[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"         "-nVNozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[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/10006018/LUAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LUAD-TP/10013791/transformed.cor.cli.txt"

nPatients in clinical file=474, in cluster file=493, common to both=462
[1]  82 462
[1] "AMP PEAK  1(1P34.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1P34.3) MUTATED AMP PEAK  1(1P34.3) WILD-TYPE 
                          127                           335 
  AMP PEAK  1(1P34.3) MUTATED AMP PEAK  1(1P34.3) WILD-TYPE 
                          127                           335 
[1] "AMP PEAK  2(1P22.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(1P22.3) MUTATED AMP PEAK  2(1P22.3) WILD-TYPE 
                          125                           337 
  AMP PEAK  2(1P22.3) MUTATED AMP PEAK  2(1P22.3) WILD-TYPE 
                          125                           337 
[1] "AMP PEAK  3(1Q21.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE 
                          332                           130 
  AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE 
                          332                           130 
[1] "AMP PEAK  4(3Q26.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE 
                          153                           309 
  AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE 
                          153                           309 
[1] "AMP PEAK  5(4Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                         90                         372 
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                         90                         372 
[1] "AMP PEAK  6(5P15.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                           302                            160 
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                           302                            160 
[1] "AMP PEAK  7(5P13.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(5P13.1) MUTATED AMP PEAK  7(5P13.1) WILD-TYPE 
                          278                           184 
  AMP PEAK  7(5P13.1) MUTATED AMP PEAK  7(5P13.1) WILD-TYPE 
                          278                           184 
[1] "AMP PEAK  8(5Q35.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(5Q35.1) MUTATED AMP PEAK  8(5Q35.1) WILD-TYPE 
                          109                           353 
  AMP PEAK  8(5Q35.1) MUTATED AMP PEAK  8(5Q35.1) WILD-TYPE 
                          109                           353 
[1] "AMP PEAK  9(6P21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE 
                          175                           287 
  AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE 
                          175                           287 
[1] "AMP PEAK 10(7P21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(7P21.1) MUTATED AMP PEAK 10(7P21.1) WILD-TYPE 
                          256                           206 
  AMP PEAK 10(7P21.1) MUTATED AMP PEAK 10(7P21.1) WILD-TYPE 
                          256                           206 
[1] "AMP PEAK 11(7P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                          250                           212 
  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                          250                           212 
[1] "AMP PEAK 12(7Q31.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(7Q31.2) MUTATED AMP PEAK 12(7Q31.2) WILD-TYPE 
                          199                           263 
  AMP PEAK 12(7Q31.2) MUTATED AMP PEAK 12(7Q31.2) WILD-TYPE 
                          199                           263 
[1] "AMP PEAK 13(8P11.23) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(8P11.23) MUTATED AMP PEAK 13(8P11.23) WILD-TYPE 
                           125                            337 
  AMP PEAK 13(8P11.23) MUTATED AMP PEAK 13(8P11.23) WILD-TYPE 
                           125                            337 
[1] "AMP PEAK 14(8P11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(8P11.21) MUTATED AMP PEAK 14(8P11.21) WILD-TYPE 
                           161                            301 
  AMP PEAK 14(8P11.21) MUTATED AMP PEAK 14(8P11.21) WILD-TYPE 
                           161                            301 
[1] "AMP PEAK 15(8Q11.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(8Q11.1) MUTATED AMP PEAK 15(8Q11.1) WILD-TYPE 
                          212                           250 
  AMP PEAK 15(8Q11.1) MUTATED AMP PEAK 15(8Q11.1) WILD-TYPE 
                          212                           250 
[1] "AMP PEAK 16(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(8Q24.21) MUTATED AMP PEAK 16(8Q24.21) WILD-TYPE 
                           294                            168 
  AMP PEAK 16(8Q24.21) MUTATED AMP PEAK 16(8Q24.21) WILD-TYPE 
                           294                            168 
[1] "AMP PEAK 17(10P15.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(10P15.1) MUTATED AMP PEAK 17(10P15.1) WILD-TYPE 
                           130                            332 
  AMP PEAK 17(10P15.1) MUTATED AMP PEAK 17(10P15.1) WILD-TYPE 
                           130                            332 
[1] "AMP PEAK 18(11Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE 
                           158                            304 
  AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE 
                           158                            304 
[1] "AMP PEAK 19(12P12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(12P12.1) MUTATED AMP PEAK 19(12P12.1) WILD-TYPE 
                           164                            298 
  AMP PEAK 19(12P12.1) MUTATED AMP PEAK 19(12P12.1) WILD-TYPE 
                           164                            298 
[1] "AMP PEAK 20(12Q14.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(12Q14.1) MUTATED AMP PEAK 20(12Q14.1) WILD-TYPE 
                           152                            310 
  AMP PEAK 20(12Q14.1) MUTATED AMP PEAK 20(12Q14.1) WILD-TYPE 
                           152                            310 
[1] "AMP PEAK 21(12Q15) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(12Q15) MUTATED AMP PEAK 21(12Q15) WILD-TYPE 
                         155                          307 
  AMP PEAK 21(12Q15) MUTATED AMP PEAK 21(12Q15) WILD-TYPE 
                         155                          307 
[1] "AMP PEAK 22(13Q33.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(13Q33.3) MUTATED AMP PEAK 22(13Q33.3) WILD-TYPE 
                            76                            386 
  AMP PEAK 22(13Q33.3) MUTATED AMP PEAK 22(13Q33.3) WILD-TYPE 
                            76                            386 
[1] "AMP PEAK 23(14Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(14Q13.3) MUTATED AMP PEAK 23(14Q13.3) WILD-TYPE 
                           206                            256 
  AMP PEAK 23(14Q13.3) MUTATED AMP PEAK 23(14Q13.3) WILD-TYPE 
                           206                            256 
[1] "AMP PEAK 24(16P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(16P11.2) MUTATED AMP PEAK 24(16P11.2) WILD-TYPE 
                           148                            314 
  AMP PEAK 24(16P11.2) MUTATED AMP PEAK 24(16P11.2) WILD-TYPE 
                           148                            314 
[1] "AMP PEAK 25(17Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 25(17Q12) MUTATED AMP PEAK 25(17Q12) WILD-TYPE 
                         209                          253 
  AMP PEAK 25(17Q12) MUTATED AMP PEAK 25(17Q12) WILD-TYPE 
                         209                          253 
[1] "AMP PEAK 26(17Q23.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 26(17Q23.1) MUTATED AMP PEAK 26(17Q23.1) WILD-TYPE 
                           227                            235 
  AMP PEAK 26(17Q23.1) MUTATED AMP PEAK 26(17Q23.1) WILD-TYPE 
                           227                            235 
[1] "AMP PEAK 27(18Q11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 27(18Q11.2) MUTATED AMP PEAK 27(18Q11.2) WILD-TYPE 
                            95                            367 
  AMP PEAK 27(18Q11.2) MUTATED AMP PEAK 27(18Q11.2) WILD-TYPE 
                            95                            367 
[1] "AMP PEAK 28(19Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 28(19Q12) MUTATED AMP PEAK 28(19Q12) WILD-TYPE 
                         128                          334 
  AMP PEAK 28(19Q12) MUTATED AMP PEAK 28(19Q12) WILD-TYPE 
                         128                          334 
[1] "AMP PEAK 29(20P11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 29(20P11.21) MUTATED AMP PEAK 29(20P11.21) WILD-TYPE 
                            179                             283 
  AMP PEAK 29(20P11.21) MUTATED AMP PEAK 29(20P11.21) WILD-TYPE 
                            179                             283 
[1] "AMP PEAK 30(20Q13.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 30(20Q13.33) MUTATED AMP PEAK 30(20Q13.33) WILD-TYPE 
                            223                             239 
  AMP PEAK 30(20Q13.33) MUTATED AMP PEAK 30(20Q13.33) WILD-TYPE 
                            223                             239 
[1] "AMP PEAK 31(22Q11.22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 31(22Q11.22) MUTATED AMP PEAK 31(22Q11.22) WILD-TYPE 
                             84                             378 
  AMP PEAK 31(22Q11.22) MUTATED AMP PEAK 31(22Q11.22) WILD-TYPE 
                             84                             378 
[1] "AMP PEAK 32(XQ28) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 32(XQ28) MUTATED AMP PEAK 32(XQ28) WILD-TYPE 
                        141                         321 
  AMP PEAK 32(XQ28) MUTATED AMP PEAK 32(XQ28) WILD-TYPE 
                        141                         321 
[1] "DEL PEAK  1(1P36.13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE 
                           107                            355 
  DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE 
                           107                            355 
[1] "DEL PEAK  2(1P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                          137                           325 
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                          137                           325 
[1] "DEL PEAK  3(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           44                           418 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           44                           418 
[1] "DEL PEAK  4(2Q37.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           61                           401 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           61                           401 
[1] "DEL PEAK  5(3P26.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(3P26.3) MUTATED DEL PEAK  5(3P26.3) WILD-TYPE 
                          209                           253 
  DEL PEAK  5(3P26.3) MUTATED DEL PEAK  5(3P26.3) WILD-TYPE 
                          209                           253 
[1] "DEL PEAK  6(3P21.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(3P21.31) MUTATED DEL PEAK  6(3P21.31) WILD-TYPE 
                           222                            240 
  DEL PEAK  6(3P21.31) MUTATED DEL PEAK  6(3P21.31) WILD-TYPE 
                           222                            240 
[1] "DEL PEAK  7(3Q11.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(3Q11.1) MUTATED DEL PEAK  7(3Q11.1) WILD-TYPE 
                          130                           332 
  DEL PEAK  7(3Q11.1) MUTATED DEL PEAK  7(3Q11.1) WILD-TYPE 
                          130                           332 
[1] "DEL PEAK  8(3Q29) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(3Q29) MUTATED DEL PEAK  8(3Q29) WILD-TYPE 
                        126                         336 
  DEL PEAK  8(3Q29) MUTATED DEL PEAK  8(3Q29) WILD-TYPE 
                        126                         336 
[1] "DEL PEAK  9(4P16.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(4P16.3) MUTATED DEL PEAK  9(4P16.3) WILD-TYPE 
                          117                           345 
  DEL PEAK  9(4P16.3) MUTATED DEL PEAK  9(4P16.3) WILD-TYPE 
                          117                           345 
[1] "DEL PEAK 10(4Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                          142                           320 
  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                          142                           320 
[1] "DEL PEAK 11(4Q35.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE 
                          169                           293 
  DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE 
                          169                           293 
[1] "DEL PEAK 12(5Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(5Q11.2) MUTATED DEL PEAK 12(5Q11.2) WILD-TYPE 
                          166                           296 
  DEL PEAK 12(5Q11.2) MUTATED DEL PEAK 12(5Q11.2) WILD-TYPE 
                          166                           296 
[1] "DEL PEAK 13(5Q31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(5Q31.1) MUTATED DEL PEAK 13(5Q31.1) WILD-TYPE 
                          192                           270 
  DEL PEAK 13(5Q31.1) MUTATED DEL PEAK 13(5Q31.1) WILD-TYPE 
                          192                           270 
[1] "DEL PEAK 14(6Q12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(6Q12) MUTATED DEL PEAK 14(6Q12) WILD-TYPE 
                        166                         296 
  DEL PEAK 14(6Q12) MUTATED DEL PEAK 14(6Q12) WILD-TYPE 
                        166                         296 
[1] "DEL PEAK 15(6Q22.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(6Q22.31) MUTATED DEL PEAK 15(6Q22.31) WILD-TYPE 
                           231                            231 
  DEL PEAK 15(6Q22.31) MUTATED DEL PEAK 15(6Q22.31) WILD-TYPE 
                           231                            231 
[1] "DEL PEAK 16(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE 
                        233                         229 
  DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE 
                        233                         229 
[1] "DEL PEAK 17(8P23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(8P23.2) MUTATED DEL PEAK 17(8P23.2) WILD-TYPE 
                          227                           235 
  DEL PEAK 17(8P23.2) MUTATED DEL PEAK 17(8P23.2) WILD-TYPE 
                          227                           235 
[1] "DEL PEAK 18(8P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(8P12) MUTATED DEL PEAK 18(8P12) WILD-TYPE 
                        202                         260 
  DEL PEAK 18(8P12) MUTATED DEL PEAK 18(8P12) WILD-TYPE 
                        202                         260 
[1] "DEL PEAK 19(8P11.21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(8P11.21) MUTATED DEL PEAK 19(8P11.21) WILD-TYPE 
                           105                            357 
  DEL PEAK 19(8P11.21) MUTATED DEL PEAK 19(8P11.21) WILD-TYPE 
                           105                            357 
[1] "DEL PEAK 20(8Q11.21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(8Q11.21) MUTATED DEL PEAK 20(8Q11.21) WILD-TYPE 
                            59                            403 
  DEL PEAK 20(8Q11.21) MUTATED DEL PEAK 20(8Q11.21) WILD-TYPE 
                            59                            403 
[1] "DEL PEAK 21(9P23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(9P23) MUTATED DEL PEAK 21(9P23) WILD-TYPE 
                        253                         209 
  DEL PEAK 21(9P23) MUTATED DEL PEAK 21(9P23) WILD-TYPE 
                        253                         209 
[1] "DEL PEAK 22(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE 
                          261                           201 
  DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE 
                          261                           201 
[1] "DEL PEAK 23(9Q21.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(9Q21.11) MUTATED DEL PEAK 23(9Q21.11) WILD-TYPE 
                           233                            229 
  DEL PEAK 23(9Q21.11) MUTATED DEL PEAK 23(9Q21.11) WILD-TYPE 
                           233                            229 
[1] "DEL PEAK 24(10P15.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE 
                           114                            348 
  DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE 
                           114                            348 
[1] "DEL PEAK 25(10Q26.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(10Q26.3) MUTATED DEL PEAK 25(10Q26.3) WILD-TYPE 
                           137                            325 
  DEL PEAK 25(10Q26.3) MUTATED DEL PEAK 25(10Q26.3) WILD-TYPE 
                           137                            325 
[1] "DEL PEAK 26(11P15.5) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(11P15.5) MUTATED DEL PEAK 26(11P15.5) WILD-TYPE 
                           129                            333 
  DEL PEAK 26(11P15.5) MUTATED DEL PEAK 26(11P15.5) WILD-TYPE 
                           129                            333 
[1] "DEL PEAK 27(11Q23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(11Q23.2) MUTATED DEL PEAK 27(11Q23.2) WILD-TYPE 
                           108                            354 
  DEL PEAK 27(11Q23.2) MUTATED DEL PEAK 27(11Q23.2) WILD-TYPE 
                           108                            354 
[1] "DEL PEAK 28(11Q25) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(11Q25) MUTATED DEL PEAK 28(11Q25) WILD-TYPE 
                         103                          359 
  DEL PEAK 28(11Q25) MUTATED DEL PEAK 28(11Q25) WILD-TYPE 
                         103                          359 
[1] "DEL PEAK 29(12P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(12P13.2) MUTATED DEL PEAK 29(12P13.2) WILD-TYPE 
                           125                            337 
  DEL PEAK 29(12P13.2) MUTATED DEL PEAK 29(12P13.2) WILD-TYPE 
                           125                            337 
[1] "DEL PEAK 30(12Q12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(12Q12) MUTATED DEL PEAK 30(12Q12) WILD-TYPE 
                          89                          373 
  DEL PEAK 30(12Q12) MUTATED DEL PEAK 30(12Q12) WILD-TYPE 
                          89                          373 
[1] "DEL PEAK 31(12Q24.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(12Q24.33) MUTATED DEL PEAK 31(12Q24.33) WILD-TYPE 
                            116                             346 
  DEL PEAK 31(12Q24.33) MUTATED DEL PEAK 31(12Q24.33) WILD-TYPE 
                            116                             346 
[1] "DEL PEAK 32(13Q12.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(13Q12.11) MUTATED DEL PEAK 32(13Q12.11) WILD-TYPE 
                            262                             200 
  DEL PEAK 32(13Q12.11) MUTATED DEL PEAK 32(13Q12.11) WILD-TYPE 
                            262                             200 
[1] "DEL PEAK 33(13Q12.13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(13Q12.13) MUTATED DEL PEAK 33(13Q12.13) WILD-TYPE 
                            261                             201 
  DEL PEAK 33(13Q12.13) MUTATED DEL PEAK 33(13Q12.13) WILD-TYPE 
                            261                             201 
[1] "DEL PEAK 34(13Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE 
                           251                            211 
  DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE 
                           251                            211 
[1] "DEL PEAK 35(13Q34) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 35(13Q34) MUTATED DEL PEAK 35(13Q34) WILD-TYPE 
                         213                          249 
  DEL PEAK 35(13Q34) MUTATED DEL PEAK 35(13Q34) WILD-TYPE 
                         213                          249 
[1] "DEL PEAK 36(14Q32.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 36(14Q32.33) MUTATED DEL PEAK 36(14Q32.33) WILD-TYPE 
                            137                             325 
  DEL PEAK 36(14Q32.33) MUTATED DEL PEAK 36(14Q32.33) WILD-TYPE 
                            137                             325 
[1] "DEL PEAK 37(15Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 37(15Q11.2) MUTATED DEL PEAK 37(15Q11.2) WILD-TYPE 
                           237                            225 
  DEL PEAK 37(15Q11.2) MUTATED DEL PEAK 37(15Q11.2) WILD-TYPE 
                           237                            225 
[1] "DEL PEAK 38(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 38(16Q23.1) MUTATED DEL PEAK 38(16Q23.1) WILD-TYPE 
                           155                            307 
  DEL PEAK 38(16Q23.1) MUTATED DEL PEAK 38(16Q23.1) WILD-TYPE 
                           155                            307 
[1] "DEL PEAK 39(17P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 39(17P13.3) MUTATED DEL PEAK 39(17P13.3) WILD-TYPE 
                           248                            214 
  DEL PEAK 39(17P13.3) MUTATED DEL PEAK 39(17P13.3) WILD-TYPE 
                           248                            214 
[1] "DEL PEAK 40(17P11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE 
                           205                            257 
  DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE 
                           205                            257 
[1] "DEL PEAK 41(18Q21.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 41(18Q21.32) MUTATED DEL PEAK 41(18Q21.32) WILD-TYPE 
                            228                             234 
  DEL PEAK 41(18Q21.32) MUTATED DEL PEAK 41(18Q21.32) WILD-TYPE 
                            228                             234 
[1] "DEL PEAK 42(18Q23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 42(18Q23) MUTATED DEL PEAK 42(18Q23) WILD-TYPE 
                         224                          238 
  DEL PEAK 42(18Q23) MUTATED DEL PEAK 42(18Q23) WILD-TYPE 
                         224                          238 
[1] "DEL PEAK 43(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE 
                           250                            212 
  DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE 
                           250                            212 
[1] "DEL PEAK 44(19P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 44(19P13.2) MUTATED DEL PEAK 44(19P13.2) WILD-TYPE 
                           245                            217 
  DEL PEAK 44(19P13.2) MUTATED DEL PEAK 44(19P13.2) WILD-TYPE 
                           245                            217 
[1] "DEL PEAK 45(19Q13.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 45(19Q13.33) MUTATED DEL PEAK 45(19Q13.33) WILD-TYPE 
                            176                             286 
  DEL PEAK 45(19Q13.33) MUTATED DEL PEAK 45(19Q13.33) WILD-TYPE 
                            176                             286 
[1] "DEL PEAK 46(20P13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 46(20P13) MUTATED DEL PEAK 46(20P13) WILD-TYPE 
                         120                          342 
  DEL PEAK 46(20P13) MUTATED DEL PEAK 46(20P13) WILD-TYPE 
                         120                          342 
[1] "DEL PEAK 47(20Q13.12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 47(20Q13.12) MUTATED DEL PEAK 47(20Q13.12) WILD-TYPE 
                             79                             383 
  DEL PEAK 47(20Q13.12) MUTATED DEL PEAK 47(20Q13.12) WILD-TYPE 
                             79                             383 
[1] "DEL PEAK 48(21Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 48(21Q11.2) MUTATED DEL PEAK 48(21Q11.2) WILD-TYPE 
                           158                            304 
  DEL PEAK 48(21Q11.2) MUTATED DEL PEAK 48(21Q11.2) WILD-TYPE 
                           158                            304 
[1] "DEL PEAK 49(22Q13.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 49(22Q13.32) MUTATED DEL PEAK 49(22Q13.32) WILD-TYPE 
                            223                             239 
  DEL PEAK 49(22Q13.32) MUTATED DEL PEAK 49(22Q13.32) WILD-TYPE 
                            223                             239 
[1] "DEL PEAK 50(XP22.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE 
                          126                           336 
  DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE 
                          126                           336 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDESEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "KARNOFSKYPERFORMANCESCORE"             
[16] "HISTOLOGICALTYPE"                      
[17] "RADIATIONS.RADIATION.REGIMENINDICATION"
[18] "NUMBERPACKYEARSSMOKED"                 
[19] "YEAROFTOBACCOSMOKINGONSET"             
[20] "COMPLETENESS.OF.RESECTION"             
[21] "RACE"                                  
[22] "ETHNICITY"                             
[23] "BATCHNUMBER"                           

Input Data has 23 rows and 462 columns.

[1] "Batch" "23"   
[1] "Last Follow UP"
TCGA-05-4244 TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 
          NA         1523           NA          607          426         1369 
TCGA-05-4390 TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 
        1126           NA           NA           NA         1431           NA 
TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 
         578          610           NA           NA          455           NA 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 
         912          365          913          669          791          791 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 
         761          761          730           NA          457          151 
TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 
         882          670           30           62           14          225 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
         182          264         2973         3674         1147         1492 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
         864         1073          354         1357          448           NA 
TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 
         133         1324         1429          400         1367          741 
TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 
        1280         1301           97          246         1130         1163 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 
        1036          190          722         1013          863          383 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
         723          328          302          845          704          658 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
         705         1938           NA         1864           NA          444 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
         592          366          218          557           NA          882 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 
         535          719          385           99          260          486 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
         466          287          337          351          415           76 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
        2318           NA           NA           NA         1081         1421 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
         428          999          268          896          157         1700 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 
         445          369          890          522          354           NA 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
          NA         2174         2146          455          785          944 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
        1499          246          282          267         1091         2370 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
         653           NA           NA          567          883          764 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
         686           NA           NA           NA           NA           NA 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8460 TCGA-53-7624 
          NA         1015           NA          255          105           NA 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 
          NA          424          280          701         1178         1479 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
        1375           87            2          993           24           NA 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
        1239           NA           25         1475           NA           NA 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
          NA           67           NA           NA         1826           NA 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
        1233         2151         1170           18           35          121 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
           6            4           95           40           NA           39 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 
          39           34           24           54           19           16 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
         197           21            3           31            5           33 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
          21          100            6           43           26            4 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8204 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
          47           15           NA           33           46           66 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
         216           44           23           29           11            8 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
          15          228            9            3          146          202 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
         536           15           48           49           66          106 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
          33           42           29           48           NA            1 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
          28            5           47          162           NA         1216 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
        1289           NA         2696         1445           NA           NA 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
          NA           NA         2067         2199           NA           NA 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 
        1246          910         1728          628         1189         1686 
TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
        1126           NA         2676           62         1305          864 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
        1559          866           31          610          573          427 
TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
         385           NA          174          141          422          202 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
         186          690          414          165          230          184 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
          70           89          382          100           77          129 
TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
         214           61         1600          711          912          800 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
         467          131           40          164           38          621 
TCGA-73-7499 TCGA-75-5122 TCGA-75-5125 TCGA-75-5126 TCGA-75-5146 TCGA-75-5147 
         519           NA           NA           NA           NA           NA 
TCGA-75-6203 TCGA-75-6205 TCGA-75-6206 TCGA-75-6207 TCGA-75-6211 TCGA-75-6212 
          NA           NA           NA           NA           NA           NA 
TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-75-7030 TCGA-75-7031 TCGA-78-7143 
          NA           NA           NA           NA           NA           NA 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
          NA           NA           NA           NA         1093           NA 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
        1202          760           NA           NA           NA           NA 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
        1221          678          215           NA         6812           NA 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
          NA           NA           NA           NA           NA          327 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
         881           NA          994         6346           NA         2360 
TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 TCGA-80-5611 TCGA-83-5908 
          NA           NA           NA           NA           NA          824 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
          NA           NA           11          630          422           NA 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
         591           NA          508          745           10           NA 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
          13           24          479          489          476          482 
TCGA-86-8280 TCGA-86-8281 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
          16           NA           19           26           35           45 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
          34           18           15          455          405           10 
TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
          30           NA           14           39          323           NA 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
          60          310           79          417          372          842 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
         224           35          492          197          174           36 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 
          44          218          297          127          186           34 
TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK 
           2          568          377          477          476          121 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
         964         1965         1932         1332          775          181 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
          NA           22          107          182           NA           87 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 
         147           15          148          115          197          271 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
         392          427          459           44          170          154 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
         114          287          282          238          578          435 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
         116            6          285          622          353           NA 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
          NA           NA           NA           NA           NA           NA 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
          NA           NA           NA           NA           NA           NA 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-MP-A5C7 
          NA          142           NA           NA           NA         1490 
Variable 1:'AGE':	nDistinctValues=50,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=118,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=279,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=8,	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:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=22,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=39,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'HISTOLOGICAL.TYPE':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'NUMBERPACKYEARSSMOKED':	nDistinctValues=90,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=57,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 23:'BATCH.NUMBER':	nDistinctValues=22,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                                   
 [2] "NEOPLASM.DISEASESTAGE"                 
 [3] "PATHOLOGY.T.STAGE"                     
 [4] "PATHOLOGY.N.STAGE"                     
 [5] "PATHOLOGY.M.STAGE"                     
 [6] "GENDER"                                
 [7] "KARNOFSKY.PERFORMANCE.SCORE"           
 [8] "HISTOLOGICAL.TYPE"                     
 [9] "RADIATIONS.RADIATION.REGIMENINDICATION"
[10] "NUMBERPACKYEARSSMOKED"                 
[11] "COMPLETENESS.OF.RESECTION"             
[12] "RACE"                                  
[13] "ETHNICITY"                             
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 462 columns, 1 survival variables, and 13 non-survival variables.
AGE, nv=50, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=8, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
143 259  40  18 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
143 259  40  18 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
143 259  40  18 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
143 259  40  18 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
295  85  70   2 
[1] "table(vv)"
vv
   N0    N1 N2+N3 
  295    85    72 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
 N0  N1  N2  N3 
295  85  70   2 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   N0    N1 N2+N3 
  295    85    72 
PATHOLOGY.M.STAGE, nv=5, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=7, binary=FALSE, numeric=TRUE
HISTOLOGICAL.TYPE, nv=12, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
NUMBERPACKYEARSSMOKED, nv=90, binary=FALSE, numeric=TRUE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK  1(1P34.3) MUTATION ANALYSIS
D1V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  1(1P34.3) MUTATED    86  27
  AMP PEAK  1(1P34.3) WILD-TYPE 235  55
  AMP PEAK  1(1P34.3) MUTATED AMP PEAK  1(1P34.3) WILD-TYPE 
                          113                           290 
  AMP PEAK  1(1P34.3) MUTATED AMP PEAK  1(1P34.3) WILD-TYPE 
                           27                            55 
$`AMP PEAK  1(1P34.3) MUTATED`
TCGA-05-4420 TCGA-05-4427 TCGA-05-4432 TCGA-05-5428 TCGA-05-5429 TCGA-38-4628 
         912          791          761          670           30         1492 
TCGA-38-4630 TCGA-38-6178 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2662 
        1073          448         1429          400         1367         1280 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6775 TCGA-44-6778 TCGA-44-6779 
         863          383          723          705         1864         1978 
TCGA-44-7660 TCGA-44-7669 TCGA-44-8119 TCGA-44-A47A TCGA-44-A4SU TCGA-49-4501 
         592         1970           99          466           76         1421 
TCGA-49-4505 TCGA-49-4510 TCGA-49-4512 TCGA-49-6742 TCGA-49-6744 TCGA-50-5045 
         428          896          157          445          890         2174 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 
        1499          246          267          567          764          686 
TCGA-50-6597 TCGA-53-7624 TCGA-55-1592 TCGA-55-6712 TCGA-55-6969 TCGA-55-6972 
        1015         1986          701           24         1239         1475 
TCGA-55-6980 TCGA-55-6987 TCGA-55-7281 TCGA-55-7573 TCGA-55-7576 TCGA-55-8091 
          67         1170           18            4           40           43 
TCGA-55-8096 TCGA-55-8206 TCGA-55-8507 TCGA-55-8508 TCGA-55-8514 TCGA-55-A48X 
          47           46            8           15          202           33 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8399 TCGA-62-A46V TCGA-64-1676 TCGA-64-1681 
          47          162         2696         2199         1728         1968 
TCGA-64-5779 TCGA-64-5781 TCGA-67-3770 TCGA-67-3772 TCGA-67-6217 TCGA-69-7760 
         864         1559           31          573          422          202 
TCGA-69-7980 TCGA-69-8254 TCGA-69-A59K TCGA-71-6725 TCGA-73-4676 TCGA-75-7025 
         382           77          214           61          164         1967 
TCGA-78-7145 TCGA-78-7147 TCGA-78-7149 TCGA-78-7155 TCGA-78-7161 TCGA-78-7162 
        1973         1950         1093         1957          215         1940 
TCGA-78-7163 TCGA-78-7167 TCGA-78-7535 TCGA-78-7542 TCGA-78-8655 TCGA-78-8662 
        1950         1937         1972         1952         1981         1964 
TCGA-86-7713 TCGA-86-7953 TCGA-86-8055 TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 
         422          591           10           24          479          482 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8668 TCGA-86-A456 TCGA-86-A4P7 TCGA-91-6831 
          16           19           45           10           14          310 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-7771 TCGA-91-8496 TCGA-95-7039 
         372          842          224          492          197           34 
TCGA-95-7944 TCGA-97-7546 TCGA-97-7553 TCGA-97-7937 TCGA-97-8177 TCGA-97-8552 
         377          964         1332          181          147          115 
TCGA-99-7458 TCGA-J2-8192 TCGA-J2-A4AG TCGA-MN-A4N1 TCGA-MP-A4SW 
         392          154          238          285         1967 

$`AMP PEAK  1(1P34.3) WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 
        1523          607          426         1369         1126         1947 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 
        1431          578          610         1958         1997          455 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4433 
         365          913          669          791          761          730 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 
         457          151          882           62           14          225 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4629 
         182          264         1952         1962         1147          864 
TCGA-38-4631 TCGA-38-4632 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2661 
         354         1357         1971          133         1324          741 
TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 
        1301           97          246         1130         1163         1036 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
         190          722         1013          328          302          845 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6776 TCGA-44-6777 TCGA-44-7659 TCGA-44-7661 
         704          658         1938         1942          444          366 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
         218          557          882          535          719          385 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
         260          486          287          337          351          415 
TCGA-49-4486 TCGA-49-4494 TCGA-49-4506 TCGA-49-4507 TCGA-49-4514 TCGA-49-6743 
        1932         1081          999          268         1700          369 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
         522          354         2146          455          785          944 
TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5942 TCGA-50-7109 
         282         1091         2370          653          883          255 
TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1595 
         105         1971          424          280         1178         1479 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6971 TCGA-55-6983 
        1375           87            2          993           25         1826 
TCGA-55-6985 TCGA-55-6986 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7574 
        1233         2151           35          121            6           95 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
        1958           39           39           34           24           54 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
          19           16          197           21            3           31 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8092 
           5           33           21          100            6           26 
TCGA-55-8094 TCGA-55-8097 TCGA-55-8205 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 
           4           15           33           66          216           44 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
          23           29           11          228            9            3 
TCGA-55-8513 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
         146          536           15           48           49           66 
TCGA-55-8621 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
         106           42           29           48         1952            1 
TCGA-55-A493 TCGA-55-A494 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8402 
          28            5         1216         1289         1970         1445 
TCGA-62-A46U TCGA-62-A471 TCGA-62-A472 TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 
        2067         1246          910          628         1189         1686 
TCGA-64-1680 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5815 TCGA-67-3771 
        1126         1959           62         1305          866          610 
TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-69-7761 TCGA-69-7763 
         427          385          174          141          186          690 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
         414          165          230          184           70           89 
TCGA-69-8253 TCGA-69-8255 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
         100          129         1600          711          912          800 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
         467          131           40           38          621          519 
TCGA-75-6214 TCGA-75-7027 TCGA-75-7031 TCGA-78-7146 TCGA-78-7148 TCGA-78-7150 
        1970         1956         1965         1988         1944         1963 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
        1202          760         1948         1961         1963         1221 
TCGA-78-7160 TCGA-78-7166 TCGA-78-7220 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
         678         1934         1965         1949         1944          327 
TCGA-78-7540 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8660 TCGA-80-5607 
         881          994         1949         1971         1954         1965 
TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 
        1972          824         1959           11          630         1968 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 TCGA-86-8076 
        1963          508          745         1963           13          489 
TCGA-86-8278 TCGA-86-8281 TCGA-86-8359 TCGA-86-8585 TCGA-86-8669 TCGA-86-8671 
         476         1955           26           35           34           18 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4D0 TCGA-86-A4P8 TCGA-91-6828 
          15          455          405           30           39          323 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 TCGA-91-6836 TCGA-91-6849 TCGA-91-8497 
        1940           60           79          417           35          174 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
          36           44          218          297          127          186 
TCGA-95-7043 TCGA-95-7567 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-97-7547 
           2          568          477          476          121         1965 
TCGA-97-7552 TCGA-97-7554 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        1932          775           22          107          182         1965 
TCGA-97-8175 TCGA-97-8179 TCGA-97-8547 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-8025 
          87           15          148          197          271          427 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
         459           44          170          114          287          282 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N4 TCGA-MN-A4N5 
         578          435          116            6          622          353 
TCGA-MP-A4SV TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
        1946         1951         1954         1954         1957         1980 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        1951         1944         1970         1970          142         1955 
TCGA-MP-A4TK TCGA-MP-A5C7 
        1971         1490 

  AMP PEAK  1(1P34.3) MUTATED AMP PEAK  1(1P34.3) WILD-TYPE 
                            4                             1 
  AMP PEAK  1(1P34.3) MUTATED AMP PEAK  1(1P34.3) WILD-TYPE 
                         2696                          2370 
  AMP PEAK  1(1P34.3) MUTATED AMP PEAK  1(1P34.3) WILD-TYPE 
                          479                           458 
[1] "4.0 - 2696.0 (479.0)" "1.0 - 2370.0 (458.0)"
[1] "hr=" "1.1"
D1V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK  1(1P34.3) MUTATED         2       29       40        15        19
  AMP PEAK  1(1P34.3) WILD-TYPE       2       84       91        28        50
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK  1(1P34.3) MUTATED           13          3        5
  AMP PEAK  1(1P34.3) WILD-TYPE         54          8       18
D1V3, multiclass
            clus
vv           AMP PEAK  1(1P34.3) MUTATED AMP PEAK  1(1P34.3) WILD-TYPE
  STAGE I                              2                             2
  STAGE IA                            29                            84
  STAGE IB                            40                            91
  STAGE IIA                           15                            28
  STAGE IIB                           19                            50
  STAGE IIIA                          13                            54
  STAGE IIIB                           3                             8
  STAGE IV                             5                            18
[1] 8 2
[1] TRUE
[1] "dimension of 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    36  78   8   5
  AMP PEAK  1(1P34.3) WILD-TYPE 107 181  32  13
D1V4, multiclass
    clus
vv   AMP PEAK  1(1P34.3) MUTATED AMP PEAK  1(1P34.3) WILD-TYPE
  T1                          36                           107
  T2                          78                           181
  T3                           8                            32
  T4                           5                            13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1 N2+N3
  AMP PEAK  1(1P34.3) MUTATED    80  29    13
  AMP PEAK  1(1P34.3) WILD-TYPE 215  56    59
D1V5, multiclass
       clus
vv      AMP PEAK  1(1P34.3) MUTATED AMP PEAK  1(1P34.3) WILD-TYPE
  N0                             80                           215
  N1                             29                            56
  N2+N3                          13                            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"
                               vv
clus                             M0  M1 M1A M1B  MX
  AMP PEAK  1(1P34.3) MUTATED    85   5   0   0  33
  AMP PEAK  1(1P34.3) WILD-TYPE 232  13   1   3  86
D1V6, multiclass
     clus
vv    AMP PEAK  1(1P34.3) MUTATED AMP PEAK  1(1P34.3) WILD-TYPE
  M0                           85                           232
  M1                            5                            13
  M1A                           0                             1
  M1B                           0                             3
  MX                           33                            86
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
                               cls
clus                              0   1
  AMP PEAK  1(1P34.3) MUTATED    73  54
  AMP PEAK  1(1P34.3) WILD-TYPE 175 160
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P34.3) MUTATED     73   54
  AMP PEAK  1(1P34.3) WILD-TYPE  175  160
        clus
vv       AMP PEAK  1(1P34.3) MUTATED AMP PEAK  1(1P34.3) WILD-TYPE
  FEMALE                          73                           175
  MALE                            54                           160
[1] 2 2
[1] FALSE
D1V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  AMP PEAK  1(1P34.3) MUTATED                            4
  AMP PEAK  1(1P34.3) WILD-TYPE                          9
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK  1(1P34.3) MUTATED                                  18
  AMP PEAK  1(1P34.3) WILD-TYPE                                75
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  1(1P34.3) MUTATED                                                   88
  AMP PEAK  1(1P34.3) WILD-TYPE                                                206
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK  1(1P34.3) MUTATED                                            1
  AMP PEAK  1(1P34.3) WILD-TYPE                                          3
                               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                                  3
                               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                            13
                               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                                             3
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK  1(1P34.3) MUTATED                              2
  AMP PEAK  1(1P34.3) WILD-TYPE                            5
D1V9, multiclass
                                                    clus
vv                                                   AMP PEAK  1(1P34.3) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           18
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          88
  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                                                 2
                                                    clus
vv                                                   AMP PEAK  1(1P34.3) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             75
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           206
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 13
  LUNG CLEAR CELL ADENOCARCINOMA                                                 2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             3
  LUNG MUCINOUS ADENOCARCINOMA                                                   2
  LUNG PAPILLARY ADENOCARCINOMA                                                 13
  LUNG SIGNET RING ADENOCARCINOMA                                                1
  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"
D1V10, binary
                               cls
clus                              0   1
  AMP PEAK  1(1P34.3) MUTATED     4 123
  AMP PEAK  1(1P34.3) WILD-TYPE  17 318
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P34.3) MUTATED      4  123
  AMP PEAK  1(1P34.3) WILD-TYPE   17  318
     clus
vv    AMP PEAK  1(1P34.3) MUTATED AMP PEAK  1(1P34.3) WILD-TYPE
  NO                            4                            17
  YES                         123                           318
[1] 2 2
[1] FALSE
D1V11, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  1(1P34.3) MUTATED    78   5   1   4
  AMP PEAK  1(1P34.3) WILD-TYPE 240   6   3  15
D1V12, multiclass
    clus
vv   AMP PEAK  1(1P34.3) MUTATED AMP PEAK  1(1P34.3) WILD-TYPE
  R0                          78                           240
  R1                           5                             6
  R2                           1                             3
  RX                           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                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  1(1P34.3) MUTATED                                  0     2
  AMP PEAK  1(1P34.3) WILD-TYPE                                1     4
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  1(1P34.3) MUTATED                          10   102
  AMP PEAK  1(1P34.3) WILD-TYPE                        16   260
D1V13, multiclass
                                  clus
vv                                 AMP PEAK  1(1P34.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 10
  WHITE                                                    102
                                  clus
vv                                 AMP PEAK  1(1P34.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   16
  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"
D1V14, binary
                               cls
clus                              0   1
  AMP PEAK  1(1P34.3) MUTATED     2  89
  AMP PEAK  1(1P34.3) WILD-TYPE   5 243
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P34.3) MUTATED      2   89
  AMP PEAK  1(1P34.3) WILD-TYPE    5  243
                        clus
vv                       AMP PEAK  1(1P34.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          89
                        clus
vv                       AMP PEAK  1(1P34.3) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           243
[1] 2 2
[1] FALSE

Clustering(2) Variable = AMP PEAK  2(1P22.3) MUTATION ANALYSIS
D2V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  2(1P22.3) MUTATED    83  29
  AMP PEAK  2(1P22.3) WILD-TYPE 238  53
  AMP PEAK  2(1P22.3) MUTATED AMP PEAK  2(1P22.3) WILD-TYPE 
                          112                           291 
  AMP PEAK  2(1P22.3) MUTATED AMP PEAK  2(1P22.3) WILD-TYPE 
                           29                            53 
$`AMP PEAK  2(1P22.3) MUTATED`
TCGA-05-4389 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4427 TCGA-05-4432 
        1369          912          365          913          791          761 
TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-35-3615 TCGA-35-4123 TCGA-38-4632 
         882          670           30           14          182         1357 
TCGA-44-2656 TCGA-44-2659 TCGA-44-2662 TCGA-44-6775 TCGA-44-6778 TCGA-44-6779 
        1429         1367         1280          705         1864         1978 
TCGA-44-7662 TCGA-44-7669 TCGA-44-8117 TCGA-44-A47B TCGA-44-A4SS TCGA-44-A4SU 
         218         1970          385          287          415           76 
TCGA-49-4505 TCGA-49-4507 TCGA-49-4512 TCGA-49-6742 TCGA-49-6744 TCGA-50-5045 
         428          268          157          445          890         2174 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 TCGA-50-5935 TCGA-50-5941 TCGA-50-5944 
        1499          246          267          653          567          764 
TCGA-50-5946 TCGA-50-6597 TCGA-55-1592 TCGA-55-6712 TCGA-55-6969 TCGA-55-6980 
         686         1015          701           24         1239           67 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7573 TCGA-55-7576 TCGA-55-7910 TCGA-55-8089 
          18           35            4           40          197          100 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8206 TCGA-55-8507 TCGA-55-8514 TCGA-55-A48X 
           4           47           46            8          202           33 
TCGA-55-A48Z TCGA-55-A4DG TCGA-62-8399 TCGA-64-1676 TCGA-64-1679 TCGA-64-1681 
          29          162         2696         1728         1686         1968 
TCGA-64-5775 TCGA-64-5781 TCGA-67-6215 TCGA-67-6217 TCGA-69-7979 TCGA-69-8254 
          62         1559          174          422           89           77 
TCGA-69-A59K TCGA-73-4662 TCGA-73-4668 TCGA-73-4676 TCGA-73-7498 TCGA-78-7145 
         214          912          467          164          621         1973 
TCGA-78-7147 TCGA-78-7149 TCGA-78-7155 TCGA-78-7158 TCGA-78-7161 TCGA-78-7162 
        1950         1093         1957         1963          215         1940 
TCGA-78-7167 TCGA-78-7535 TCGA-78-7542 TCGA-78-8640 TCGA-78-8655 TCGA-86-7953 
        1937         1972         1952         1949         1981          591 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 TCGA-86-8280 
         745           10           24          479          482           16 
TCGA-86-8585 TCGA-86-A456 TCGA-86-A4P7 TCGA-91-6831 TCGA-91-6836 TCGA-91-6840 
          35           10           14          310          417          372 
TCGA-91-6847 TCGA-91-8499 TCGA-93-8067 TCGA-95-7944 TCGA-97-7546 TCGA-97-7553 
         842           36          186          377          964         1332 
TCGA-97-7937 TCGA-99-7458 TCGA-J2-8192 TCGA-J2-A4AG TCGA-MN-A4N1 TCGA-MP-A4T8 
         181          392          154          238          285         1957 
TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A5C7 
        1944         1970         1970         1490 

$`AMP PEAK  2(1P22.3) WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4390 TCGA-05-4396 TCGA-05-4398 
        1523          607          426         1126         1947         1431 
TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 TCGA-05-4425 
         578          610         1958         1997          455          669 
TCGA-05-4426 TCGA-05-4430 TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5715 
         791          761          730          457          151           62 
TCGA-35-4122 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
         225          264         1952         1962         1147         1492 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F 
         864         1073          354          448         1971          133 
TCGA-44-2655 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
        1324          400          741         1301           97          246 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
        1130         1163         1036          190          722         1013 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
         863          383          723          328          302          845 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6776 TCGA-44-6777 TCGA-44-7659 TCGA-44-7660 
         704          658         1938         1942          444          592 
TCGA-44-7661 TCGA-44-7667 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8119 
         366          557          882          535          719           99 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47F TCGA-44-A47G TCGA-49-4486 
         260          486          466          337          351         1932 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4506 TCGA-49-4510 TCGA-49-4514 TCGA-49-6743 
        1081         1421          999          896         1700          369 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
         522          354         2146          455          785          944 
TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 TCGA-50-5942 TCGA-50-7109 TCGA-50-8460 
         282         1091         2370          883          255          105 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1595 
        1986         1971          424          280         1178         1479 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6971 TCGA-55-6972 
        1375           87            2          993           25         1475 
TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7284 TCGA-55-7570 
        1826         1233         2151         1170          121            6 
TCGA-55-7574 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
          95         1958           39           39           34           24 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
          54           19           16           21            3           31 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
           5           33           21            6           43           26 
TCGA-55-8097 TCGA-55-8205 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
          15           33           66          216           44           23 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
          29           11           15          228            9            3 
TCGA-55-8513 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
         146          536           15           48           49           66 
TCGA-55-8621 TCGA-55-A48Y TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
         106           42           48         1952            1           28 
TCGA-55-A494 TCGA-55-A4DF TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8402 
           5           47         1216         1289         1970         1445 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 TCGA-64-1677 TCGA-64-1678 
        2067         2199         1246          910          628         1189 
TCGA-64-1680 TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 TCGA-67-3770 
        1126         1959         1305          864          866           31 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6216 TCGA-69-7760 
         610          573          427          385          141          202 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
         186          690          414          165          230          184 
TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8255 TCGA-71-6725 TCGA-73-4658 
          70          382          100          129           61         1600 
TCGA-73-4659 TCGA-73-4666 TCGA-73-4670 TCGA-73-4675 TCGA-73-4677 TCGA-73-7499 
         711          800          131           40           38          519 
TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 TCGA-78-7146 TCGA-78-7148 
        1970         1967         1956         1965         1988         1944 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7159 
        1963         1202          760         1948         1961         1221 
TCGA-78-7160 TCGA-78-7163 TCGA-78-7166 TCGA-78-7220 TCGA-78-7536 TCGA-78-7537 
         678         1950         1934         1965         1949         1944 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7633 TCGA-78-8648 TCGA-78-8660 TCGA-78-8662 
         327          881          994         1971         1954         1964 
TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
        1965         1972          824         1959           11          630 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7954 TCGA-86-7955 TCGA-86-8056 TCGA-86-8073 
         422         1968         1963          508         1963           13 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8281 TCGA-86-8358 TCGA-86-8359 TCGA-86-8668 
         489          476         1955           19           26           45 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4D0 
          34           18           15          455          405           30 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 TCGA-91-6848 
          39          323         1940           60           79          224 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD 
          35          492          197          174           44          218 
TCGA-93-7347 TCGA-93-7348 TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-95-7947 
         297          127           34            2          568          477 
TCGA-95-7948 TCGA-95-A4VK TCGA-97-7547 TCGA-97-7552 TCGA-97-7554 TCGA-97-7941 
         476          121         1965         1932          775           22 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 
         107          182         1965           87          147           15 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-8025 TCGA-99-8028 
         148          115          197          271          427          459 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E5 
          44          170          114          287          282          578 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
         435          116            6          622          353         1946 
TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TA 
        1967         1951         1954         1954         1980         1951 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
         142         1955         1971 

  AMP PEAK  2(1P22.3) MUTATED AMP PEAK  2(1P22.3) WILD-TYPE 
                            4                             1 
  AMP PEAK  2(1P22.3) MUTATED AMP PEAK  2(1P22.3) WILD-TYPE 
                         2696                          2370 
  AMP PEAK  2(1P22.3) MUTATED AMP PEAK  2(1P22.3) WILD-TYPE 
                          456                           466 
[1] "4.0 - 2696.0 (456.0)" "1.0 - 2370.0 (466.0)"
[1] "hr=" "1.4"
D2V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK  2(1P22.3) MUTATED         0       31       34        17        17
  AMP PEAK  2(1P22.3) WILD-TYPE       4       82       97        26        52
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK  2(1P22.3) MUTATED           16          4        5
  AMP PEAK  2(1P22.3) WILD-TYPE         51          7       18
D2V3, multiclass
            clus
vv           AMP PEAK  2(1P22.3) MUTATED AMP PEAK  2(1P22.3) WILD-TYPE
  STAGE I                              0                             4
  STAGE IA                            31                            82
  STAGE IB                            34                            97
  STAGE IIA                           17                            26
  STAGE IIB                           17                            52
  STAGE IIIA                          16                            51
  STAGE IIIB                           4                             7
  STAGE IV                             5                            18
[1] 8 2
[1] TRUE
[1] "dimension of 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(1P22.3) MUTATED    40  71   8   6
  AMP PEAK  2(1P22.3) WILD-TYPE 103 188  32  12
D2V4, multiclass
    clus
vv   AMP PEAK  2(1P22.3) MUTATED AMP PEAK  2(1P22.3) WILD-TYPE
  T1                          40                           103
  T2                          71                           188
  T3                           8                            32
  T4                           6                            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  2(1P22.3) MUTATED    77  30    16
  AMP PEAK  2(1P22.3) WILD-TYPE 218  55    56
D2V5, multiclass
       clus
vv      AMP PEAK  2(1P22.3) MUTATED AMP PEAK  2(1P22.3) WILD-TYPE
  N0                             77                           218
  N1                             30                            55
  N2+N3                          16                            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"
                               vv
clus                             M0  M1 M1A M1B  MX
  AMP PEAK  2(1P22.3) MUTATED    88   4   0   1  31
  AMP PEAK  2(1P22.3) WILD-TYPE 229  14   1   2  88
D2V6, multiclass
     clus
vv    AMP PEAK  2(1P22.3) MUTATED AMP PEAK  2(1P22.3) WILD-TYPE
  M0                           88                           229
  M1                            4                            14
  M1A                           0                             1
  M1B                           1                             2
  MX                           31                            88
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
                               cls
clus                              0   1
  AMP PEAK  2(1P22.3) MUTATED    68  57
  AMP PEAK  2(1P22.3) WILD-TYPE 180 157
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1P22.3) MUTATED     68   57
  AMP PEAK  2(1P22.3) WILD-TYPE  180  157
        clus
vv       AMP PEAK  2(1P22.3) MUTATED AMP PEAK  2(1P22.3) WILD-TYPE
  FEMALE                          68                           180
  MALE                            57                           157
[1] 2 2
[1] FALSE
D2V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  AMP PEAK  2(1P22.3) MUTATED                            4
  AMP PEAK  2(1P22.3) WILD-TYPE                          9
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK  2(1P22.3) MUTATED                                  22
  AMP PEAK  2(1P22.3) WILD-TYPE                                71
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  2(1P22.3) MUTATED                                                   84
  AMP PEAK  2(1P22.3) WILD-TYPE                                                210
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK  2(1P22.3) MUTATED                                            0
  AMP PEAK  2(1P22.3) WILD-TYPE                                          4
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK  2(1P22.3) MUTATED                                               7
  AMP PEAK  2(1P22.3) WILD-TYPE                                            12
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK  2(1P22.3) MUTATED                                0
  AMP PEAK  2(1P22.3) WILD-TYPE                              2
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK  2(1P22.3) MUTATED                                    2
  AMP PEAK  2(1P22.3) WILD-TYPE                                  2
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK  2(1P22.3) MUTATED                              0
  AMP PEAK  2(1P22.3) WILD-TYPE                            2
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK  2(1P22.3) MUTATED                               3
  AMP PEAK  2(1P22.3) WILD-TYPE                            16
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK  2(1P22.3) MUTATED                                 0
  AMP PEAK  2(1P22.3) WILD-TYPE                               1
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK  2(1P22.3) MUTATED                                               2
  AMP PEAK  2(1P22.3) WILD-TYPE                                             2
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK  2(1P22.3) MUTATED                              1
  AMP PEAK  2(1P22.3) WILD-TYPE                            6
D2V9, multiclass
                                                    clus
vv                                                   AMP PEAK  2(1P22.3) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           22
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          84
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                   0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                7
  LUNG CLEAR CELL ADENOCARCINOMA                                               0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                           2
  LUNG MUCINOUS ADENOCARCINOMA                                                 0
  LUNG PAPILLARY ADENOCARCINOMA                                                3
  LUNG SIGNET RING ADENOCARCINOMA                                              0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                2
  MUCINOUS (COLLOID) CARCINOMA                                                 1
                                                    clus
vv                                                   AMP PEAK  2(1P22.3) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             71
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           210
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     4
  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                                  2
  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"
D2V10, binary
                               cls
clus                              0   1
  AMP PEAK  2(1P22.3) MUTATED     5 120
  AMP PEAK  2(1P22.3) WILD-TYPE  16 321
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1P22.3) MUTATED      5  120
  AMP PEAK  2(1P22.3) WILD-TYPE   16  321
     clus
vv    AMP PEAK  2(1P22.3) MUTATED AMP PEAK  2(1P22.3) WILD-TYPE
  NO                            5                            16
  YES                         120                           321
[1] 2 2
[1] FALSE
D2V11, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  2(1P22.3) MUTATED    84   5   1   4
  AMP PEAK  2(1P22.3) WILD-TYPE 234   6   3  15
D2V12, multiclass
    clus
vv   AMP PEAK  2(1P22.3) MUTATED AMP PEAK  2(1P22.3) WILD-TYPE
  R0                          84                           234
  R1                           5                             6
  R2                           1                             3
  RX                           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                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  2(1P22.3) MUTATED                                  1     2
  AMP PEAK  2(1P22.3) WILD-TYPE                                0     4
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  2(1P22.3) MUTATED                           9    97
  AMP PEAK  2(1P22.3) WILD-TYPE                        17   265
D2V13, multiclass
                                  clus
vv                                 AMP PEAK  2(1P22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                  9
  WHITE                                                     97
                                  clus
vv                                 AMP PEAK  2(1P22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   17
  WHITE                                                      265
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V14, binary
                               cls
clus                              0   1
  AMP PEAK  2(1P22.3) MUTATED     1  84
  AMP PEAK  2(1P22.3) WILD-TYPE   6 248
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1P22.3) MUTATED      1   84
  AMP PEAK  2(1P22.3) WILD-TYPE    6  248
                        clus
vv                       AMP PEAK  2(1P22.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          84
                        clus
vv                       AMP PEAK  2(1P22.3) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           248
[1] 2 2
[1] FALSE

Clustering(3) Variable = AMP PEAK  3(1Q21.3) MUTATION ANALYSIS
D3V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  3(1Q21.3) MUTATED   231  64
  AMP PEAK  3(1Q21.3) WILD-TYPE  90  18
  AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE 
                          295                           108 
  AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE 
                           64                            18 
$`AMP PEAK  3(1Q21.3) MUTATED`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 
        1523          607          426         1369         1126         1947 
TCGA-05-4398 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 TCGA-05-4422 
        1431          610         1958         1997          455          365 
TCGA-05-4424 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-5420 TCGA-05-5423 
         913          791          761          761          457          151 
TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4123 
         882          670           30           62           14          182 
TCGA-35-5375 TCGA-38-4625 TCGA-38-4628 TCGA-38-4629 TCGA-38-4632 TCGA-38-6178 
         264         1952         1492          864         1357          448 
TCGA-38-7271 TCGA-44-2655 TCGA-44-2656 TCGA-44-2659 TCGA-44-2662 TCGA-44-2665 
        1971         1324         1429         1367         1280         1301 
TCGA-44-2668 TCGA-44-3918 TCGA-44-4112 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 
         246         1036          722          863          383          723 
TCGA-44-6147 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
         845          705         1938         1942         1864         1978 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 
         444          592          218         1970          882          535 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
         719          385           99          466          287          337 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
         415           76         1932         1081         1421          428 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-6742 TCGA-49-6743 
         999          268          896          157          445          369 
TCGA-49-6744 TCGA-49-6761 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5066 
         890          354         2174         2146          455          944 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
        1499          246          282          267         1091         2370 
TCGA-50-5935 TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 TCGA-50-6597 TCGA-50-7109 
         653          567          764          686         1015          255 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
         105         1986         1971          424          280          701 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6971 
        1479           87          993           24         1239           25 
TCGA-55-6972 TCGA-55-6980 TCGA-55-6983 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 
        1475           67         1826         1170           18           35 
TCGA-55-7284 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7725 TCGA-55-7815 
         121            4           95           40           39           54 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 
          19           16          197            3            5           33 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8206 
          21          100           26            4           47           46 
TCGA-55-8207 TCGA-55-8301 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
          66           44            8           15          228            9 
TCGA-55-8514 TCGA-55-8615 TCGA-55-8616 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
         202           15           48           33           42           29 
TCGA-55-A490 TCGA-55-A492 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8398 
          48            1            5           47          162         1970 
TCGA-62-8399 TCGA-62-A46U TCGA-62-A46V TCGA-64-1676 TCGA-64-1679 TCGA-64-1680 
        2696         2067         2199         1728         1686         1126 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-67-3771 
        1968         1959         1305          864         1559          610 
TCGA-67-3772 TCGA-67-3774 TCGA-67-6215 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
         573          385          174          422          202          186 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7979 TCGA-69-7980 
         690          414          165          230           89          382 
TCGA-69-8253 TCGA-69-8254 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 
         100           77          214           61         1600          711 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
         912          800          467          131           40          164 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 
          38          621          519         1967         1956         1965 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        1988         1950         1944         1093         1963         1202 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
         760         1948         1961         1963         1221          678 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
         215         1940         1950         1934         1937         1965 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7633 TCGA-78-8640 
        1972         1949         1944          327          994         1949 
TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
        1981         1964         1972         1959           11          630 
TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
         422          591         1963          508          745           10 
TCGA-86-8056 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
        1963           24          479          489          476          482 
TCGA-86-8280 TCGA-86-8281 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8669 
          16         1955           19           26           35           34 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 
          15          455          405           10           30           14 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
         323         1940          310           79          417          372 
TCGA-91-6847 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
         842           35          492          197          174           36 
TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 
         127          186           34            2          568          377 
TCGA-95-7947 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 TCGA-97-7553 TCGA-97-7554 
         477          121          964         1965         1332          775 
TCGA-97-7937 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8179 TCGA-97-8547 
         181          107          182         1965           15          148 
TCGA-97-8552 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8032 TCGA-99-8033 
         115          271          392          427           44          170 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L9-A443 TCGA-L9-A444 
         114          287          238          578          116            6 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T7 
         285          622          353         1946         1967         1954 
TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TK 
        1957         1944         1970         1970          142         1971 
TCGA-MP-A5C7 
        1490 

$`AMP PEAK  3(1Q21.3) WILD-TYPE`
TCGA-05-4403 TCGA-05-4420 TCGA-05-4425 TCGA-05-4426 TCGA-05-4433 TCGA-35-4122 
         578          912          669          791          730          225 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4630 TCGA-38-4631 TCGA-38-A44F TCGA-44-2657 
        1962         1147         1073          354          133          400 
TCGA-44-2661 TCGA-44-2666 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-5643 
         741           97         1130         1163          190         1013 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6148 TCGA-44-6774 TCGA-44-7661 TCGA-44-7667 
         328          302          704          658          366          557 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47G TCGA-49-4514 TCGA-49-6745 TCGA-50-5055 
         260          486          351         1700          522          785 
TCGA-50-5942 TCGA-55-1594 TCGA-55-1596 TCGA-55-6543 TCGA-55-6985 TCGA-55-6986 
         883         1178         1375            2         1233         2151 
TCGA-55-7570 TCGA-55-7724 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7911 
           6         1958           39           34           24           21 
TCGA-55-7994 TCGA-55-8090 TCGA-55-8091 TCGA-55-8097 TCGA-55-8205 TCGA-55-8299 
          31            6           43           15           33          216 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 
          23           29           11            3          146          536 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A491 TCGA-55-A493 TCGA-62-8395 
          49           66          106         1952           28         1216 
TCGA-62-8397 TCGA-62-8402 TCGA-62-A471 TCGA-62-A472 TCGA-64-1677 TCGA-64-1678 
        1289         1445         1246          910          628         1189 
TCGA-64-5775 TCGA-64-5815 TCGA-67-3770 TCGA-67-3773 TCGA-67-6216 TCGA-69-7974 
          62          866           31          427          141          184 
TCGA-69-7978 TCGA-69-8255 TCGA-75-6214 TCGA-78-7145 TCGA-78-7155 TCGA-78-7540 
          70          129         1970         1973         1957          881 
TCGA-78-7542 TCGA-78-8648 TCGA-78-8660 TCGA-80-5607 TCGA-83-5908 TCGA-86-7714 
        1952         1971         1954         1965          824         1968 
TCGA-86-8073 TCGA-86-8668 TCGA-86-8671 TCGA-86-A4P8 TCGA-91-6830 TCGA-91-6848 
          13           45           18           39           60          224 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-95-7948 TCGA-97-7552 TCGA-97-7941 
          44          218          297          476         1932           22 
TCGA-97-8175 TCGA-97-8177 TCGA-97-A4M2 TCGA-99-8028 TCGA-J2-8192 TCGA-J2-A4AE 
          87          147          197          459          154          282 
TCGA-L4-A4E6 TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TI 
         435         1951         1954         1980         1951         1955 

  AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE 
                            1                             2 
  AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE 
                         2696                          2151 
  AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE 
                          476                           431 
[1] "1.0 - 2696.0 (476.0)" "2.0 - 2151.0 (431.0)"
[1] "hr=" "1"  
D3V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK  3(1Q21.3) MUTATED         4       81       95        32        45
  AMP PEAK  3(1Q21.3) WILD-TYPE       0       32       36        11        24
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK  3(1Q21.3) MUTATED           46         11       17
  AMP PEAK  3(1Q21.3) WILD-TYPE         21          0        6
D3V3, multiclass
            clus
vv           AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE
  STAGE I                              4                             0
  STAGE IA                            81                            32
  STAGE IB                            95                            36
  STAGE IIA                           32                            11
  STAGE IIB                           45                            24
  STAGE IIIA                          46                            21
  STAGE IIIB                          11                             0
  STAGE IV                            17                             6
[1] 8 2
[1] TRUE
[1] "dimension of 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(1Q21.3) MUTATED    99 189  27  15
  AMP PEAK  3(1Q21.3) WILD-TYPE  44  70  13   3
D3V4, multiclass
    clus
vv   AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE
  T1                          99                            44
  T2                         189                            70
  T3                          27                            13
  T4                          15                             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  3(1Q21.3) MUTATED   209  62    52
  AMP PEAK  3(1Q21.3) WILD-TYPE  86  23    20
D3V5, multiclass
       clus
vv      AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE
  N0                            209                            86
  N1                             62                            23
  N2+N3                          52                            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"
                               vv
clus                             M0  M1 M1A M1B  MX
  AMP PEAK  3(1Q21.3) MUTATED   230  14   1   1  82
  AMP PEAK  3(1Q21.3) WILD-TYPE  87   4   0   2  37
D3V6, multiclass
     clus
vv    AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE
  M0                          230                            87
  M1                           14                             4
  M1A                           1                             0
  M1B                           1                             2
  MX                           82                            37
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
                               cls
clus                              0   1
  AMP PEAK  3(1Q21.3) MUTATED   170 162
  AMP PEAK  3(1Q21.3) WILD-TYPE  78  52
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q21.3) MUTATED    170  162
  AMP PEAK  3(1Q21.3) WILD-TYPE   78   52
        clus
vv       AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE
  FEMALE                         170                            78
  MALE                           162                            52
[1] 2 2
[1] FALSE
D3V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  AMP PEAK  3(1Q21.3) MUTATED                           12
  AMP PEAK  3(1Q21.3) WILD-TYPE                          1
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK  3(1Q21.3) MUTATED                                  70
  AMP PEAK  3(1Q21.3) WILD-TYPE                                23
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  3(1Q21.3) MUTATED                                                  207
  AMP PEAK  3(1Q21.3) WILD-TYPE                                                 87
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK  3(1Q21.3) MUTATED                                            0
  AMP PEAK  3(1Q21.3) WILD-TYPE                                          4
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK  3(1Q21.3) MUTATED                                              16
  AMP PEAK  3(1Q21.3) WILD-TYPE                                             3
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK  3(1Q21.3) MUTATED                                2
  AMP PEAK  3(1Q21.3) WILD-TYPE                              0
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK  3(1Q21.3) MUTATED                                    3
  AMP PEAK  3(1Q21.3) WILD-TYPE                                  1
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK  3(1Q21.3) MUTATED                              0
  AMP PEAK  3(1Q21.3) WILD-TYPE                            2
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK  3(1Q21.3) MUTATED                              15
  AMP PEAK  3(1Q21.3) WILD-TYPE                             4
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK  3(1Q21.3) MUTATED                                 1
  AMP PEAK  3(1Q21.3) WILD-TYPE                               0
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK  3(1Q21.3) MUTATED                                               2
  AMP PEAK  3(1Q21.3) WILD-TYPE                                             2
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK  3(1Q21.3) MUTATED                              4
  AMP PEAK  3(1Q21.3) WILD-TYPE                            3
D3V9, multiclass
                                                    clus
vv                                                   AMP PEAK  3(1Q21.3) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                  12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           70
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         207
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                   0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                               16
  LUNG CLEAR CELL ADENOCARCINOMA                                               2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                           3
  LUNG MUCINOUS ADENOCARCINOMA                                                 0
  LUNG PAPILLARY ADENOCARCINOMA                                               15
  LUNG SIGNET RING ADENOCARCINOMA                                              1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                2
  MUCINOUS (COLLOID) CARCINOMA                                                 4
                                                    clus
vv                                                   AMP PEAK  3(1Q21.3) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             23
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            87
  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                                                   3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V10, binary
                               cls
clus                              0   1
  AMP PEAK  3(1Q21.3) MUTATED    17 315
  AMP PEAK  3(1Q21.3) WILD-TYPE   4 126
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q21.3) MUTATED     17  315
  AMP PEAK  3(1Q21.3) WILD-TYPE    4  126
     clus
vv    AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE
  NO                           17                             4
  YES                         315                           126
[1] 2 2
[1] FALSE
D3V11, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  3(1Q21.3) MUTATED   225   8   2  16
  AMP PEAK  3(1Q21.3) WILD-TYPE  93   3   2   3
D3V12, multiclass
    clus
vv   AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE
  R0                         225                            93
  R1                           8                             3
  R2                           2                             2
  RX                          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                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  3(1Q21.3) MUTATED                                  1     5
  AMP PEAK  3(1Q21.3) WILD-TYPE                                0     1
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  3(1Q21.3) MUTATED                          19   260
  AMP PEAK  3(1Q21.3) WILD-TYPE                         7   102
D3V13, multiclass
                                  clus
vv                                 AMP PEAK  3(1Q21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      5
  BLACK OR AFRICAN AMERICAN                                 19
  WHITE                                                    260
                                  clus
vv                                 AMP PEAK  3(1Q21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                    7
  WHITE                                                      102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V14, binary
                               cls
clus                              0   1
  AMP PEAK  3(1Q21.3) MUTATED     5 236
  AMP PEAK  3(1Q21.3) WILD-TYPE   2  96
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q21.3) MUTATED      5  236
  AMP PEAK  3(1Q21.3) WILD-TYPE    2   96
                        clus
vv                       AMP PEAK  3(1Q21.3) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         236
                        clus
vv                       AMP PEAK  3(1Q21.3) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            96
[1] 2 2
[1] FALSE

Clustering(4) Variable = AMP PEAK  4(3Q26.2) MUTATION ANALYSIS
D4V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  4(3Q26.2) MUTATED   105  25
  AMP PEAK  4(3Q26.2) WILD-TYPE 216  57
  AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE 
                          130                           273 
  AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE 
                           25                            57 
$`AMP PEAK  4(3Q26.2) MUTATED`
TCGA-05-4382 TCGA-05-4389 TCGA-05-4398 TCGA-05-4410 TCGA-05-4417 TCGA-05-4420 
         607         1369         1431         1958          455          912 
TCGA-05-4424 TCGA-05-4427 TCGA-05-4430 TCGA-05-5420 TCGA-05-5425 TCGA-05-5429 
         913          791          761          457          882           30 
TCGA-35-4122 TCGA-35-5375 TCGA-38-4626 TCGA-38-4628 TCGA-38-4630 TCGA-38-4631 
         225          264         1962         1492         1073          354 
TCGA-44-2662 TCGA-44-2668 TCGA-44-3918 TCGA-44-5643 TCGA-44-6145 TCGA-44-6147 
        1280          246         1036         1013          328          845 
TCGA-44-6779 TCGA-44-7660 TCGA-44-7669 TCGA-44-7670 TCGA-44-7672 TCGA-44-A47B 
        1978          592         1970          882          719          287 
TCGA-49-4507 TCGA-49-6743 TCGA-49-6744 TCGA-50-5055 TCGA-50-5072 TCGA-50-5931 
         268          369          890          785          246          267 
TCGA-50-5941 TCGA-50-5946 TCGA-53-7624 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1596 
         567          686         1986          280         1178         1375 
TCGA-55-5899 TCGA-55-6642 TCGA-55-6969 TCGA-55-6972 TCGA-55-6985 TCGA-55-6987 
          87          993         1239         1475         1233         1170 
TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7726 TCGA-55-7815 TCGA-55-7907 
         121            4         1958           39           54           16 
TCGA-55-7910 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8094 TCGA-55-8205 
         197           31            5           33            4           33 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8614 TCGA-55-8620 TCGA-55-A490 TCGA-55-A491 
           8           15          536           66           48         1952 
TCGA-55-A493 TCGA-55-A4DF TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-5781 
          28           47         1728          628         1686         1559 
TCGA-64-5815 TCGA-67-3771 TCGA-69-7760 TCGA-69-7761 TCGA-69-7978 TCGA-69-7979 
         866          610          202          186           70           89 
TCGA-69-7980 TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 
         382          214           61          711          800          467 
TCGA-73-4676 TCGA-73-7499 TCGA-75-6214 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
         164          519         1970         1973         1988         1950 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7220 TCGA-78-7539 TCGA-78-7540 TCGA-78-8662 
        1948         1957         1965          327          881         1964 
TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7953 TCGA-86-8055 
         824         1959           11          630          591           10 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8278 TCGA-86-8358 TCGA-86-8669 TCGA-86-8673 
          24          479          476           19           34          455 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 TCGA-91-6840 TCGA-91-6848 
         323         1940           60           79          372          224 
TCGA-91-7771 TCGA-91-8497 TCGA-91-8499 TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 
         492          174           36          186           34            2 
TCGA-95-7567 TCGA-95-7947 TCGA-97-7553 TCGA-J2-A4AD TCGA-L9-A443 TCGA-L9-A444 
         568          477         1332          287          116            6 
TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4TF TCGA-MP-A4TK 
         622         1946         1970         1971 

$`AMP PEAK  4(3Q26.2) WILD-TYPE`
TCGA-05-4249 TCGA-05-4384 TCGA-05-4390 TCGA-05-4396 TCGA-05-4403 TCGA-05-4405 
        1523          426         1126         1947          578          610 
TCGA-05-4415 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4432 TCGA-05-4433 
        1997          365          669          791          761          730 
TCGA-05-5423 TCGA-05-5428 TCGA-05-5715 TCGA-35-3615 TCGA-35-4123 TCGA-38-4625 
         151          670           62           14          182         1952 
TCGA-38-4627 TCGA-38-4629 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F 
        1147          864         1357          448         1971          133 
TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2665 
        1324         1429          400         1367          741         1301 
TCGA-44-2666 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5644 
          97         1130         1163          190          722          863 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6146 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
         383          723          302          704          658          705 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-7659 TCGA-44-7661 TCGA-44-7662 
        1938         1942         1864          444          366          218 
TCGA-44-7667 TCGA-44-7671 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 
         557          535          385           99          260          486 
TCGA-44-A47A TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
         466          337          351          415           76         1932 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4510 TCGA-49-4512 
        1081         1421          428          999          896          157 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-50-5045 TCGA-50-5049 
        1700          445          522          354         2174         2146 
TCGA-50-5051 TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 
         455          944         1499          282         1091         2370 
TCGA-50-5935 TCGA-50-5942 TCGA-50-5944 TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 
         653          883          764         1015          255          105 
TCGA-53-7626 TCGA-53-7813 TCGA-55-1592 TCGA-55-1595 TCGA-55-6543 TCGA-55-6712 
        1971          424          701         1479            2           24 
TCGA-55-6971 TCGA-55-6980 TCGA-55-6983 TCGA-55-6986 TCGA-55-7281 TCGA-55-7283 
          25           67         1826         2151           18           35 
TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7725 TCGA-55-7727 TCGA-55-7728 
           6           95           40           39           34           24 
TCGA-55-7903 TCGA-55-7911 TCGA-55-7914 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
          19           21            3           21          100            6 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8207 
          43           26           47           15           46           66 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8510 
         216           44           23           29           11          228 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8615 TCGA-55-8616 
           9            3          146          202           15           48 
TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A492 
          49          106           33           42           29            1 
TCGA-55-A494 TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
           5          162         1216         1289         1970         2696 
TCGA-62-8402 TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 TCGA-64-1678 
        1445         2067         2199         1246          910         1189 
TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
        1126         1968         1959           62         1305          864 
TCGA-67-3770 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 
          31          573          427          385          174          141 
TCGA-67-6217 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
         422          690          414          165          230          184 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-73-4658 TCGA-73-4662 TCGA-73-4670 
         100           77          129         1600          912          131 
TCGA-73-4675 TCGA-73-4677 TCGA-73-7498 TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 
          40           38          621         1967         1956         1965 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7156 
        1944         1093         1963         1202          760         1961 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        1963         1221          678          215         1940         1950 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7542 
        1934         1937         1972         1949         1944         1952 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-80-5607 
         994         1949         1971         1981         1954         1965 
TCGA-80-5608 TCGA-86-7713 TCGA-86-7714 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
        1972          422         1968         1963          508          745 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8076 TCGA-86-8279 TCGA-86-8280 TCGA-86-8281 
        1963           13          489          482           16         1955 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 
          26           35           45           18           15          405 
TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6831 TCGA-91-6836 
          10           30           14           39          310          417 
TCGA-91-6847 TCGA-91-6849 TCGA-91-8496 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
         842           35          197           44          218          297 
TCGA-93-7348 TCGA-95-7944 TCGA-95-7948 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 
         127          377          476          121          964         1965 
TCGA-97-7552 TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
        1932          775          181           22          107          182 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
        1965           87          147           15          148          115 
TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
         197          271          392          427          459           44 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
         170          154          114          282          238          578 
TCGA-L4-A4E6 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 
         435          285          353         1967         1951         1954 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TE 
        1954         1957         1980         1951         1944         1970 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A5C7 
         142         1955         1490 

  AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE 
                            2                             1 
  AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE 
                         1988                          2696 
  AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE 
                        505.5                         444.0 
[1] "2.0 - 1988.0 (505.5)" "1.0 - 2696.0 (444.0)"
[1] "hr=" "1.1"
D4V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK  4(3Q26.2) MUTATED         1       36       41        19        24
  AMP PEAK  4(3Q26.2) WILD-TYPE       3       77       90        24        45
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK  4(3Q26.2) MUTATED           19          3       10
  AMP PEAK  4(3Q26.2) WILD-TYPE         48          8       13
D4V3, multiclass
            clus
vv           AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE
  STAGE I                              1                             3
  STAGE IA                            36                            77
  STAGE IB                            41                            90
  STAGE IIA                           19                            24
  STAGE IIB                           24                            45
  STAGE IIIA                          19                            48
  STAGE IIIB                           3                             8
  STAGE IV                            10                            13
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK  4(3Q26.2) MUTATED    47  88  12   5
  AMP PEAK  4(3Q26.2) WILD-TYPE  96 171  28  13
D4V4, multiclass
    clus
vv   AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE
  T1                          47                            96
  T2                          88                           171
  T3                          12                            28
  T4                           5                            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  4(3Q26.2) MUTATED    96  35    20
  AMP PEAK  4(3Q26.2) WILD-TYPE 199  50    52
D4V5, multiclass
       clus
vv      AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE
  N0                             96                           199
  N1                             35                            50
  N2+N3                          20                            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"
                               vv
clus                             M0  M1 M1A M1B  MX
  AMP PEAK  4(3Q26.2) MUTATED   102   8   0   2  41
  AMP PEAK  4(3Q26.2) WILD-TYPE 215  10   1   1  78
D4V6, multiclass
     clus
vv    AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE
  M0                          102                           215
  M1                            8                            10
  M1A                           0                             1
  M1B                           2                             1
  MX                           41                            78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
                               cls
clus                              0   1
  AMP PEAK  4(3Q26.2) MUTATED    84  69
  AMP PEAK  4(3Q26.2) WILD-TYPE 164 145
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(3Q26.2) MUTATED     84   69
  AMP PEAK  4(3Q26.2) WILD-TYPE  164  145
        clus
vv       AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE
  FEMALE                          84                           164
  MALE                            69                           145
[1] 2 2
[1] FALSE
D4V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  AMP PEAK  4(3Q26.2) MUTATED                            5
  AMP PEAK  4(3Q26.2) WILD-TYPE                          8
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK  4(3Q26.2) MUTATED                                  32
  AMP PEAK  4(3Q26.2) WILD-TYPE                                61
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  4(3Q26.2) MUTATED                                                  101
  AMP PEAK  4(3Q26.2) WILD-TYPE                                                193
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK  4(3Q26.2) MUTATED                                            1
  AMP PEAK  4(3Q26.2) WILD-TYPE                                          3
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK  4(3Q26.2) MUTATED                                               5
  AMP PEAK  4(3Q26.2) WILD-TYPE                                            14
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK  4(3Q26.2) MUTATED                                1
  AMP PEAK  4(3Q26.2) WILD-TYPE                              1
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK  4(3Q26.2) MUTATED                                    1
  AMP PEAK  4(3Q26.2) WILD-TYPE                                  3
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK  4(3Q26.2) MUTATED                              0
  AMP PEAK  4(3Q26.2) WILD-TYPE                            2
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK  4(3Q26.2) MUTATED                               4
  AMP PEAK  4(3Q26.2) WILD-TYPE                            15
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK  4(3Q26.2) MUTATED                                 1
  AMP PEAK  4(3Q26.2) WILD-TYPE                               0
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK  4(3Q26.2) MUTATED                                               1
  AMP PEAK  4(3Q26.2) WILD-TYPE                                             3
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK  4(3Q26.2) MUTATED                              1
  AMP PEAK  4(3Q26.2) WILD-TYPE                            6
D4V9, multiclass
                                                    clus
vv                                                   AMP PEAK  4(3Q26.2) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           32
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         101
  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                                                4
  LUNG SIGNET RING ADENOCARCINOMA                                              1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                1
  MUCINOUS (COLLOID) CARCINOMA                                                 1
                                                    clus
vv                                                   AMP PEAK  4(3Q26.2) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             61
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           193
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 14
  LUNG CLEAR CELL ADENOCARCINOMA                                                 1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             3
  LUNG MUCINOUS ADENOCARCINOMA                                                   2
  LUNG PAPILLARY ADENOCARCINOMA                                                 15
  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"
D4V10, binary
                               cls
clus                              0   1
  AMP PEAK  4(3Q26.2) MUTATED     6 147
  AMP PEAK  4(3Q26.2) WILD-TYPE  15 294
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(3Q26.2) MUTATED      6  147
  AMP PEAK  4(3Q26.2) WILD-TYPE   15  294
     clus
vv    AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE
  NO                            6                            15
  YES                         147                           294
[1] 2 2
[1] FALSE
D4V11, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  4(3Q26.2) MUTATED   105   3   3   6
  AMP PEAK  4(3Q26.2) WILD-TYPE 213   8   1  13
D4V12, multiclass
    clus
vv   AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE
  R0                         105                           213
  R1                           3                             8
  R2                           3                             1
  RX                           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                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  4(3Q26.2) MUTATED                                  1     3
  AMP PEAK  4(3Q26.2) WILD-TYPE                                0     3
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  4(3Q26.2) MUTATED                           6   117
  AMP PEAK  4(3Q26.2) WILD-TYPE                        20   245
D4V13, multiclass
                                  clus
vv                                 AMP PEAK  4(3Q26.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                  6
  WHITE                                                    117
                                  clus
vv                                 AMP PEAK  4(3Q26.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        3
  BLACK OR AFRICAN AMERICAN                                   20
  WHITE                                                      245
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V14, binary
                               cls
clus                              0   1
  AMP PEAK  4(3Q26.2) MUTATED     4 105
  AMP PEAK  4(3Q26.2) WILD-TYPE   3 227
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(3Q26.2) MUTATED      4  105
  AMP PEAK  4(3Q26.2) WILD-TYPE    3  227
                        clus
vv                       AMP PEAK  4(3Q26.2) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         105
                        clus
vv                       AMP PEAK  4(3Q26.2) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           227
[1] 2 2
[1] FALSE

Clustering(5) Variable = AMP PEAK  5(4Q12) MUTATION ANALYSIS
D5V1, survival
                             sevent
clus2                           0   1
  AMP PEAK  5(4Q12) MUTATED    59  17
  AMP PEAK  5(4Q12) WILD-TYPE 262  65
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                         76                         327 
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                         17                          65 
$`AMP PEAK  5(4Q12) MUTATED`
TCGA-05-4420 TCGA-05-4432 TCGA-05-5423 TCGA-05-5425 TCGA-38-4628 TCGA-38-4629 
         912          761          151          882         1492          864 
TCGA-38-6178 TCGA-44-2656 TCGA-44-2659 TCGA-44-2662 TCGA-44-4112 TCGA-44-5645 
         448         1429         1367         1280          722          383 
TCGA-44-6775 TCGA-44-6778 TCGA-44-7661 TCGA-44-7670 TCGA-44-8117 TCGA-44-A4SU 
         705         1864          366          882          385           76 
TCGA-49-4507 TCGA-53-7624 TCGA-53-7813 TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 
         268         1986          424          701         1178         1479 
TCGA-55-1596 TCGA-55-6712 TCGA-55-7283 TCGA-55-7573 TCGA-55-7576 TCGA-55-7995 
        1375           24           35            4           40            5 
TCGA-55-8089 TCGA-55-8091 TCGA-55-8092 TCGA-55-8620 TCGA-55-A490 TCGA-55-A493 
         100           43           26           66           48           28 
TCGA-55-A4DF TCGA-62-8402 TCGA-62-A471 TCGA-64-1676 TCGA-64-1680 TCGA-69-7979 
          47         1445         1246         1728         1126           89 
TCGA-69-7980 TCGA-69-8253 TCGA-73-4662 TCGA-75-6214 TCGA-78-7145 TCGA-78-7150 
         382          100          912         1970         1973         1963 
TCGA-78-7154 TCGA-78-7161 TCGA-78-7163 TCGA-78-7535 TCGA-78-7542 TCGA-78-8662 
        1948          215         1950         1972         1952         1964 
TCGA-86-7953 TCGA-86-7955 TCGA-86-8054 TCGA-86-8074 TCGA-86-8278 TCGA-86-8279 
         591          508          745           24          476          482 
TCGA-86-8669 TCGA-86-8673 TCGA-86-A456 TCGA-91-6848 TCGA-91-8499 TCGA-95-7039 
          34          455           10          224           36           34 
TCGA-95-7567 TCGA-95-7948 TCGA-97-7937 TCGA-97-8179 TCGA-J2-8194 TCGA-L4-A4E5 
         568          476          181           15          114          578 
TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4TF TCGA-MP-A4TK 
         353         1967         1970         1971 

$`AMP PEAK  5(4Q12) WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 
        1523          607          426         1369         1126         1947 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 
        1431          578          610         1958         1997          455 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 
         365          913          669          791          791          761 
TCGA-05-4433 TCGA-05-5420 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
         730          457          670           30           62           14 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
         225          182          264         1952         1962         1147 
TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 
        1073          354         1357         1971          133         1324 
TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 
         400          741         1301           97          246         1130 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 
        1163         1036          190         1013          863          723 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6776 
         328          302          845          704          658         1938 
TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 
        1942         1978          444          592          218          557 
TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 
        1970          535          719           99          260          486 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 
         466          287          337          351          415         1932 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4510 TCGA-49-4512 
        1081         1421          428          999          896          157 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
        1700          445          369          890          522          354 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
        2174         2146          455          785          944         1499 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
         246          282          267         1091         2370          653 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6597 TCGA-50-7109 
         567          883          764          686         1015          255 
TCGA-50-8460 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
         105         1971          280           87            2          993 
TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 
        1239           25         1475           67         1826         1233 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7284 TCGA-55-7570 TCGA-55-7574 
        2151         1170           18          121            6           95 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
        1958           39           39           34           24           54 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
          19           16          197           21            3           31 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
          33           21            6            4           47           15 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
          33           46           66          216           44           23 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
          29           11            8           15          228            9 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
           3          146          202          536           15           48 
TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 
          49          106           33           42           29         1952 
TCGA-55-A492 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
           1            5          162         1216         1289         1970 
TCGA-62-8399 TCGA-62-A46U TCGA-62-A46V TCGA-62-A472 TCGA-64-1677 TCGA-64-1678 
        2696         2067         2199          910          628         1189 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
        1686         1968         1959           62         1305          864 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
        1559          866           31          610          573          427 
TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
         385          174          141          422          202          186 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
         690          414          165          230          184           70 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 
          77          129          214           61         1600          711 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
         800          467          131           40          164           38 
TCGA-73-7498 TCGA-73-7499 TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 TCGA-78-7146 
         621          519         1967         1956         1965         1988 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7155 
        1950         1944         1093         1202          760         1957 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7162 TCGA-78-7166 
        1961         1963         1221          678         1940         1934 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
        1937         1965         1949         1944          327          881 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-80-5607 
         994         1949         1971         1981         1954         1965 
TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
        1972          824         1959           11          630          422 
TCGA-86-7714 TCGA-86-7954 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 
        1968         1963           10         1963           13          479 
TCGA-86-8076 TCGA-86-8280 TCGA-86-8281 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
         489           16         1955           19           26           35 
TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 TCGA-86-A4D0 TCGA-86-A4P7 
          45           18           15          405           30           14 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
          39          323         1940           60          310           79 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
         417          372          842           35          492          197 
TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
         174           44          218          297          127          186 
TCGA-95-7043 TCGA-95-7944 TCGA-95-7947 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 
           2          377          477          121          964         1965 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
        1932         1332          775           22          107          182 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 
        1965           87          147          148          115          197 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
         271          392          427          459           44          170 
TCGA-J2-8192 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 
         154          287          282          238          435          116 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4T2 TCGA-MP-A4T4 
           6          285          622         1946         1951         1954 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TE 
        1954         1957         1980         1951         1944         1970 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A5C7 
         142         1955         1490 

  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                          4                           1 
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                       1986                        2696 
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                        495                         455 
[1] "4.0 - 1986.0 (495.0)" "1.0 - 2696.0 (455.0)"
[1] "hr=" "1.2"
D5V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK  5(4Q12) MUTATED         2       17       28         6        21
  AMP PEAK  5(4Q12) WILD-TYPE       2       96      103        37        48
                             vv
clus                          STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK  5(4Q12) MUTATED           10          1        5
  AMP PEAK  5(4Q12) WILD-TYPE         57         10       18
D5V3, multiclass
            clus
vv           AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  STAGE I                            2                           2
  STAGE IA                          17                          96
  STAGE IB                          28                         103
  STAGE IIA                          6                          37
  STAGE IIB                         21                          48
  STAGE IIIA                        10                          57
  STAGE IIIB                         1                          10
  STAGE IV                           5                          18
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2  T3  T4
  AMP PEAK  5(4Q12) MUTATED    24  54  10   2
  AMP PEAK  5(4Q12) WILD-TYPE 119 205  30  16
D5V4, multiclass
    clus
vv   AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  T1                        24                         119
  T2                        54                         205
  T3                        10                          30
  T4                         2                          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  5(4Q12) MUTATED    57  22    10
  AMP PEAK  5(4Q12) WILD-TYPE 238  63    62
D5V5, multiclass
       clus
vv      AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  N0                           57                         238
  N1                           22                          63
  N2+N3                        10                          62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           M0  M1 M1A M1B  MX
  AMP PEAK  5(4Q12) MUTATED    64   4   0   1  19
  AMP PEAK  5(4Q12) WILD-TYPE 253  14   1   2 100
D5V6, multiclass
     clus
vv    AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  M0                         64                         253
  M1                          4                          14
  M1A                         0                           1
  M1B                         1                           2
  MX                         19                         100
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
                             cls
clus                            0   1
  AMP PEAK  5(4Q12) MUTATED    46  44
  AMP PEAK  5(4Q12) WILD-TYPE 202 170
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(4Q12) MUTATED     46   44
  AMP PEAK  5(4Q12) WILD-TYPE  202  170
        clus
vv       AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  FEMALE                        46                         202
  MALE                          44                         170
[1] 2 2
[1] FALSE
D5V8, continuous
                             vv
clus                          LUNG ACINAR ADENOCARCINOMA
  AMP PEAK  5(4Q12) MUTATED                            3
  AMP PEAK  5(4Q12) WILD-TYPE                         10
                             vv
clus                          LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK  5(4Q12) MUTATED                                  12
  AMP PEAK  5(4Q12) WILD-TYPE                                81
                             vv
clus                          LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  5(4Q12) MUTATED                                                   67
  AMP PEAK  5(4Q12) WILD-TYPE                                                227
                             vv
clus                          LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK  5(4Q12) MUTATED                                            0
  AMP PEAK  5(4Q12) WILD-TYPE                                          4
                             vv
clus                          LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK  5(4Q12) MUTATED                                               4
  AMP PEAK  5(4Q12) WILD-TYPE                                            15
                             vv
clus                          LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK  5(4Q12) MUTATED                                1
  AMP PEAK  5(4Q12) WILD-TYPE                              1
                             vv
clus                          LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK  5(4Q12) MUTATED                                    1
  AMP PEAK  5(4Q12) WILD-TYPE                                  3
                             vv
clus                          LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK  5(4Q12) MUTATED                              0
  AMP PEAK  5(4Q12) WILD-TYPE                            2
                             vv
clus                          LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK  5(4Q12) MUTATED                               1
  AMP PEAK  5(4Q12) WILD-TYPE                            18
                             vv
clus                          LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK  5(4Q12) MUTATED                                 0
  AMP PEAK  5(4Q12) WILD-TYPE                               1
                             vv
clus                          LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK  5(4Q12) MUTATED                                               1
  AMP PEAK  5(4Q12) WILD-TYPE                                             3
                             vv
clus                          MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK  5(4Q12) MUTATED                              0
  AMP PEAK  5(4Q12) WILD-TYPE                            7
D5V9, multiclass
                                                    clus
vv                                                   AMP PEAK  5(4Q12) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                 3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                         12
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                        67
  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                                              1
  LUNG SIGNET RING ADENOCARCINOMA                                            0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                              1
  MUCINOUS (COLLOID) CARCINOMA                                               0
                                                    clus
vv                                                   AMP PEAK  5(4Q12) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                  10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           81
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         227
  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"
D5V10, binary
                             cls
clus                            0   1
  AMP PEAK  5(4Q12) MUTATED     2  88
  AMP PEAK  5(4Q12) WILD-TYPE  19 353
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(4Q12) MUTATED      2   88
  AMP PEAK  5(4Q12) WILD-TYPE   19  353
     clus
vv    AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  NO                          2                          19
  YES                        88                         353
[1] 2 2
[1] FALSE
D5V11, continuous
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK  5(4Q12) MUTATED    59   3   0   3
  AMP PEAK  5(4Q12) WILD-TYPE 259   8   4  16
D5V12, multiclass
    clus
vv   AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  R0                        59                         259
  R1                         3                           8
  R2                         0                           4
  RX                         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                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  5(4Q12) MUTATED                                  0     3
  AMP PEAK  5(4Q12) WILD-TYPE                                1     3
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  5(4Q12) MUTATED                           5    68
  AMP PEAK  5(4Q12) WILD-TYPE                        21   294
D5V13, multiclass
                                  clus
vv                                 AMP PEAK  5(4Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    3
  BLACK OR AFRICAN AMERICAN                                5
  WHITE                                                   68
                                  clus
vv                                 AMP PEAK  5(4Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 21
  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"
D5V14, binary
                             cls
clus                            0   1
  AMP PEAK  5(4Q12) MUTATED     3  62
  AMP PEAK  5(4Q12) WILD-TYPE   4 270
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(4Q12) MUTATED      3   62
  AMP PEAK  5(4Q12) WILD-TYPE    4  270
                        clus
vv                       AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  HISPANIC OR LATINO                             3                           4
  NOT HISPANIC OR LATINO                        62                         270
[1] 2 2
[1] FALSE

Clustering(6) Variable = AMP PEAK  6(5P15.33) MUTATION ANALYSIS
D6V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  6(5P15.33) MUTATED   210  56
  AMP PEAK  6(5P15.33) WILD-TYPE 111  26
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                           266                            137 
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                            56                             26 
$`AMP PEAK  6(5P15.33) MUTATED`
TCGA-05-4382 TCGA-05-4389 TCGA-05-4396 TCGA-05-4398 TCGA-05-4405 TCGA-05-4410 
         607         1369         1947         1431          610         1958 
TCGA-05-4415 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4426 TCGA-05-4430 
        1997          912          365          913          791          761 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5715 TCGA-35-3615 TCGA-35-4123 
         151          882          670           62           14          182 
TCGA-35-5375 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4631 
         264         1962         1147         1492          864          354 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 
        1357          448         1971         1324         1429          400 
TCGA-44-2659 TCGA-44-2662 TCGA-44-2668 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
        1367         1280          246         1163         1036          190 
TCGA-44-4112 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6147 TCGA-44-6774 
         722          863          383          723          845          658 
TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 
         705         1942         1864          444          592          218 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
         557         1970          882          719          385           99 
TCGA-44-A47A TCGA-44-A47F TCGA-44-A4SS TCGA-49-4486 TCGA-49-4501 TCGA-49-4505 
         466          337          415         1932         1421          428 
TCGA-49-4506 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 
         999          896          157         1700          369          890 
TCGA-49-6761 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5066 TCGA-50-5068 
         354         2174         2146          455          944         1499 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 
         246          282          267         2370          653          567 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6597 TCGA-50-7109 TCGA-53-7624 TCGA-53-7626 
         764          686         1015          255         1986         1971 
TCGA-53-7813 TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 
         424          701         1178         1479         1375           87 
TCGA-55-6543 TCGA-55-6712 TCGA-55-6969 TCGA-55-6972 TCGA-55-6980 TCGA-55-6983 
           2           24         1239         1475           67         1826 
TCGA-55-6985 TCGA-55-6987 TCGA-55-7281 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        1233         1170           18            6            4           95 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7903 TCGA-55-7910 
        1958           39           39           34           19          197 
TCGA-55-7911 TCGA-55-7994 TCGA-55-8091 TCGA-55-8094 TCGA-55-8096 TCGA-55-8206 
          21           31           43            4           47           46 
TCGA-55-8207 TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
          66           44           23           11            8           15 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
         228            9          202          536           15           48 
TCGA-55-8620 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A490 TCGA-55-A491 TCGA-55-A493 
          66           33           42           48         1952           28 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 TCGA-62-8399 TCGA-62-8402 
           5           47          162         1216         2696         1445 
TCGA-62-A46U TCGA-62-A471 TCGA-62-A472 TCGA-64-1677 TCGA-64-1679 TCGA-64-1680 
        2067         1246          910          628         1686         1126 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 TCGA-64-5781 TCGA-67-3770 TCGA-67-6215 
        1968         1959         1305         1559           31          174 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
         141          422          202          690          414          165 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8255 
         230          184           89          382          100          129 
TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4662 TCGA-73-4668 TCGA-73-4675 
         214           61         1600          912          467           40 
TCGA-73-4676 TCGA-73-7499 TCGA-75-6214 TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 
         164          519         1970         1965         1973         1988 
TCGA-78-7147 TCGA-78-7149 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7159 
        1950         1093          760         1948         1957         1221 
TCGA-78-7160 TCGA-78-7163 TCGA-78-7166 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
         678         1950         1934         1965         1972         1949 
TCGA-78-7539 TCGA-78-7633 TCGA-78-8640 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 
         327          994         1949         1981         1964         1972 
TCGA-83-5908 TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 
         824         1959          630          422          591         1963 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
         508          745           10           13           24          479 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8671 
         482           16           19           26           35           18 
TCGA-86-8672 TCGA-86-8673 TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
          15          455           30          323         1940           60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6848 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
         417          372          224           36           44          218 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 
         297          127          186           34            2          568 
TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 TCGA-97-7553 
         477          476          121          964         1965         1332 
TCGA-97-7554 TCGA-97-7937 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8179 
         775          181          107          182         1965           15 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
         148          115          271          392          427          459 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L9-A444 
         170          154          287          282          578            6 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 
         285          622          353         1967         1951         1954 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TF 
        1954         1957         1980         1951         1944         1970 
TCGA-MP-A4TH TCGA-MP-A4TK 
         142         1971 

$`AMP PEAK  6(5P15.33) WILD-TYPE`
TCGA-05-4249 TCGA-05-4384 TCGA-05-4390 TCGA-05-4403 TCGA-05-4417 TCGA-05-4425 
        1523          426         1126          578          455          669 
TCGA-05-4427 TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 TCGA-05-5429 TCGA-35-4122 
         791          761          730          457           30          225 
TCGA-38-4625 TCGA-38-4630 TCGA-38-A44F TCGA-44-2661 TCGA-44-2665 TCGA-44-2666 
        1952         1073          133          741         1301           97 
TCGA-44-3396 TCGA-44-5643 TCGA-44-6145 TCGA-44-6146 TCGA-44-6148 TCGA-44-6776 
        1130         1013          328          302          704         1938 
TCGA-44-6779 TCGA-44-7661 TCGA-44-7671 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B 
        1978          366          535          260          486          287 
TCGA-44-A47G TCGA-44-A4SU TCGA-49-4494 TCGA-49-4507 TCGA-49-6742 TCGA-49-6745 
         351           76         1081          268          445          522 
TCGA-50-5055 TCGA-50-5932 TCGA-50-5942 TCGA-50-8460 TCGA-53-A4EZ TCGA-55-6642 
         785         1091          883          105          280          993 
TCGA-55-6971 TCGA-55-6986 TCGA-55-7283 TCGA-55-7284 TCGA-55-7576 TCGA-55-7728 
          25         2151           35          121           40           24 
TCGA-55-7815 TCGA-55-7907 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
          54           16            3            5           33           21 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8092 TCGA-55-8097 TCGA-55-8205 TCGA-55-8299 
         100            6           26           15           33          216 
TCGA-55-8505 TCGA-55-8512 TCGA-55-8513 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48Z 
          29            3          146           49          106           29 
TCGA-55-A492 TCGA-62-8397 TCGA-62-8398 TCGA-62-A46V TCGA-64-1676 TCGA-64-1678 
           1         1289         1970         2199         1728         1189 
TCGA-64-5775 TCGA-64-5779 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
          62          864          866          610          573          427 
TCGA-67-3774 TCGA-69-7761 TCGA-69-7978 TCGA-69-8254 TCGA-73-4659 TCGA-73-4666 
         385          186           70           77          711          800 
TCGA-73-4670 TCGA-73-4677 TCGA-73-7498 TCGA-75-7025 TCGA-75-7027 TCGA-78-7148 
         131           38          621         1967         1956         1944 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7156 TCGA-78-7158 TCGA-78-7161 TCGA-78-7162 
        1963         1202         1961         1963          215         1940 
TCGA-78-7167 TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-8648 TCGA-78-8660 
        1937         1944          881         1952         1971         1954 
TCGA-80-5607 TCGA-86-7701 TCGA-86-7714 TCGA-86-8056 TCGA-86-8076 TCGA-86-8278 
        1965           11         1968         1963          489          476 
TCGA-86-8281 TCGA-86-8668 TCGA-86-8669 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 
        1955           45           34          405           10           14 
TCGA-86-A4P8 TCGA-91-6831 TCGA-91-6835 TCGA-91-6847 TCGA-91-6849 TCGA-91-7771 
          39          310           79          842           35          492 
TCGA-91-8496 TCGA-91-8497 TCGA-95-7944 TCGA-97-7552 TCGA-97-7941 TCGA-97-8175 
         197          174          377         1932           22           87 
TCGA-97-8177 TCGA-97-A4M2 TCGA-99-8032 TCGA-J2-8194 TCGA-J2-A4AG TCGA-L4-A4E6 
         147          197           44          114          238          435 
TCGA-L9-A443 TCGA-MP-A4SV TCGA-MP-A4TE TCGA-MP-A4TI TCGA-MP-A5C7 
         116         1946         1970         1955         1490 

  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                             2                              1 
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                          2696                           2199 
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                         480.5                          427.0 
[1] "2.0 - 2696.0 (480.5)" "1.0 - 2199.0 (427.0)"
[1] "hr=" "1.1"
D6V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK  6(5P15.33) MUTATED         4       75       83        33        40
  AMP PEAK  6(5P15.33) WILD-TYPE       0       38       48        10        29
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK  6(5P15.33) MUTATED           45          8       14
  AMP PEAK  6(5P15.33) WILD-TYPE         22          3        9
D6V3, multiclass
            clus
vv           AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE
  STAGE I                               4                              0
  STAGE IA                             75                             38
  STAGE IB                             83                             48
  STAGE IIA                            33                             10
  STAGE IIB                            40                             29
  STAGE IIIA                           45                             22
  STAGE IIIB                            8                              3
  STAGE IV                             14                              9
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK  6(5P15.33) MUTATED    97 170  21  12
  AMP PEAK  6(5P15.33) WILD-TYPE  46  89  19   6
D6V4, multiclass
    clus
vv   AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE
  T1                           97                             46
  T2                          170                             89
  T3                           21                             19
  T4                           12                              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1 N2+N3
  AMP PEAK  6(5P15.33) MUTATED   187  56    52
  AMP PEAK  6(5P15.33) WILD-TYPE 108  29    20
D6V5, multiclass
       clus
vv      AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE
  N0                             187                            108
  N1                              56                             29
  N2+N3                           52                             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"
                                vv
clus                              M0  M1 M1A M1B  MX
  AMP PEAK  6(5P15.33) MUTATED   206  10   1   2  80
  AMP PEAK  6(5P15.33) WILD-TYPE 111   8   0   1  39
D6V6, multiclass
     clus
vv    AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE
  M0                           206                            111
  M1                            10                              8
  M1A                            1                              0
  M1B                            2                              1
  MX                            80                             39
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
                                cls
clus                               0   1
  AMP PEAK  6(5P15.33) MUTATED   169 133
  AMP PEAK  6(5P15.33) WILD-TYPE  79  81
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(5P15.33) MUTATED    169  133
  AMP PEAK  6(5P15.33) WILD-TYPE   79   81
        clus
vv       AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE
  FEMALE                          169                             79
  MALE                            133                             81
[1] 2 2
[1] FALSE
D6V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  AMP PEAK  6(5P15.33) MUTATED                            9
  AMP PEAK  6(5P15.33) WILD-TYPE                          4
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK  6(5P15.33) MUTATED                                  56
  AMP PEAK  6(5P15.33) WILD-TYPE                                37
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  6(5P15.33) MUTATED                                                  201
  AMP PEAK  6(5P15.33) WILD-TYPE                                                 93
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK  6(5P15.33) MUTATED                                            1
  AMP PEAK  6(5P15.33) WILD-TYPE                                          3
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK  6(5P15.33) MUTATED                                              13
  AMP PEAK  6(5P15.33) WILD-TYPE                                             6
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK  6(5P15.33) MUTATED                                2
  AMP PEAK  6(5P15.33) WILD-TYPE                              0
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK  6(5P15.33) MUTATED                                    3
  AMP PEAK  6(5P15.33) WILD-TYPE                                  1
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK  6(5P15.33) MUTATED                              0
  AMP PEAK  6(5P15.33) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK  6(5P15.33) MUTATED                              12
  AMP PEAK  6(5P15.33) WILD-TYPE                             7
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK  6(5P15.33) MUTATED                                 0
  AMP PEAK  6(5P15.33) WILD-TYPE                               1
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK  6(5P15.33) MUTATED                                               3
  AMP PEAK  6(5P15.33) WILD-TYPE                                             1
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK  6(5P15.33) MUTATED                              2
  AMP PEAK  6(5P15.33) WILD-TYPE                            5
D6V9, multiclass
                                                    clus
vv                                                   AMP PEAK  6(5P15.33) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            56
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          201
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                13
  LUNG CLEAR CELL ADENOCARCINOMA                                                2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            3
  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(5P15.33) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              37
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             93
  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                                                   7
  LUNG SIGNET RING ADENOCARCINOMA                                                 1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                   1
  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"
D6V10, binary
                                cls
clus                               0   1
  AMP PEAK  6(5P15.33) MUTATED    16 286
  AMP PEAK  6(5P15.33) WILD-TYPE   5 155
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(5P15.33) MUTATED     16  286
  AMP PEAK  6(5P15.33) WILD-TYPE    5  155
     clus
vv    AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE
  NO                            16                              5
  YES                          286                            155
[1] 2 2
[1] FALSE
D6V11, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK  6(5P15.33) MUTATED   206   7   2  14
  AMP PEAK  6(5P15.33) WILD-TYPE 112   4   2   5
D6V12, multiclass
    clus
vv   AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE
  R0                          206                            112
  R1                            7                              4
  R2                            2                              2
  RX                           14                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  6(5P15.33) MUTATED                                  1     5
  AMP PEAK  6(5P15.33) WILD-TYPE                                0     1
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  6(5P15.33) MUTATED                          18   239
  AMP PEAK  6(5P15.33) WILD-TYPE                         8   123
D6V13, multiclass
                                  clus
vv                                 AMP PEAK  6(5P15.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  18
  WHITE                                                     239
                                  clus
vv                                 AMP PEAK  6(5P15.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         1
  BLACK OR AFRICAN AMERICAN                                     8
  WHITE                                                       123
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V14, binary
                                cls
clus                               0   1
  AMP PEAK  6(5P15.33) MUTATED     5 219
  AMP PEAK  6(5P15.33) WILD-TYPE   2 113
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(5P15.33) MUTATED      5  219
  AMP PEAK  6(5P15.33) WILD-TYPE    2  113
                        clus
vv                       AMP PEAK  6(5P15.33) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          219
                        clus
vv                       AMP PEAK  6(5P15.33) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            113
[1] 2 2
[1] FALSE

Clustering(7) Variable = AMP PEAK  7(5P13.1) MUTATION ANALYSIS
D7V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  7(5P13.1) MUTATED   199  46
  AMP PEAK  7(5P13.1) WILD-TYPE 122  36
  AMP PEAK  7(5P13.1) MUTATED AMP PEAK  7(5P13.1) WILD-TYPE 
                          245                           158 
  AMP PEAK  7(5P13.1) MUTATED AMP PEAK  7(5P13.1) WILD-TYPE 
                           46                            36 
$`AMP PEAK  7(5P13.1) MUTATED`
TCGA-05-4389 TCGA-05-4396 TCGA-05-4398 TCGA-05-4405 TCGA-05-4410 TCGA-05-4420 
        1369         1947         1431          610         1958          912 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4426 TCGA-05-4430 TCGA-05-5423 TCGA-05-5425 
         365          913          791          761          151          882 
TCGA-05-5428 TCGA-05-5715 TCGA-35-3615 TCGA-35-4123 TCGA-35-5375 TCGA-38-4626 
         670           62           14          182          264         1962 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
        1147         1492          864          354         1357          448 
TCGA-38-7271 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2662 TCGA-44-2665 
        1971         1429          400         1367         1280         1301 
TCGA-44-2668 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5644 
         246         1163         1036          190          722          863 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6147 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 
         383          723          845          658          705         1942 
TCGA-44-6778 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
        1864          444          592          218          557         1970 
TCGA-44-7670 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-A47A TCGA-44-A47F 
         882          719          385           99          466          337 
TCGA-44-A4SS TCGA-49-4501 TCGA-49-4505 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
         415         1421          428          896          157         1700 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6761 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
         369          890          354         2174         2146          455 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 TCGA-50-5935 TCGA-50-5941 
         944         1499          282          267          653          567 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6597 TCGA-50-7109 TCGA-53-7624 TCGA-53-7626 
         764          686         1015          255         1986         1971 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-5899 
         424          280          701         1178         1479           87 
TCGA-55-6543 TCGA-55-6969 TCGA-55-6972 TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 
           2         1239         1475           67         1826         1233 
TCGA-55-6987 TCGA-55-7281 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7724 
        1170           18            6            4           95         1958 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 
          39           39           34           19          197           21 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8091 TCGA-55-8094 TCGA-55-8096 TCGA-55-8206 
          31            5           43            4           47           46 
TCGA-55-8207 TCGA-55-8302 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
          66           23           11            8           15          228 
TCGA-55-8511 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 
           9          202          536           15           48           66 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A493 
          33           42           29           48         1952           28 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 TCGA-62-8399 TCGA-62-8402 
           5           47          162         1216         2696         1445 
TCGA-62-A46U TCGA-62-A471 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-5774 
        2067         1246         1189         1686         1126         1959 
TCGA-64-5778 TCGA-64-5781 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
        1305         1559          427          174          141          422 
TCGA-69-7760 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7980 
         202          690          414          165          230          382 
TCGA-69-8253 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4668 
         100          129          214           61         1600          467 
TCGA-73-4675 TCGA-73-4676 TCGA-73-7499 TCGA-75-6214 TCGA-75-7031 TCGA-78-7147 
          40          164          519         1970         1965         1950 
TCGA-78-7149 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7159 TCGA-78-7160 
        1093          760         1948         1957         1221          678 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 
        1950         1934         1965         1972         1949          327 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 
         994         1949         1981         1964         1972          824 
TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
        1959          630          422          591         1963          508 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 
         745           10           13           24          479          482 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8672 TCGA-86-8673 
          16           19           26           35           15          455 
TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6836 
          30          323         1940           60          310          417 
TCGA-91-6840 TCGA-91-6848 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
         372          224           36           44          218          297 
TCGA-93-7348 TCGA-95-7039 TCGA-95-7043 TCGA-95-7947 TCGA-95-7948 TCGA-97-7546 
         127           34            2          477          476          964 
TCGA-97-7547 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-8172 TCGA-97-8174 
        1965         1332          775          181          182         1965 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M7 TCGA-99-8025 TCGA-99-8033 
          15          148          115          271          427          170 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
         287          282          578            6          285          622 
TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 
         353         1967         1951         1954         1954         1957 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TK 
        1951         1944         1970          142         1971 

$`AMP PEAK  7(5P13.1) WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4390 TCGA-05-4403 TCGA-05-4415 
        1523          607          426         1126          578         1997 
TCGA-05-4417 TCGA-05-4425 TCGA-05-4427 TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 
         455          669          791          761          730          457 
TCGA-05-5429 TCGA-35-4122 TCGA-38-4625 TCGA-38-4630 TCGA-38-A44F TCGA-44-2655 
          30          225         1952         1073          133         1324 
TCGA-44-2661 TCGA-44-2666 TCGA-44-3396 TCGA-44-5643 TCGA-44-6145 TCGA-44-6146 
         741           97         1130         1013          328          302 
TCGA-44-6148 TCGA-44-6776 TCGA-44-6779 TCGA-44-7661 TCGA-44-7671 TCGA-44-8120 
         704         1938         1978          366          535          260 
TCGA-44-A479 TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 
         486          287          351           76         1932         1081 
TCGA-49-4506 TCGA-49-4507 TCGA-49-6742 TCGA-49-6745 TCGA-50-5055 TCGA-50-5072 
         999          268          445          522          785          246 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5942 TCGA-50-8460 TCGA-55-1596 TCGA-55-6642 
        1091         2370          883          105         1375          993 
TCGA-55-6712 TCGA-55-6971 TCGA-55-6986 TCGA-55-7283 TCGA-55-7284 TCGA-55-7576 
          24           25         2151           35          121           40 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7907 TCGA-55-7914 TCGA-55-8085 TCGA-55-8087 
          24           54           16            3           33           21 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8092 TCGA-55-8097 TCGA-55-8205 TCGA-55-8299 
         100            6           26           15           33          216 
TCGA-55-8301 TCGA-55-8505 TCGA-55-8512 TCGA-55-8513 TCGA-55-8619 TCGA-55-8621 
          44           29            3          146           49          106 
TCGA-55-A492 TCGA-62-8397 TCGA-62-8398 TCGA-62-A46V TCGA-62-A472 TCGA-64-1676 
           1         1289         1970         2199          910         1728 
TCGA-64-1677 TCGA-64-1681 TCGA-64-5775 TCGA-64-5779 TCGA-64-5815 TCGA-67-3770 
         628         1968           62          864          866           31 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3774 TCGA-69-7761 TCGA-69-7974 TCGA-69-7978 
         610          573          385          186          184           70 
TCGA-69-7979 TCGA-69-8254 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4670 
          89           77          711          912          800          131 
TCGA-73-4677 TCGA-73-7498 TCGA-75-7025 TCGA-75-7027 TCGA-78-7145 TCGA-78-7146 
          38          621         1967         1956         1973         1988 
TCGA-78-7148 TCGA-78-7150 TCGA-78-7152 TCGA-78-7156 TCGA-78-7158 TCGA-78-7161 
        1944         1963         1202         1961         1963          215 
TCGA-78-7162 TCGA-78-7167 TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-8648 
        1940         1937         1944          881         1952         1971 
TCGA-78-8660 TCGA-80-5607 TCGA-86-7701 TCGA-86-7714 TCGA-86-8056 TCGA-86-8076 
        1954         1965           11         1968         1963          489 
TCGA-86-8278 TCGA-86-8281 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8674 
         476         1955           45           34           18          405 
TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6835 TCGA-91-6847 TCGA-91-6849 
          10           14           39           79          842           35 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-93-8067 TCGA-95-7567 TCGA-95-7944 
         492          197          174          186          568          377 
TCGA-95-A4VK TCGA-97-7552 TCGA-97-7941 TCGA-97-8171 TCGA-97-8175 TCGA-97-8177 
         121         1932           22          107           87          147 
TCGA-97-A4M2 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 TCGA-J2-8192 TCGA-J2-8194 
         197          392          459           44          154          114 
TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 TCGA-MP-A4SV TCGA-MP-A4T9 TCGA-MP-A4TE 
         238          435          116         1946         1980         1970 
TCGA-MP-A4TI TCGA-MP-A5C7 
        1955         1490 

  AMP PEAK  7(5P13.1) MUTATED AMP PEAK  7(5P13.1) WILD-TYPE 
                            2                             1 
  AMP PEAK  7(5P13.1) MUTATED AMP PEAK  7(5P13.1) WILD-TYPE 
                         2696                          2370 
  AMP PEAK  7(5P13.1) MUTATED AMP PEAK  7(5P13.1) WILD-TYPE 
                          476                           456 
[1] "2.0 - 2696.0 (476.0)" "1.0 - 2370.0 (456.0)"
[1] "hr=" "1.1"
D7V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK  7(5P13.1) MUTATED         4       70       82        33        33
  AMP PEAK  7(5P13.1) WILD-TYPE       0       43       49        10        36
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK  7(5P13.1) MUTATED           37          7       12
  AMP PEAK  7(5P13.1) WILD-TYPE         30          4       11
D7V3, multiclass
            clus
vv           AMP PEAK  7(5P13.1) MUTATED AMP PEAK  7(5P13.1) WILD-TYPE
  STAGE I                              4                             0
  STAGE IA                            70                            43
  STAGE IB                            82                            49
  STAGE IIA                           33                            10
  STAGE IIB                           33                            36
  STAGE IIIA                          37                            30
  STAGE IIIB                           7                             4
  STAGE IV                            12                            11
[1] 8 2
[1] TRUE
[1] "dimension of 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(5P13.1) MUTATED    94 155  19   8
  AMP PEAK  7(5P13.1) WILD-TYPE  49 104  21  10
D7V4, multiclass
    clus
vv   AMP PEAK  7(5P13.1) MUTATED AMP PEAK  7(5P13.1) WILD-TYPE
  T1                          94                            49
  T2                         155                           104
  T3                          19                            21
  T4                           8                            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  7(5P13.1) MUTATED   180  49    43
  AMP PEAK  7(5P13.1) WILD-TYPE 115  36    29
D7V5, multiclass
       clus
vv      AMP PEAK  7(5P13.1) MUTATED AMP PEAK  7(5P13.1) WILD-TYPE
  N0                            180                           115
  N1                             49                            36
  N2+N3                          43                            29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B  MX
  AMP PEAK  7(5P13.1) MUTATED   189   9   0   2  75
  AMP PEAK  7(5P13.1) WILD-TYPE 128   9   1   1  44
D7V6, multiclass
     clus
vv    AMP PEAK  7(5P13.1) MUTATED AMP PEAK  7(5P13.1) WILD-TYPE
  M0                          189                           128
  M1                            9                             9
  M1A                           0                             1
  M1B                           2                             1
  MX                           75                            44
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
                               cls
clus                              0   1
  AMP PEAK  7(5P13.1) MUTATED   156 122
  AMP PEAK  7(5P13.1) WILD-TYPE  92  92
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(5P13.1) MUTATED    156  122
  AMP PEAK  7(5P13.1) WILD-TYPE   92   92
        clus
vv       AMP PEAK  7(5P13.1) MUTATED AMP PEAK  7(5P13.1) WILD-TYPE
  FEMALE                         156                            92
  MALE                           122                            92
[1] 2 2
[1] FALSE
D7V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  AMP PEAK  7(5P13.1) MUTATED                            9
  AMP PEAK  7(5P13.1) WILD-TYPE                          4
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK  7(5P13.1) MUTATED                                  50
  AMP PEAK  7(5P13.1) WILD-TYPE                                43
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  7(5P13.1) MUTATED                                                  186
  AMP PEAK  7(5P13.1) WILD-TYPE                                                108
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK  7(5P13.1) MUTATED                                            1
  AMP PEAK  7(5P13.1) WILD-TYPE                                          3
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK  7(5P13.1) MUTATED                                              12
  AMP PEAK  7(5P13.1) WILD-TYPE                                             7
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK  7(5P13.1) MUTATED                                2
  AMP PEAK  7(5P13.1) WILD-TYPE                              0
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK  7(5P13.1) MUTATED                                    3
  AMP PEAK  7(5P13.1) WILD-TYPE                                  1
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK  7(5P13.1) MUTATED                              0
  AMP PEAK  7(5P13.1) WILD-TYPE                            2
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK  7(5P13.1) MUTATED                              10
  AMP PEAK  7(5P13.1) WILD-TYPE                             9
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK  7(5P13.1) MUTATED                                 0
  AMP PEAK  7(5P13.1) WILD-TYPE                               1
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK  7(5P13.1) MUTATED                                               3
  AMP PEAK  7(5P13.1) WILD-TYPE                                             1
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK  7(5P13.1) MUTATED                              2
  AMP PEAK  7(5P13.1) WILD-TYPE                            5
D7V9, multiclass
                                                    clus
vv                                                   AMP PEAK  7(5P13.1) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           50
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         186
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                   1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                               12
  LUNG CLEAR CELL ADENOCARCINOMA                                               2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                           3
  LUNG MUCINOUS ADENOCARCINOMA                                                 0
  LUNG PAPILLARY ADENOCARCINOMA                                               10
  LUNG SIGNET RING ADENOCARCINOMA                                              0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                3
  MUCINOUS (COLLOID) CARCINOMA                                                 2
                                                    clus
vv                                                   AMP PEAK  7(5P13.1) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             43
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           108
  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                                                  9
  LUNG SIGNET RING ADENOCARCINOMA                                                1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                  1
  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"
D7V10, binary
                               cls
clus                              0   1
  AMP PEAK  7(5P13.1) MUTATED    13 265
  AMP PEAK  7(5P13.1) WILD-TYPE   8 176
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(5P13.1) MUTATED     13  265
  AMP PEAK  7(5P13.1) WILD-TYPE    8  176
     clus
vv    AMP PEAK  7(5P13.1) MUTATED AMP PEAK  7(5P13.1) WILD-TYPE
  NO                           13                             8
  YES                         265                           176
[1] 2 2
[1] FALSE
D7V11, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  7(5P13.1) MUTATED   194   5   1  12
  AMP PEAK  7(5P13.1) WILD-TYPE 124   6   3   7
D7V12, multiclass
    clus
vv   AMP PEAK  7(5P13.1) MUTATED AMP PEAK  7(5P13.1) WILD-TYPE
  R0                         194                           124
  R1                           5                             6
  R2                           1                             3
  RX                          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                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  7(5P13.1) MUTATED                                  1     2
  AMP PEAK  7(5P13.1) WILD-TYPE                                0     4
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  7(5P13.1) MUTATED                          17   224
  AMP PEAK  7(5P13.1) WILD-TYPE                         9   138
D7V13, multiclass
                                  clus
vv                                 AMP PEAK  7(5P13.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 17
  WHITE                                                    224
                                  clus
vv                                 AMP PEAK  7(5P13.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                    9
  WHITE                                                      138
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V14, binary
                               cls
clus                              0   1
  AMP PEAK  7(5P13.1) MUTATED     6 204
  AMP PEAK  7(5P13.1) WILD-TYPE   1 128
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(5P13.1) MUTATED      6  204
  AMP PEAK  7(5P13.1) WILD-TYPE    1  128
                        clus
vv                       AMP PEAK  7(5P13.1) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                         204
                        clus
vv                       AMP PEAK  7(5P13.1) WILD-TYPE
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                           128
[1] 2 2
[1] FALSE

Clustering(8) Variable = AMP PEAK  8(5Q35.1) MUTATION ANALYSIS
D8V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  8(5Q35.1) MUTATED    79  16
  AMP PEAK  8(5Q35.1) WILD-TYPE 242  66
  AMP PEAK  8(5Q35.1) MUTATED AMP PEAK  8(5Q35.1) WILD-TYPE 
                           95                           308 
  AMP PEAK  8(5Q35.1) MUTATED AMP PEAK  8(5Q35.1) WILD-TYPE 
                           16                            66 
$`AMP PEAK  8(5Q35.1) MUTATED`
TCGA-05-4426 TCGA-05-5423 TCGA-35-3615 TCGA-35-5375 TCGA-38-6178 TCGA-44-2657 
         791          151           14          264          448          400 
TCGA-44-2659 TCGA-44-2662 TCGA-44-2665 TCGA-44-3398 TCGA-44-4112 TCGA-44-5645 
        1367         1280         1301         1163          722          383 
TCGA-44-6777 TCGA-44-7659 TCGA-44-7672 TCGA-44-A47A TCGA-44-A47F TCGA-49-4501 
        1942          444          719          466          337         1421 
TCGA-49-4512 TCGA-49-6744 TCGA-49-6761 TCGA-50-5045 TCGA-50-5051 TCGA-50-5068 
         157          890          354         2174          455         1499 
TCGA-50-5935 TCGA-50-5944 TCGA-50-6597 TCGA-53-7813 TCGA-55-1595 TCGA-55-6543 
         653          764         1015          424         1479            2 
TCGA-55-6642 TCGA-55-6972 TCGA-55-6980 TCGA-55-6983 TCGA-55-6987 TCGA-55-7281 
         993         1475           67         1826         1170           18 
TCGA-55-7573 TCGA-55-7727 TCGA-55-7911 TCGA-55-8091 TCGA-55-8206 TCGA-55-8207 
           4           34           21           43           46           66 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8508 TCGA-55-A48Z TCGA-55-A491 
         216           44           23           15           29         1952 
TCGA-55-A493 TCGA-55-A4DG TCGA-62-A46U TCGA-64-1679 TCGA-64-1680 TCGA-64-5775 
          28          162         2067         1686         1126           62 
TCGA-64-5815 TCGA-67-3770 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
         866           31          174          141          422          202 
TCGA-69-7763 TCGA-69-7764 TCGA-69-8253 TCGA-73-4675 TCGA-73-7499 TCGA-75-6214 
         690          414          100           40          519         1970 
TCGA-78-7147 TCGA-78-7153 TCGA-78-7154 TCGA-78-7163 TCGA-78-7539 TCGA-78-7633 
        1950          760         1948         1950          327          994 
TCGA-86-7953 TCGA-86-7954 TCGA-86-8055 TCGA-86-8056 TCGA-86-8280 TCGA-86-8669 
         591         1963           10         1963           16           34 
TCGA-91-A4BD TCGA-93-7348 TCGA-95-7043 TCGA-97-7546 TCGA-97-7547 TCGA-97-8174 
         218          127            2          964         1965         1965 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M7 TCGA-99-8028 TCGA-99-8032 
         147           15          115          271          459           44 
TCGA-J2-A4AE TCGA-MP-A4T2 TCGA-MP-A4T7 TCGA-MP-A4TF TCGA-MP-A4TH 
         282         1951         1954         1970          142 

$`AMP PEAK  8(5Q35.1) WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 
        1523          607          426         1369         1126         1947 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 
        1431          578          610         1958         1997          455 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4427 TCGA-05-4430 
         912          365          913          669          791          761 
TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
         761          730          457          882          670           30 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
          62          225          182         1952         1962         1147 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-7271 
        1492          864         1073          354         1357         1971 
TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2661 TCGA-44-2666 TCGA-44-2668 
         133         1324         1429          741           97          246 
TCGA-44-3396 TCGA-44-3918 TCGA-44-3919 TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 
        1130         1036          190         1013          863          723 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
         328          302          845          704          658          705 
TCGA-44-6776 TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
        1938         1864         1978          592          366          218 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-8117 TCGA-44-8119 
         557         1970          882          535          385           99 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
         260          486          287          351          415           76 
TCGA-49-4486 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
        1932         1081          428          999          268          896 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6745 TCGA-50-5049 TCGA-50-5055 
        1700          445          369          522         2146          785 
TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
         944          246          282          267         1091         2370 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5946 TCGA-50-7109 TCGA-50-8460 TCGA-53-7624 
         567          883          686          255          105         1986 
TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 
        1971          280          701         1178         1375           87 
TCGA-55-6712 TCGA-55-6969 TCGA-55-6971 TCGA-55-6985 TCGA-55-6986 TCGA-55-7283 
          24         1239           25         1233         2151           35 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
         121            6           95           40         1958           39 
TCGA-55-7726 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
          39           24           54           19           16          197 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
           3           31            5           33           21          100 
TCGA-55-8090 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 
           6           26            4           47           15           33 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
          29           11            8          228            9            3 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
         146          202          536           15           48           49 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A490 TCGA-55-A492 
          66          106           33           42           48            1 
TCGA-55-A494 TCGA-55-A4DF TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
           5           47         1216         1289         1970         2696 
TCGA-62-8402 TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
        1445         2199         1246          910         1728          628 
TCGA-64-1678 TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
        1189         1968         1959         1305          864         1559 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-69-7761 TCGA-69-7765 
         610          573          427          385          186          165 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8254 
         230          184           70           89          382           77 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
         129          214           61         1600          711          912 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
         800          467          131          164           38          621 
TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 
        1967         1956         1965         1973         1988         1944 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
        1093         1963         1202         1957         1961         1963 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7166 TCGA-78-7167 
        1221          678          215         1940         1934         1937 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 
        1965         1972         1949         1944          881         1952 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 
        1949         1971         1981         1954         1964         1965 
TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
        1972          824         1959           11          630          422 
TCGA-86-7714 TCGA-86-7955 TCGA-86-8054 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
        1968          508          745           13           24          479 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8281 TCGA-86-8358 TCGA-86-8359 
         489          476          482         1955           19           26 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
          35           45           18           15          455          405 
TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
          10           30           14           39          323         1940 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
          60          310           79          417          372          842 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
         224           35          492          197          174           36 
TCGA-91-A4BC TCGA-93-7347 TCGA-93-8067 TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 
          44          297          186           34          568          377 
TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
         477          476          121         1932         1332          775 
TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 TCGA-97-8547 
         181           22          107          182           87          148 
TCGA-97-A4M2 TCGA-99-7458 TCGA-99-8025 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
         197          392          427          170          154          114 
TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
         287          238          578          435          116            6 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T4 
         285          622          353         1946         1967         1954 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TI 
        1957         1980         1951         1944         1970         1955 
TCGA-MP-A4TK TCGA-MP-A5C7 
        1971         1490 

  AMP PEAK  8(5Q35.1) MUTATED AMP PEAK  8(5Q35.1) WILD-TYPE 
                            2                             1 
  AMP PEAK  8(5Q35.1) MUTATED AMP PEAK  8(5Q35.1) WILD-TYPE 
                         2174                          2696 
  AMP PEAK  8(5Q35.1) MUTATED AMP PEAK  8(5Q35.1) WILD-TYPE 
                        424.0                         480.5 
[1] "2.0 - 2174.0 (424.0)" "1.0 - 2696.0 (480.5)"
[1] "hr=" "1"  
D8V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK  8(5Q35.1) MUTATED         1       36       27         9        12
  AMP PEAK  8(5Q35.1) WILD-TYPE       3       77      104        34        57
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK  8(5Q35.1) MUTATED           18          2        4
  AMP PEAK  8(5Q35.1) WILD-TYPE         49          9       19
D8V3, multiclass
            clus
vv           AMP PEAK  8(5Q35.1) MUTATED AMP PEAK  8(5Q35.1) WILD-TYPE
  STAGE I                              1                             3
  STAGE IA                            36                            77
  STAGE IB                            27                           104
  STAGE IIA                            9                            34
  STAGE IIB                           12                            57
  STAGE IIIA                          18                            49
  STAGE IIIB                           2                             9
  STAGE IV                             4                            19
[1] 8 2
[1] TRUE
[1] "dimension of 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(5Q35.1) MUTATED    41  59   5   3
  AMP PEAK  8(5Q35.1) WILD-TYPE 102 200  35  15
D8V4, multiclass
    clus
vv   AMP PEAK  8(5Q35.1) MUTATED AMP PEAK  8(5Q35.1) WILD-TYPE
  T1                          41                           102
  T2                          59                           200
  T3                           5                            35
  T4                           3                            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  8(5Q35.1) MUTATED    70  18    18
  AMP PEAK  8(5Q35.1) WILD-TYPE 225  67    54
D8V5, multiclass
       clus
vv      AMP PEAK  8(5Q35.1) MUTATED AMP PEAK  8(5Q35.1) WILD-TYPE
  N0                             70                           225
  N1                             18                            67
  N2+N3                          18                            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"
                               vv
clus                             M0  M1 M1A M1B  MX
  AMP PEAK  8(5Q35.1) MUTATED    72   4   0   0  31
  AMP PEAK  8(5Q35.1) WILD-TYPE 245  14   1   3  88
D8V6, multiclass
     clus
vv    AMP PEAK  8(5Q35.1) MUTATED AMP PEAK  8(5Q35.1) WILD-TYPE
  M0                           72                           245
  M1                            4                            14
  M1A                           0                             1
  M1B                           0                             3
  MX                           31                            88
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
                               cls
clus                              0   1
  AMP PEAK  8(5Q35.1) MUTATED    67  42
  AMP PEAK  8(5Q35.1) WILD-TYPE 181 172
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(5Q35.1) MUTATED     67   42
  AMP PEAK  8(5Q35.1) WILD-TYPE  181  172
        clus
vv       AMP PEAK  8(5Q35.1) MUTATED AMP PEAK  8(5Q35.1) WILD-TYPE
  FEMALE                          67                           181
  MALE                            42                           172
[1] 2 2
[1] FALSE
D8V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  AMP PEAK  8(5Q35.1) MUTATED                            5
  AMP PEAK  8(5Q35.1) WILD-TYPE                          8
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK  8(5Q35.1) MUTATED                                  19
  AMP PEAK  8(5Q35.1) WILD-TYPE                                74
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  8(5Q35.1) MUTATED                                                   70
  AMP PEAK  8(5Q35.1) WILD-TYPE                                                224
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK  8(5Q35.1) MUTATED                                            1
  AMP PEAK  8(5Q35.1) WILD-TYPE                                          3
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK  8(5Q35.1) MUTATED                                               6
  AMP PEAK  8(5Q35.1) WILD-TYPE                                            13
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK  8(5Q35.1) MUTATED                                1
  AMP PEAK  8(5Q35.1) WILD-TYPE                              1
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK  8(5Q35.1) MUTATED                                    0
  AMP PEAK  8(5Q35.1) WILD-TYPE                                  4
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK  8(5Q35.1) MUTATED                              0
  AMP PEAK  8(5Q35.1) WILD-TYPE                            2
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK  8(5Q35.1) MUTATED                               5
  AMP PEAK  8(5Q35.1) WILD-TYPE                            14
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK  8(5Q35.1) MUTATED                                 0
  AMP PEAK  8(5Q35.1) WILD-TYPE                               1
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK  8(5Q35.1) MUTATED                                               0
  AMP PEAK  8(5Q35.1) WILD-TYPE                                             4
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK  8(5Q35.1) MUTATED                              2
  AMP PEAK  8(5Q35.1) WILD-TYPE                            5
D8V9, multiclass
                                                    clus
vv                                                   AMP PEAK  8(5Q35.1) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           19
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          70
  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                                                5
  LUNG SIGNET RING ADENOCARCINOMA                                              0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                0
  MUCINOUS (COLLOID) CARCINOMA                                                 2
                                                    clus
vv                                                   AMP PEAK  8(5Q35.1) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             74
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           224
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 13
  LUNG CLEAR CELL ADENOCARCINOMA                                                 1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             4
  LUNG MUCINOUS ADENOCARCINOMA                                                   2
  LUNG PAPILLARY ADENOCARCINOMA                                                 14
  LUNG SIGNET RING ADENOCARCINOMA                                                1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                  4
  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"
D8V10, binary
                               cls
clus                              0   1
  AMP PEAK  8(5Q35.1) MUTATED     4 105
  AMP PEAK  8(5Q35.1) WILD-TYPE  17 336
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(5Q35.1) MUTATED      4  105
  AMP PEAK  8(5Q35.1) WILD-TYPE   17  336
     clus
vv    AMP PEAK  8(5Q35.1) MUTATED AMP PEAK  8(5Q35.1) WILD-TYPE
  NO                            4                            17
  YES                         105                           336
[1] 2 2
[1] FALSE
D8V11, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  8(5Q35.1) MUTATED    75   3   0   5
  AMP PEAK  8(5Q35.1) WILD-TYPE 243   8   4  14
D8V12, multiclass
    clus
vv   AMP PEAK  8(5Q35.1) MUTATED AMP PEAK  8(5Q35.1) WILD-TYPE
  R0                          75                           243
  R1                           3                             8
  R2                           0                             4
  RX                           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                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  8(5Q35.1) MUTATED                                  0     1
  AMP PEAK  8(5Q35.1) WILD-TYPE                                1     5
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  8(5Q35.1) MUTATED                           6    94
  AMP PEAK  8(5Q35.1) WILD-TYPE                        20   268
D8V13, multiclass
                                  clus
vv                                 AMP PEAK  8(5Q35.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  6
  WHITE                                                     94
                                  clus
vv                                 AMP PEAK  8(5Q35.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                   20
  WHITE                                                      268
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V14, binary
                               cls
clus                              0   1
  AMP PEAK  8(5Q35.1) MUTATED     0  84
  AMP PEAK  8(5Q35.1) WILD-TYPE   7 248
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(5Q35.1) MUTATED      0   84
  AMP PEAK  8(5Q35.1) WILD-TYPE    7  248
                        clus
vv                       AMP PEAK  8(5Q35.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          84
                        clus
vv                       AMP PEAK  8(5Q35.1) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           248
[1] 2 2
[1] FALSE

Clustering(9) Variable = AMP PEAK  9(6P21.1) MUTATION ANALYSIS
D9V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  9(6P21.1) MUTATED   129  27
  AMP PEAK  9(6P21.1) WILD-TYPE 192  55
  AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE 
                          156                           247 
  AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE 
                           27                            55 
$`AMP PEAK  9(6P21.1) MUTATED`
TCGA-05-4249 TCGA-05-4389 TCGA-05-4410 TCGA-05-4420 TCGA-05-4427 TCGA-05-4430 
        1523         1369         1958          912          791          761 
TCGA-05-5425 TCGA-35-3615 TCGA-35-5375 TCGA-38-4625 TCGA-38-4628 TCGA-38-6178 
         882           14          264         1952         1492          448 
TCGA-44-2659 TCGA-44-3918 TCGA-44-6147 TCGA-44-6774 TCGA-44-7660 TCGA-44-7662 
        1367         1036          845          658          592          218 
TCGA-44-7667 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-44-A4SU 
         557          882          535           99          337           76 
TCGA-49-4510 TCGA-49-4512 TCGA-49-6742 TCGA-49-6761 TCGA-50-5931 TCGA-50-5932 
         896          157          445          354          267         1091 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 TCGA-50-6597 
        2370          653          567          764          686         1015 
TCGA-50-7109 TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 
         255         1986          424          280          701         1479 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6642 TCGA-55-6972 TCGA-55-6985 TCGA-55-7283 
        1375           87          993         1475         1233           35 
TCGA-55-7573 TCGA-55-7576 TCGA-55-7815 TCGA-55-7903 TCGA-55-7914 TCGA-55-7994 
           4           40           54           19            3           31 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
           5           33           15           33           46           66 
TCGA-55-8507 TCGA-55-8511 TCGA-55-8512 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
           8            9            3          202          536           15 
TCGA-55-8616 TCGA-55-8620 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A490 TCGA-55-A494 
          48           66           33           42           48            5 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 
        1970         2696         1445         2067         2199         1246 
TCGA-64-1677 TCGA-64-1680 TCGA-64-5774 TCGA-64-5779 TCGA-67-3773 TCGA-67-6215 
         628         1126         1959          864          427          174 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7979 TCGA-69-7980 TCGA-69-8255 
         690          414          165           89          382          129 
TCGA-71-6725 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4677 
          61          912          800          467          131           38 
TCGA-73-7498 TCGA-73-7499 TCGA-75-6214 TCGA-78-7145 TCGA-78-7147 TCGA-78-7149 
         621          519         1970         1973         1950         1093 
TCGA-78-7155 TCGA-78-7158 TCGA-78-7159 TCGA-78-7161 TCGA-78-7162 TCGA-78-7167 
        1957         1963         1221          215         1940         1937 
TCGA-78-7220 TCGA-78-7539 TCGA-78-7542 TCGA-78-7633 TCGA-78-8655 TCGA-78-8662 
        1965          327         1952          994         1981         1964 
TCGA-80-5608 TCGA-86-6851 TCGA-86-7713 TCGA-86-7954 TCGA-86-8074 TCGA-86-8075 
        1972         1959          422         1963           24          479 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8281 TCGA-86-8358 TCGA-86-8359 TCGA-86-8672 
         482           16         1955           19           26           15 
TCGA-86-8674 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
         405          310           79          372          842          224 
TCGA-91-8499 TCGA-95-7567 TCGA-95-7944 TCGA-95-7948 TCGA-97-7546 TCGA-97-7553 
          36          568          377          476          964         1332 
TCGA-97-7554 TCGA-97-8171 TCGA-97-8174 TCGA-97-8177 TCGA-97-8179 TCGA-97-A4M2 
         775          107         1965          147           15          197 
TCGA-97-A4M7 TCGA-99-8033 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L9-A444 
         271          170          114          287          282            6 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A5C7 
         622          353         1946         1970         1970         1490 

$`AMP PEAK  9(6P21.1) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4390 TCGA-05-4396 TCGA-05-4398 TCGA-05-4403 
         607          426         1126         1947         1431          578 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
         610         1997          455          365          913          669 
TCGA-05-4426 TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5428 
         791          761          730          457          151          670 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-38-4626 TCGA-38-4627 
          30           62          225          182         1962         1147 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-7271 TCGA-38-A44F 
         864         1073          354         1357         1971          133 
TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 
        1324         1429          400          741         1280         1301 
TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 
          97          246         1130         1163          190          722 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
        1013          863          383          723          328          302 
TCGA-44-6148 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
         704          705         1938         1942         1864         1978 
TCGA-44-7659 TCGA-44-7661 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 
         444          366         1970          719          385          260 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 
         486          466          287          351          415         1932 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4514 
        1081         1421          428          999          268         1700 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
         369          890          522         2174         2146          455 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5942 
         785          944         1499          246          282          883 
TCGA-50-8460 TCGA-53-7626 TCGA-55-1594 TCGA-55-6543 TCGA-55-6712 TCGA-55-6969 
         105         1971         1178            2           24         1239 
TCGA-55-6971 TCGA-55-6980 TCGA-55-6983 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 
          25           67         1826         2151         1170           18 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7574 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
         121            6           95         1958           39           39 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-8087 
          34           24           16          197           21           21 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
         100            6           43           26            4           47 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 
         216           44           23           29           11           15 
TCGA-55-8510 TCGA-55-8513 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48Z TCGA-55-A491 
         228          146           49          106           29         1952 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 
           1           28           47          162         1216         1289 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 TCGA-64-5775 
         910         1728         1189         1686         1968           62 
TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 
        1305         1559          866           31          610          573 
TCGA-67-3774 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7973 
         385          141          422          202          186          230 
TCGA-69-7974 TCGA-69-7978 TCGA-69-8253 TCGA-69-8254 TCGA-69-A59K TCGA-73-4658 
         184           70          100           77          214         1600 
TCGA-73-4659 TCGA-73-4675 TCGA-73-4676 TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 
         711           40          164         1967         1956         1965 
TCGA-78-7146 TCGA-78-7148 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
        1988         1944         1963         1202          760         1948 
TCGA-78-7156 TCGA-78-7160 TCGA-78-7163 TCGA-78-7166 TCGA-78-7535 TCGA-78-7536 
        1961          678         1950         1934         1972         1949 
TCGA-78-7537 TCGA-78-7540 TCGA-78-8640 TCGA-78-8648 TCGA-78-8660 TCGA-80-5607 
        1944          881         1949         1971         1954         1965 
TCGA-83-5908 TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 TCGA-86-7953 TCGA-86-7955 
         824           11          630         1968          591          508 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8076 TCGA-86-8278 
         745           10         1963           13          489          476 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 TCGA-86-A456 
          35           45           34           18          455           10 
TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
          30           14           39          323         1940           60 
TCGA-91-6836 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC 
         417           35          492          197          174           44 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 
         218          297          127          186           34            2 
TCGA-95-7947 TCGA-95-A4VK TCGA-97-7547 TCGA-97-7552 TCGA-97-7937 TCGA-97-7941 
         477          121         1965         1932          181           22 
TCGA-97-8172 TCGA-97-8175 TCGA-97-8547 TCGA-97-8552 TCGA-99-7458 TCGA-99-8025 
         182           87          148          115          392          427 
TCGA-99-8028 TCGA-99-8032 TCGA-J2-8192 TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
         459           44          154          238          578          435 
TCGA-L9-A443 TCGA-MN-A4N1 TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 
         116          285         1967         1951         1954         1954 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TH TCGA-MP-A4TI 
        1957         1980         1951         1944          142         1955 
TCGA-MP-A4TK 
        1971 

  AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE 
                            3                             1 
  AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE 
                         2696                          2174 
  AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE 
                        480.5                         455.0 
[1] "3.0 - 2696.0 (480.5)" "1.0 - 2174.0 (455.0)"
[1] "hr=" "1.5"
D9V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK  9(6P21.1) MUTATED         2       47       49        16        22
  AMP PEAK  9(6P21.1) WILD-TYPE       2       66       82        27        47
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK  9(6P21.1) MUTATED           22          5       12
  AMP PEAK  9(6P21.1) WILD-TYPE         45          6       11
D9V3, multiclass
            clus
vv           AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE
  STAGE I                              2                             2
  STAGE IA                            47                            66
  STAGE IB                            49                            82
  STAGE IIA                           16                            27
  STAGE IIB                           22                            47
  STAGE IIIA                          22                            45
  STAGE IIIB                           5                             6
  STAGE IV                            12                            11
[1] 8 2
[1] TRUE
[1] "dimension of 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(6P21.1) MUTATED    58  97  12   7
  AMP PEAK  9(6P21.1) WILD-TYPE  85 162  28  11
D9V4, multiclass
    clus
vv   AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE
  T1                          58                            85
  T2                          97                           162
  T3                          12                            28
  T4                           7                            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(6P21.1) MUTATED   118  26    27
  AMP PEAK  9(6P21.1) WILD-TYPE 177  59    45
D9V5, multiclass
       clus
vv      AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE
  N0                            118                           177
  N1                             26                            59
  N2+N3                          27                            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"
                               vv
clus                             M0  M1 M1A M1B  MX
  AMP PEAK  9(6P21.1) MUTATED   119   8   1   2  44
  AMP PEAK  9(6P21.1) WILD-TYPE 198  10   0   1  75
D9V6, multiclass
     clus
vv    AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE
  M0                          119                           198
  M1                            8                            10
  M1A                           1                             0
  M1B                           2                             1
  MX                           44                            75
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
                               cls
clus                              0   1
  AMP PEAK  9(6P21.1) MUTATED    94  81
  AMP PEAK  9(6P21.1) WILD-TYPE 154 133
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(6P21.1) MUTATED     94   81
  AMP PEAK  9(6P21.1) WILD-TYPE  154  133
        clus
vv       AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE
  FEMALE                          94                           154
  MALE                            81                           133
[1] 2 2
[1] FALSE
D9V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  AMP PEAK  9(6P21.1) MUTATED                            8
  AMP PEAK  9(6P21.1) WILD-TYPE                          5
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK  9(6P21.1) MUTATED                                  35
  AMP PEAK  9(6P21.1) WILD-TYPE                                58
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  9(6P21.1) MUTATED                                                  109
  AMP PEAK  9(6P21.1) WILD-TYPE                                                185
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK  9(6P21.1) MUTATED                                            0
  AMP PEAK  9(6P21.1) WILD-TYPE                                          4
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK  9(6P21.1) MUTATED                                               8
  AMP PEAK  9(6P21.1) WILD-TYPE                                            11
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK  9(6P21.1) MUTATED                                1
  AMP PEAK  9(6P21.1) WILD-TYPE                              1
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK  9(6P21.1) MUTATED                                    1
  AMP PEAK  9(6P21.1) WILD-TYPE                                  3
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK  9(6P21.1) MUTATED                              0
  AMP PEAK  9(6P21.1) WILD-TYPE                            2
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK  9(6P21.1) MUTATED                              11
  AMP PEAK  9(6P21.1) WILD-TYPE                             8
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK  9(6P21.1) MUTATED                                 0
  AMP PEAK  9(6P21.1) WILD-TYPE                               1
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK  9(6P21.1) MUTATED                                               1
  AMP PEAK  9(6P21.1) WILD-TYPE                                             3
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK  9(6P21.1) MUTATED                              1
  AMP PEAK  9(6P21.1) WILD-TYPE                            6
D9V9, multiclass
                                                    clus
vv                                                   AMP PEAK  9(6P21.1) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           35
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         109
  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                                               11
  LUNG SIGNET RING ADENOCARCINOMA                                              0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                1
  MUCINOUS (COLLOID) CARCINOMA                                                 1
                                                    clus
vv                                                   AMP PEAK  9(6P21.1) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             58
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           185
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 11
  LUNG CLEAR CELL ADENOCARCINOMA                                                 1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             3
  LUNG MUCINOUS ADENOCARCINOMA                                                   2
  LUNG PAPILLARY ADENOCARCINOMA                                                  8
  LUNG SIGNET RING ADENOCARCINOMA                                                1
  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"
D9V10, binary
                               cls
clus                              0   1
  AMP PEAK  9(6P21.1) MUTATED     7 168
  AMP PEAK  9(6P21.1) WILD-TYPE  14 273
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(6P21.1) MUTATED      7  168
  AMP PEAK  9(6P21.1) WILD-TYPE   14  273
     clus
vv    AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE
  NO                            7                            14
  YES                         168                           273
[1] 2 2
[1] FALSE
D9V11, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  9(6P21.1) MUTATED   121   6   0   6
  AMP PEAK  9(6P21.1) WILD-TYPE 197   5   4  13
D9V12, multiclass
    clus
vv   AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE
  R0                         121                           197
  R1                           6                             5
  R2                           0                             4
  RX                           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                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  9(6P21.1) MUTATED                                  1     4
  AMP PEAK  9(6P21.1) WILD-TYPE                                0     2
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  9(6P21.1) MUTATED                           5   150
  AMP PEAK  9(6P21.1) WILD-TYPE                        21   212
D9V13, multiclass
                                  clus
vv                                 AMP PEAK  9(6P21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                  5
  WHITE                                                    150
                                  clus
vv                                 AMP PEAK  9(6P21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   21
  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"
D9V14, binary
                               cls
clus                              0   1
  AMP PEAK  9(6P21.1) MUTATED     4 134
  AMP PEAK  9(6P21.1) WILD-TYPE   3 198
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(6P21.1) MUTATED      4  134
  AMP PEAK  9(6P21.1) WILD-TYPE    3  198
                        clus
vv                       AMP PEAK  9(6P21.1) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         134
                        clus
vv                       AMP PEAK  9(6P21.1) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           198
[1] 2 2
[1] FALSE

Clustering(10) Variable = AMP PEAK 10(7P21.1) MUTATION ANALYSIS
D10V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 10(7P21.1) MUTATED   178  42
  AMP PEAK 10(7P21.1) WILD-TYPE 143  40
  AMP PEAK 10(7P21.1) MUTATED AMP PEAK 10(7P21.1) WILD-TYPE 
                          220                           183 
  AMP PEAK 10(7P21.1) MUTATED AMP PEAK 10(7P21.1) WILD-TYPE 
                           42                            40 
$`AMP PEAK 10(7P21.1) MUTATED`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4398 TCGA-05-4405 
         607          426         1369         1126         1431          610 
TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-5423 TCGA-05-5425 
        1958         1997          455          912          151          882 
TCGA-05-5428 TCGA-35-4123 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4631 
         670          182         1147         1492          864          354 
TCGA-38-4632 TCGA-38-6178 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 
        1357          448         1429          400         1367          741 
TCGA-44-2662 TCGA-44-3396 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5644 
        1280         1130         1036          190          722          863 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6147 TCGA-44-6775 TCGA-44-6777 TCGA-44-6779 
         383          723          845          705         1942         1978 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-8117 
         592          366          218          557         1970          385 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
          99          260          486          337          351          415 
TCGA-44-A4SU TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4510 
          76         1081         1421          428          999          896 
TCGA-49-4512 TCGA-49-6742 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-50-5045 
         157          445          890          522          354         2174 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 TCGA-50-5933 
        2146          455          785          944          246         2370 
TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 TCGA-50-6597 TCGA-53-7624 TCGA-55-1595 
         567          764          686         1015         1986         1479 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6712 TCGA-55-6971 TCGA-55-6972 
        1375           87            2           24           25         1475 
TCGA-55-6980 TCGA-55-6985 TCGA-55-6987 TCGA-55-7283 TCGA-55-7284 TCGA-55-7573 
          67         1233         1170           35          121            4 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7726 TCGA-55-7727 TCGA-55-7815 TCGA-55-7907 
          40         1958           39           34           54           16 
TCGA-55-7910 TCGA-55-7994 TCGA-55-8085 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
         197           31           33            6           43           26 
TCGA-55-8096 TCGA-55-8205 TCGA-55-8206 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
          47           33           46           44           23           29 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8514 TCGA-55-8615 TCGA-55-8616 TCGA-55-A48Y 
         228            9          202           15           48           42 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
          29           48         1952            1           28            5 
TCGA-55-A4DG TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A472 
         162         1289         1970         2696         1445          910 
TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5779 
        1728         1189         1686         1126         1968          864 
TCGA-64-5781 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-6217 TCGA-69-7760 
        1559           31          610          573          422          202 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 TCGA-69-7979 TCGA-69-7980 TCGA-69-8255 
         414          165          184           89          382          129 
TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4662 TCGA-73-4668 TCGA-73-4670 
         214           61         1600          912          467          131 
TCGA-73-4675 TCGA-73-4676 TCGA-73-7499 TCGA-75-6214 TCGA-75-7025 TCGA-78-7145 
          40          164          519         1970         1967         1973 
TCGA-78-7147 TCGA-78-7150 TCGA-78-7154 TCGA-78-7155 TCGA-78-7160 TCGA-78-7161 
        1950         1963         1948         1957          678          215 
TCGA-78-7163 TCGA-78-7535 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8655 
        1950         1972          327          881         1952         1981 
TCGA-78-8662 TCGA-83-5908 TCGA-86-7701 TCGA-86-7713 TCGA-86-7953 TCGA-86-7955 
        1964          824           11          422          591          508 
TCGA-86-8055 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8278 TCGA-86-8279 
          10           13           24          479          476          482 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8668 TCGA-86-8673 TCGA-86-A456 
          16           19           26           45          455           10 
TCGA-86-A4P7 TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 TCGA-91-6847 TCGA-91-6848 
          14         1940          310           79          842          224 
TCGA-91-8496 TCGA-91-A4BC TCGA-93-7348 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
         197           44          127          568          377          477 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-8171 TCGA-97-8175 TCGA-97-8177 
        1332          775          181          107           87          147 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M7 TCGA-99-8025 TCGA-99-8033 
          15          148          115          271          427          170 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L9-A443 
         154          114          287          282          578          116 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4T2 TCGA-MP-A4T8 
           6          285          622          353         1951         1957 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TK 
        1980         1951         1944         1971 

$`AMP PEAK 10(7P21.1) WILD-TYPE`
TCGA-05-4249 TCGA-05-4396 TCGA-05-4403 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
        1523         1947          578          365          913          669 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 
         791          791          761          761          730          457 
TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-5375 TCGA-38-4625 
          30           62           14          225          264         1952 
TCGA-38-4626 TCGA-38-4630 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2665 
        1962         1073         1971          133         1324         1301 
TCGA-44-2666 TCGA-44-2668 TCGA-44-3398 TCGA-44-5643 TCGA-44-6145 TCGA-44-6146 
          97          246         1163         1013          328          302 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6776 TCGA-44-6778 TCGA-44-7659 TCGA-44-7670 
         704          658         1938         1864          444          882 
TCGA-44-7671 TCGA-44-7672 TCGA-44-A47A TCGA-44-A47B TCGA-49-4486 TCGA-49-4507 
         535          719          466          287         1932          268 
TCGA-49-4514 TCGA-49-6743 TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
        1700          369         1499          282          267         1091 
TCGA-50-5935 TCGA-50-5942 TCGA-50-7109 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 
         653          883          255          105         1971          424 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-6642 TCGA-55-6969 TCGA-55-6983 
         280          701         1178          993         1239         1826 
TCGA-55-6986 TCGA-55-7281 TCGA-55-7570 TCGA-55-7574 TCGA-55-7725 TCGA-55-7728 
        2151           18            6           95           39           24 
TCGA-55-7903 TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 TCGA-55-8087 TCGA-55-8089 
          19           21            3            5           21          100 
TCGA-55-8094 TCGA-55-8097 TCGA-55-8207 TCGA-55-8299 TCGA-55-8506 TCGA-55-8507 
           4           15           66          216           11            8 
TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-8619 TCGA-55-8620 
          15            3          146          536           49           66 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A4DF TCGA-62-8395 TCGA-62-A46U TCGA-62-A46V 
         106           33           47         1216         2067         2199 
TCGA-62-A471 TCGA-64-1677 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5815 
        1246          628         1959           62         1305          866 
TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-69-7761 TCGA-69-7763 
         427          385          174          141          186          690 
TCGA-69-7973 TCGA-69-7978 TCGA-69-8253 TCGA-69-8254 TCGA-73-4659 TCGA-73-4666 
         230           70          100           77          711          800 
TCGA-73-4677 TCGA-73-7498 TCGA-75-7027 TCGA-75-7031 TCGA-78-7146 TCGA-78-7148 
          38          621         1956         1965         1988         1944 
TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
        1093         1202          760         1961         1963         1221 
TCGA-78-7162 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 TCGA-78-7537 
        1940         1934         1937         1965         1949         1944 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8660 TCGA-80-5607 TCGA-80-5608 
         994         1949         1971         1954         1965         1972 
TCGA-86-6851 TCGA-86-7711 TCGA-86-7714 TCGA-86-7954 TCGA-86-8054 TCGA-86-8056 
        1959          630         1968         1963          745         1963 
TCGA-86-8076 TCGA-86-8281 TCGA-86-8585 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
         489         1955           35           34           18           15 
TCGA-86-8674 TCGA-86-A4D0 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 TCGA-91-6836 
         405           30           39          323           60          417 
TCGA-91-6840 TCGA-91-6849 TCGA-91-7771 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD 
         372           35          492          174           36          218 
TCGA-93-7347 TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-95-7948 TCGA-95-A4VK 
         297          186           34            2          476          121 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7941 TCGA-97-8172 TCGA-97-8174 
         964         1965         1932           22          182         1965 
TCGA-97-A4M2 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 TCGA-J2-A4AG TCGA-L4-A4E6 
         197          392          459           44          238          435 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4TE TCGA-MP-A4TF 
        1946         1967         1954         1954         1970         1970 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A5C7 
         142         1955         1490 

  AMP PEAK 10(7P21.1) MUTATED AMP PEAK 10(7P21.1) WILD-TYPE 
                            1                             2 
  AMP PEAK 10(7P21.1) MUTATED AMP PEAK 10(7P21.1) WILD-TYPE 
                         2696                          2199 
  AMP PEAK 10(7P21.1) MUTATED AMP PEAK 10(7P21.1) WILD-TYPE 
                        446.5                         535.0 
[1] "1.0 - 2696.0 (446.5)" "2.0 - 2199.0 (535.0)"
[1] "hr=" "1.1"
D10V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 10(7P21.1) MUTATED         3       57       72        24        36
  AMP PEAK 10(7P21.1) WILD-TYPE       1       56       59        19        33
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 10(7P21.1) MUTATED           45          6       13
  AMP PEAK 10(7P21.1) WILD-TYPE         22          5       10
D10V3, multiclass
            clus
vv           AMP PEAK 10(7P21.1) MUTATED AMP PEAK 10(7P21.1) WILD-TYPE
  STAGE I                              3                             1
  STAGE IA                            57                            56
  STAGE IB                            72                            59
  STAGE IIA                           24                            19
  STAGE IIB                           36                            33
  STAGE IIIA                          45                            22
  STAGE IIIB                           6                             5
  STAGE IV                            13                            10
[1] 8 2
[1] TRUE
[1] "dimension of 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(7P21.1) MUTATED    73 149  25   8
  AMP PEAK 10(7P21.1) WILD-TYPE  70 110  15  10
D10V4, multiclass
    clus
vv   AMP PEAK 10(7P21.1) MUTATED AMP PEAK 10(7P21.1) WILD-TYPE
  T1                          73                            70
  T2                         149                           110
  T3                          25                            15
  T4                           8                            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 10(7P21.1) MUTATED   153  43    53
  AMP PEAK 10(7P21.1) WILD-TYPE 142  42    19
D10V5, multiclass
       clus
vv      AMP PEAK 10(7P21.1) MUTATED AMP PEAK 10(7P21.1) WILD-TYPE
  N0                            153                           142
  N1                             43                            42
  N2+N3                          53                            19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B  MX
  AMP PEAK 10(7P21.1) MUTATED   173  11   1   0  68
  AMP PEAK 10(7P21.1) WILD-TYPE 144   7   0   3  51
D10V6, multiclass
     clus
vv    AMP PEAK 10(7P21.1) MUTATED AMP PEAK 10(7P21.1) WILD-TYPE
  M0                          173                           144
  M1                           11                             7
  M1A                           1                             0
  M1B                           0                             3
  MX                           68                            51
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
                               cls
clus                              0   1
  AMP PEAK 10(7P21.1) MUTATED   142 114
  AMP PEAK 10(7P21.1) WILD-TYPE 106 100
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7P21.1) MUTATED    142  114
  AMP PEAK 10(7P21.1) WILD-TYPE  106  100
        clus
vv       AMP PEAK 10(7P21.1) MUTATED AMP PEAK 10(7P21.1) WILD-TYPE
  FEMALE                         142                           106
  MALE                           114                           100
[1] 2 2
[1] FALSE
D10V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 10(7P21.1) MUTATED                            5
  AMP PEAK 10(7P21.1) WILD-TYPE                          8
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 10(7P21.1) MUTATED                                  46
  AMP PEAK 10(7P21.1) WILD-TYPE                                47
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 10(7P21.1) MUTATED                                                  174
  AMP PEAK 10(7P21.1) WILD-TYPE                                                120
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 10(7P21.1) MUTATED                                            3
  AMP PEAK 10(7P21.1) WILD-TYPE                                          1
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 10(7P21.1) MUTATED                                              11
  AMP PEAK 10(7P21.1) WILD-TYPE                                             8
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 10(7P21.1) MUTATED                                1
  AMP PEAK 10(7P21.1) WILD-TYPE                              1
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 10(7P21.1) MUTATED                                    3
  AMP PEAK 10(7P21.1) WILD-TYPE                                  1
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 10(7P21.1) MUTATED                              0
  AMP PEAK 10(7P21.1) WILD-TYPE                            2
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 10(7P21.1) MUTATED                               8
  AMP PEAK 10(7P21.1) WILD-TYPE                            11
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 10(7P21.1) MUTATED                                 0
  AMP PEAK 10(7P21.1) WILD-TYPE                               1
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 10(7P21.1) MUTATED                                               3
  AMP PEAK 10(7P21.1) WILD-TYPE                                             1
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 10(7P21.1) MUTATED                              2
  AMP PEAK 10(7P21.1) WILD-TYPE                            5
D10V9, multiclass
                                                    clus
vv                                                   AMP PEAK 10(7P21.1) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           46
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         174
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                   3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                               11
  LUNG CLEAR CELL ADENOCARCINOMA                                               1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                           3
  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                                                   AMP PEAK 10(7P21.1) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             47
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           120
  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                                                 11
  LUNG SIGNET RING ADENOCARCINOMA                                                1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                  1
  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"
D10V10, binary
                               cls
clus                              0   1
  AMP PEAK 10(7P21.1) MUTATED     9 247
  AMP PEAK 10(7P21.1) WILD-TYPE  12 194
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7P21.1) MUTATED      9  247
  AMP PEAK 10(7P21.1) WILD-TYPE   12  194
     clus
vv    AMP PEAK 10(7P21.1) MUTATED AMP PEAK 10(7P21.1) WILD-TYPE
  NO                            9                            12
  YES                         247                           194
[1] 2 2
[1] FALSE
D10V11, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 10(7P21.1) MUTATED   171   5   3  12
  AMP PEAK 10(7P21.1) WILD-TYPE 147   6   1   7
D10V12, multiclass
    clus
vv   AMP PEAK 10(7P21.1) MUTATED AMP PEAK 10(7P21.1) WILD-TYPE
  R0                         171                           147
  R1                           5                             6
  R2                           3                             1
  RX                          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                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 10(7P21.1) MUTATED                                  1     5
  AMP PEAK 10(7P21.1) WILD-TYPE                                0     1
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 10(7P21.1) MUTATED                          17   200
  AMP PEAK 10(7P21.1) WILD-TYPE                         9   162
D10V13, multiclass
                                  clus
vv                                 AMP PEAK 10(7P21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      5
  BLACK OR AFRICAN AMERICAN                                 17
  WHITE                                                    200
                                  clus
vv                                 AMP PEAK 10(7P21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                    9
  WHITE                                                      162
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V14, binary
                               cls
clus                              0   1
  AMP PEAK 10(7P21.1) MUTATED     3 189
  AMP PEAK 10(7P21.1) WILD-TYPE   4 143
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7P21.1) MUTATED      3  189
  AMP PEAK 10(7P21.1) WILD-TYPE    4  143
                        clus
vv                       AMP PEAK 10(7P21.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                         189
                        clus
vv                       AMP PEAK 10(7P21.1) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           143
[1] 2 2
[1] FALSE

Clustering(11) Variable = AMP PEAK 11(7P11.2) MUTATION ANALYSIS
D11V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 11(7P11.2) MUTATED   169  43
  AMP PEAK 11(7P11.2) WILD-TYPE 152  39
  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                          212                           191 
  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                           43                            39 
$`AMP PEAK 11(7P11.2) MUTATED`
TCGA-05-4382 TCGA-05-4390 TCGA-05-4398 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 
         607         1126         1431          610         1958         1997 
TCGA-05-4417 TCGA-05-4420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-35-4123 
         455          912          151          882          670          182 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
        1147         1492          864          354         1357          448 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-3396 
        1429          400         1367          741         1280         1130 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 
        1036          190          722          863          383          723 
TCGA-44-6147 TCGA-44-6775 TCGA-44-6777 TCGA-44-6779 TCGA-44-7660 TCGA-44-7661 
         845          705         1942         1978          592          366 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 
         218          557         1970          385          260          486 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4494 TCGA-49-4501 
         337          351          415           76         1081         1421 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4510 TCGA-49-4512 TCGA-49-6742 TCGA-49-6745 
         428          999          896          157          445          522 
TCGA-49-6761 TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 
         354         2174         2146          785          944          246 
TCGA-50-5930 TCGA-50-5933 TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 TCGA-53-7624 
         282         2370          567          764          686         1986 
TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6712 
         280         1178         1375           87            2           24 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 TCGA-55-6985 TCGA-55-6987 TCGA-55-7283 
          25         1475           67         1233         1170           35 
TCGA-55-7284 TCGA-55-7576 TCGA-55-7724 TCGA-55-7726 TCGA-55-7727 TCGA-55-7907 
         121           40         1958           39           34           16 
TCGA-55-7910 TCGA-55-7994 TCGA-55-8085 TCGA-55-8089 TCGA-55-8091 TCGA-55-8092 
         197           31           33          100           43           26 
TCGA-55-8096 TCGA-55-8205 TCGA-55-8206 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
          47           33           46           44           23           29 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8514 TCGA-55-8615 TCGA-55-8616 TCGA-55-A48Z 
         228            9          202           15           48           29 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG 
          48         1952            1           28            5          162 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-A472 TCGA-64-1676 TCGA-64-1679 
        1289         1970         2696          910         1728         1686 
TCGA-64-1680 TCGA-64-1681 TCGA-64-5779 TCGA-64-5781 TCGA-67-3770 TCGA-67-3771 
        1126         1968          864         1559           31          610 
TCGA-67-3772 TCGA-67-6217 TCGA-69-7760 TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 
         573          422          202          414          165          184 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
          70           89          382          129          214           61 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
        1600          711          912          467          131           40 
TCGA-73-4676 TCGA-73-7499 TCGA-75-6214 TCGA-75-7025 TCGA-78-7145 TCGA-78-7146 
         164          519         1970         1967         1973         1988 
TCGA-78-7147 TCGA-78-7150 TCGA-78-7154 TCGA-78-7155 TCGA-78-7160 TCGA-78-7161 
        1950         1963         1948         1957          678          215 
TCGA-78-7163 TCGA-78-7535 TCGA-78-7540 TCGA-78-8655 TCGA-78-8662 TCGA-83-5908 
        1950         1972          881         1981         1964          824 
TCGA-86-7701 TCGA-86-7713 TCGA-86-7953 TCGA-86-7955 TCGA-86-8055 TCGA-86-8073 
          11          422          591          508           10           13 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 
          24          479          476          482           16           26 
TCGA-86-8668 TCGA-86-8673 TCGA-86-A456 TCGA-86-A4P7 TCGA-91-6831 TCGA-91-6835 
          45          455           10           14          310           79 
TCGA-91-6847 TCGA-91-6848 TCGA-91-8496 TCGA-91-A4BC TCGA-93-7348 TCGA-95-7039 
         842          224          197           44          127           34 
TCGA-95-7944 TCGA-95-7947 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-8171 
         377          477         1332          775          181          107 
TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M7 
          87          147           15          148          115          271 
TCGA-99-8025 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
         427          170          154          114          287          282 
TCGA-L4-A4E5 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
         578          116            6          285          622          353 
TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
        1967         1951         1957         1980         1951         1944 
TCGA-MP-A4TF TCGA-MP-A4TK 
        1970         1971 

$`AMP PEAK 11(7P11.2) WILD-TYPE`
TCGA-05-4249 TCGA-05-4384 TCGA-05-4389 TCGA-05-4396 TCGA-05-4403 TCGA-05-4422 
        1523          426         1369         1947          578          365 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
         913          669          791          791          761          761 
TCGA-05-4433 TCGA-05-5420 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 
         730          457           30           62           14          225 
TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4630 TCGA-38-7271 TCGA-38-A44F 
         264         1952         1962         1073         1971          133 
TCGA-44-2655 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3398 TCGA-44-5643 
        1324         1301           97          246         1163         1013 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6148 TCGA-44-6774 TCGA-44-6776 TCGA-44-6778 
         328          302          704          658         1938         1864 
TCGA-44-7659 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8119 TCGA-44-A47A 
         444          882          535          719           99          466 
TCGA-44-A47B TCGA-49-4486 TCGA-49-4507 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 
         287         1932          268         1700          369          890 
TCGA-50-5051 TCGA-50-5068 TCGA-50-5931 TCGA-50-5932 TCGA-50-5935 TCGA-50-5942 
         455         1499          267         1091          653          883 
TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-55-1592 
        1015          255          105         1971          424          701 
TCGA-55-1595 TCGA-55-6642 TCGA-55-6969 TCGA-55-6983 TCGA-55-6986 TCGA-55-7281 
        1479          993         1239         1826         2151           18 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7725 TCGA-55-7728 TCGA-55-7815 
           6            4           95           39           24           54 
TCGA-55-7903 TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 TCGA-55-8087 TCGA-55-8090 
          19           21            3            5           21            6 
TCGA-55-8094 TCGA-55-8097 TCGA-55-8207 TCGA-55-8299 TCGA-55-8506 TCGA-55-8507 
           4           15           66          216           11            8 
TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-8619 TCGA-55-8620 
          15            3          146          536           49           66 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A4DF TCGA-62-8395 TCGA-62-8402 
         106           33           42           47         1216         1445 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 TCGA-64-1677 TCGA-64-1678 TCGA-64-5774 
        2067         2199         1246          628         1189         1959 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5815 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 
          62         1305          866          427          385          174 
TCGA-67-6216 TCGA-69-7761 TCGA-69-7763 TCGA-69-7973 TCGA-69-8253 TCGA-69-8254 
         141          186          690          230          100           77 
TCGA-73-4666 TCGA-73-4677 TCGA-73-7498 TCGA-75-7027 TCGA-75-7031 TCGA-78-7148 
         800           38          621         1956         1965         1944 
TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
        1093         1202          760         1961         1963         1221 
TCGA-78-7162 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 TCGA-78-7537 
        1940         1934         1937         1965         1949         1944 
TCGA-78-7539 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8660 
         327         1952          994         1949         1971         1954 
TCGA-80-5607 TCGA-80-5608 TCGA-86-6851 TCGA-86-7711 TCGA-86-7714 TCGA-86-7954 
        1965         1972         1959          630         1968         1963 
TCGA-86-8054 TCGA-86-8056 TCGA-86-8076 TCGA-86-8281 TCGA-86-8358 TCGA-86-8585 
         745         1963          489         1955           19           35 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 TCGA-86-A4D0 TCGA-86-A4P8 
          34           18           15          405           30           39 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6836 TCGA-91-6840 TCGA-91-6849 
         323         1940           60          417          372           35 
TCGA-91-7771 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-8067 
         492          174           36          218          297          186 
TCGA-95-7043 TCGA-95-7567 TCGA-95-7948 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 
           2          568          476          121          964         1965 
TCGA-97-7552 TCGA-97-7941 TCGA-97-8172 TCGA-97-8174 TCGA-97-A4M2 TCGA-99-7458 
        1932           22          182         1965          197          392 
TCGA-99-8028 TCGA-99-8032 TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-MP-A4SV TCGA-MP-A4T4 
         459           44          238          435         1946         1954 
TCGA-MP-A4T7 TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A5C7 
        1954         1970          142         1955         1490 

  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                            1                             2 
  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                         2696                          2199 
  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                        436.5                         535.0 
[1] "1.0 - 2696.0 (436.5)" "2.0 - 2199.0 (535.0)"
[1] "hr=" "1.1"
D11V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 11(7P11.2) MUTATED         3       54       70        22        37
  AMP PEAK 11(7P11.2) WILD-TYPE       1       59       61        21        32
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 11(7P11.2) MUTATED           46          6       12
  AMP PEAK 11(7P11.2) WILD-TYPE         21          5       11
D11V3, multiclass
            clus
vv           AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  STAGE I                              3                             1
  STAGE IA                            54                            59
  STAGE IB                            70                            61
  STAGE IIA                           22                            21
  STAGE IIB                           37                            32
  STAGE IIIA                          46                            21
  STAGE IIIB                           6                             5
  STAGE IV                            12                            11
[1] 8 2
[1] TRUE
[1] "dimension of 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(7P11.2) MUTATED    70 146  25   8
  AMP PEAK 11(7P11.2) WILD-TYPE  73 113  15  10
D11V4, multiclass
    clus
vv   AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  T1                          70                            73
  T2                         146                           113
  T3                          25                            15
  T4                           8                            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 11(7P11.2) MUTATED   146  44    53
  AMP PEAK 11(7P11.2) WILD-TYPE 149  41    19
D11V5, multiclass
       clus
vv      AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  N0                            146                           149
  N1                             44                            41
  N2+N3                          53                            19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B  MX
  AMP PEAK 11(7P11.2) MUTATED   169  10   1   0  67
  AMP PEAK 11(7P11.2) WILD-TYPE 148   8   0   3  52
D11V6, multiclass
     clus
vv    AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  M0                          169                           148
  M1                           10                             8
  M1A                           1                             0
  M1B                           0                             3
  MX                           67                            52
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, binary
                               cls
clus                              0   1
  AMP PEAK 11(7P11.2) MUTATED   139 111
  AMP PEAK 11(7P11.2) WILD-TYPE 109 103
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7P11.2) MUTATED    139  111
  AMP PEAK 11(7P11.2) WILD-TYPE  109  103
        clus
vv       AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  FEMALE                         139                           109
  MALE                           111                           103
[1] 2 2
[1] FALSE
D11V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 11(7P11.2) MUTATED                            6
  AMP PEAK 11(7P11.2) WILD-TYPE                          7
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 11(7P11.2) MUTATED                                  45
  AMP PEAK 11(7P11.2) WILD-TYPE                                48
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 11(7P11.2) MUTATED                                                  170
  AMP PEAK 11(7P11.2) WILD-TYPE                                                124
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 11(7P11.2) MUTATED                                            3
  AMP PEAK 11(7P11.2) WILD-TYPE                                          1
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 11(7P11.2) MUTATED                                              10
  AMP PEAK 11(7P11.2) WILD-TYPE                                             9
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 11(7P11.2) MUTATED                                0
  AMP PEAK 11(7P11.2) WILD-TYPE                              2
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 11(7P11.2) MUTATED                                    3
  AMP PEAK 11(7P11.2) WILD-TYPE                                  1
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 11(7P11.2) MUTATED                              0
  AMP PEAK 11(7P11.2) WILD-TYPE                            2
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 11(7P11.2) MUTATED                               8
  AMP PEAK 11(7P11.2) WILD-TYPE                            11
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 11(7P11.2) MUTATED                                 0
  AMP PEAK 11(7P11.2) WILD-TYPE                               1
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 11(7P11.2) MUTATED                                               3
  AMP PEAK 11(7P11.2) WILD-TYPE                                             1
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 11(7P11.2) MUTATED                              2
  AMP PEAK 11(7P11.2) WILD-TYPE                            5
D11V9, multiclass
                                                    clus
vv                                                   AMP PEAK 11(7P11.2) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           45
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         170
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                   3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                               10
  LUNG CLEAR CELL ADENOCARCINOMA                                               0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                           3
  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                                                   AMP PEAK 11(7P11.2) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             48
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           124
  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                                                 11
  LUNG SIGNET RING ADENOCARCINOMA                                                1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                  1
  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"
D11V10, binary
                               cls
clus                              0   1
  AMP PEAK 11(7P11.2) MUTATED    10 240
  AMP PEAK 11(7P11.2) WILD-TYPE  11 201
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7P11.2) MUTATED     10  240
  AMP PEAK 11(7P11.2) WILD-TYPE   11  201
     clus
vv    AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  NO                           10                            11
  YES                         240                           201
[1] 2 2
[1] FALSE
D11V11, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 11(7P11.2) MUTATED   166   5   3  11
  AMP PEAK 11(7P11.2) WILD-TYPE 152   6   1   8
D11V12, multiclass
    clus
vv   AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  R0                         166                           152
  R1                           5                             6
  R2                           3                             1
  RX                          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                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 11(7P11.2) MUTATED                                  1     4
  AMP PEAK 11(7P11.2) WILD-TYPE                                0     2
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 11(7P11.2) MUTATED                          17   198
  AMP PEAK 11(7P11.2) WILD-TYPE                         9   164
D11V13, multiclass
                                  clus
vv                                 AMP PEAK 11(7P11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 17
  WHITE                                                    198
                                  clus
vv                                 AMP PEAK 11(7P11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                    9
  WHITE                                                      164
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V14, binary
                               cls
clus                              0   1
  AMP PEAK 11(7P11.2) MUTATED     4 186
  AMP PEAK 11(7P11.2) WILD-TYPE   3 146
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7P11.2) MUTATED      4  186
  AMP PEAK 11(7P11.2) WILD-TYPE    3  146
                        clus
vv                       AMP PEAK 11(7P11.2) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         186
                        clus
vv                       AMP PEAK 11(7P11.2) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           146
[1] 2 2
[1] FALSE

Clustering(12) Variable = AMP PEAK 12(7Q31.2) MUTATION ANALYSIS
D12V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 12(7Q31.2) MUTATED   139  34
  AMP PEAK 12(7Q31.2) WILD-TYPE 182  48
  AMP PEAK 12(7Q31.2) MUTATED AMP PEAK 12(7Q31.2) WILD-TYPE 
                          173                           230 
  AMP PEAK 12(7Q31.2) MUTATED AMP PEAK 12(7Q31.2) WILD-TYPE 
                           34                            48 
$`AMP PEAK 12(7Q31.2) MUTATED`
TCGA-05-4398 TCGA-05-4405 TCGA-05-4410 TCGA-05-4420 TCGA-05-4427 TCGA-05-5423 
        1431          610         1958          912          791          151 
TCGA-05-5425 TCGA-05-5428 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
         882          670          225          182          264         1952 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
        1147         1492          864          354         1357          448 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2662 TCGA-44-3396 TCGA-44-3918 
        1429          400         1367         1280         1130         1036 
TCGA-44-3919 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6147 TCGA-44-6777 
         190          383          723          328          845         1942 
TCGA-44-6778 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7669 TCGA-44-8117 
        1864          592          366          218         1970          385 
TCGA-44-A47F TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4494 TCGA-49-4505 TCGA-49-4512 
         337          415           76         1081          428          157 
TCGA-49-6745 TCGA-50-5045 TCGA-50-5049 TCGA-50-5066 TCGA-50-5930 TCGA-50-5935 
         522         2174         2146          944          282          653 
TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1596 
         567          764          686          280          701         1375 
TCGA-55-6543 TCGA-55-6712 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 
           2           24         1239           25         1475           67 
TCGA-55-6983 TCGA-55-6985 TCGA-55-6987 TCGA-55-7283 TCGA-55-7284 TCGA-55-7576 
        1826         1233         1170           35          121           40 
TCGA-55-7724 TCGA-55-7726 TCGA-55-7907 TCGA-55-7910 TCGA-55-7994 TCGA-55-7995 
        1958           39           16          197           31            5 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8205 TCGA-55-8206 TCGA-55-8301 TCGA-55-8302 
          43           26           33           46           44           23 
TCGA-55-8505 TCGA-55-8507 TCGA-55-8510 TCGA-55-8511 TCGA-55-8514 TCGA-55-8616 
          29            8          228            9          202           48 
TCGA-55-8620 TCGA-55-A490 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-62-8397 
          66           48            1           28            5         1289 
TCGA-62-8398 TCGA-62-8399 TCGA-62-A472 TCGA-64-1676 TCGA-64-1679 TCGA-64-1680 
        1970         2696          910         1728         1686         1126 
TCGA-64-1681 TCGA-64-5781 TCGA-67-3772 TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 
        1968         1559          573          414          165          184 
TCGA-69-7978 TCGA-69-7979 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 
          70           89          214           61         1600          711 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-7499 
         912          800          131           40          164          519 
TCGA-78-7145 TCGA-78-7147 TCGA-78-7154 TCGA-78-7160 TCGA-78-7163 TCGA-78-7220 
        1973         1950         1948          678         1950         1965 
TCGA-78-7536 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8655 TCGA-83-5908 
        1949          881         1952         1949         1981          824 
TCGA-86-7701 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 
          11          422          591         1963          508           10 
TCGA-86-8073 TCGA-86-8075 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8672 
          13          479           16           19           26           15 
TCGA-86-8673 TCGA-86-A4P7 TCGA-91-6835 TCGA-91-6836 TCGA-91-6847 TCGA-91-6848 
         455           14           79          417          842          224 
TCGA-91-8496 TCGA-91-A4BC TCGA-93-7348 TCGA-95-7039 TCGA-95-7043 TCGA-95-7944 
         197           44          127           34            2          377 
TCGA-95-7947 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-8171 TCGA-97-8175 
         477         1332          775          181          107           87 
TCGA-97-8179 TCGA-97-8552 TCGA-99-8025 TCGA-99-8033 TCGA-J2-8192 TCGA-L4-A4E5 
          15          115          427          170          154          578 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4T2 TCGA-MP-A4T4 
           6          285          622         1946         1951         1954 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TK 
        1957         1980         1951         1944         1971 

$`AMP PEAK 12(7Q31.2) WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 
        1523          607          426         1369         1126         1947 
TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
         578         1997          455          365          913          669 
TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 TCGA-05-5429 
         791          761          761          730          457           30 
TCGA-05-5715 TCGA-35-3615 TCGA-38-4626 TCGA-38-4630 TCGA-38-7271 TCGA-38-A44F 
          62           14         1962         1073         1971          133 
TCGA-44-2655 TCGA-44-2661 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3398 
        1324          741         1301           97          246         1163 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-6146 TCGA-44-6148 TCGA-44-6774 
         722         1013          863          302          704          658 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6779 TCGA-44-7659 TCGA-44-7667 TCGA-44-7670 
         705         1938         1978          444          557          882 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
         535          719           99          260          486          466 
TCGA-44-A47B TCGA-44-A47G TCGA-49-4486 TCGA-49-4501 TCGA-49-4506 TCGA-49-4507 
         287          351         1932         1421          999          268 
TCGA-49-4510 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6761 
         896         1700          445          369          890          354 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 TCGA-50-5932 
         455          785         1499          246          267         1091 
TCGA-50-5933 TCGA-50-5942 TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 TCGA-53-7624 
        2370          883         1015          255          105         1986 
TCGA-53-7626 TCGA-53-7813 TCGA-55-1594 TCGA-55-1595 TCGA-55-5899 TCGA-55-6642 
        1971          424         1178         1479           87          993 
TCGA-55-6986 TCGA-55-7281 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7725 
        2151           18            6            4           95           39 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 TCGA-55-7914 
          34           24           54           19           21            3 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8094 TCGA-55-8096 
          33           21          100            6            4           47 
TCGA-55-8097 TCGA-55-8207 TCGA-55-8299 TCGA-55-8506 TCGA-55-8508 TCGA-55-8512 
          15           66          216           11           15            3 
TCGA-55-8513 TCGA-55-8614 TCGA-55-8615 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
         146          536           15           49          106           33 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 
          42           29         1952           47          162         1216 
TCGA-62-8402 TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 TCGA-64-1677 TCGA-64-1678 
        1445         2067         2199         1246          628         1189 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 TCGA-67-3770 
        1959           62         1305          864          866           31 
TCGA-67-3771 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
         610          427          385          174          141          422 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7973 TCGA-69-7980 TCGA-69-8253 
         202          186          690          230          382          100 
TCGA-69-8254 TCGA-69-8255 TCGA-73-4668 TCGA-73-4677 TCGA-73-7498 TCGA-75-6214 
          77          129          467           38          621         1970 
TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 
        1967         1956         1965         1988         1944         1093 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
        1963         1202          760         1957         1961         1963 
TCGA-78-7159 TCGA-78-7161 TCGA-78-7162 TCGA-78-7166 TCGA-78-7167 TCGA-78-7535 
        1221          215         1940         1934         1937         1972 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7633 TCGA-78-8648 TCGA-78-8660 TCGA-78-8662 
        1944          327          994         1971         1954         1964 
TCGA-80-5607 TCGA-80-5608 TCGA-86-6851 TCGA-86-7711 TCGA-86-7714 TCGA-86-8054 
        1965         1972         1959          630         1968          745 
TCGA-86-8056 TCGA-86-8074 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8281 
        1963           24          489          476          482         1955 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8674 TCGA-86-A456 
          35           45           34           18          405           10 
TCGA-86-A4D0 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
          30           39          323         1940           60          310 
TCGA-91-6840 TCGA-91-6849 TCGA-91-7771 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD 
         372           35          492          174           36          218 
TCGA-93-7347 TCGA-93-8067 TCGA-95-7567 TCGA-95-7948 TCGA-95-A4VK TCGA-97-7546 
         297          186          568          476          121          964 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7941 TCGA-97-8172 TCGA-97-8174 TCGA-97-8177 
        1965         1932           22          182         1965          147 
TCGA-97-8547 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 
         148          197          271          392          459           44 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 
         114          287          282          238          435          116 
TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T7 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
         353         1967         1954         1970         1970          142 
TCGA-MP-A4TI TCGA-MP-A5C7 
        1955         1490 

  AMP PEAK 12(7Q31.2) MUTATED AMP PEAK 12(7Q31.2) WILD-TYPE 
                            1                             3 
  AMP PEAK 12(7Q31.2) MUTATED AMP PEAK 12(7Q31.2) WILD-TYPE 
                         2696                          2370 
  AMP PEAK 12(7Q31.2) MUTATED AMP PEAK 12(7Q31.2) WILD-TYPE 
                        448.0                         471.5 
[1] "1.0 - 2696.0 (448.0)" "3.0 - 2370.0 (471.5)"
[1] "hr=" "1.1"
D12V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 12(7Q31.2) MUTATED         2       44       56        18        28
  AMP PEAK 12(7Q31.2) WILD-TYPE       2       69       75        25        41
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 12(7Q31.2) MUTATED           37          2       12
  AMP PEAK 12(7Q31.2) WILD-TYPE         30          9       11
D12V3, multiclass
            clus
vv           AMP PEAK 12(7Q31.2) MUTATED AMP PEAK 12(7Q31.2) WILD-TYPE
  STAGE I                              2                             2
  STAGE IA                            44                            69
  STAGE IB                            56                            75
  STAGE IIA                           18                            25
  STAGE IIB                           28                            41
  STAGE IIIA                          37                            30
  STAGE IIIB                           2                             9
  STAGE IV                            12                            11
[1] 8 2
[1] TRUE
[1] "dimension of 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(7Q31.2) MUTATED    54 118  20   5
  AMP PEAK 12(7Q31.2) WILD-TYPE  89 141  20  13
D12V4, multiclass
    clus
vv   AMP PEAK 12(7Q31.2) MUTATED AMP PEAK 12(7Q31.2) WILD-TYPE
  T1                          54                            89
  T2                         118                           141
  T3                          20                            20
  T4                           5                            13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1 N2+N3
  AMP PEAK 12(7Q31.2) MUTATED   117  35    40
  AMP PEAK 12(7Q31.2) WILD-TYPE 178  50    32
D12V5, multiclass
       clus
vv      AMP PEAK 12(7Q31.2) MUTATED AMP PEAK 12(7Q31.2) WILD-TYPE
  N0                            117                           178
  N1                             35                            50
  N2+N3                          40                            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"
                               vv
clus                             M0  M1 M1A M1B  MX
  AMP PEAK 12(7Q31.2) MUTATED   131   9   1   1  55
  AMP PEAK 12(7Q31.2) WILD-TYPE 186   9   0   2  64
D12V6, multiclass
     clus
vv    AMP PEAK 12(7Q31.2) MUTATED AMP PEAK 12(7Q31.2) WILD-TYPE
  M0                          131                           186
  M1                            9                             9
  M1A                           1                             0
  M1B                           1                             2
  MX                           55                            64
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V7, binary
                               cls
clus                              0   1
  AMP PEAK 12(7Q31.2) MUTATED   105  94
  AMP PEAK 12(7Q31.2) WILD-TYPE 143 120
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(7Q31.2) MUTATED    105   94
  AMP PEAK 12(7Q31.2) WILD-TYPE  143  120
        clus
vv       AMP PEAK 12(7Q31.2) MUTATED AMP PEAK 12(7Q31.2) WILD-TYPE
  FEMALE                         105                           143
  MALE                            94                           120
[1] 2 2
[1] FALSE
D12V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 12(7Q31.2) MUTATED                            4
  AMP PEAK 12(7Q31.2) WILD-TYPE                          9
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 12(7Q31.2) MUTATED                                  34
  AMP PEAK 12(7Q31.2) WILD-TYPE                                59
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 12(7Q31.2) MUTATED                                                  138
  AMP PEAK 12(7Q31.2) WILD-TYPE                                                156
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 12(7Q31.2) MUTATED                                            2
  AMP PEAK 12(7Q31.2) WILD-TYPE                                          2
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 12(7Q31.2) MUTATED                                              11
  AMP PEAK 12(7Q31.2) WILD-TYPE                                             8
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 12(7Q31.2) MUTATED                                0
  AMP PEAK 12(7Q31.2) WILD-TYPE                              2
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 12(7Q31.2) MUTATED                                    1
  AMP PEAK 12(7Q31.2) WILD-TYPE                                  3
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 12(7Q31.2) MUTATED                              0
  AMP PEAK 12(7Q31.2) WILD-TYPE                            2
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 12(7Q31.2) MUTATED                               7
  AMP PEAK 12(7Q31.2) WILD-TYPE                            12
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 12(7Q31.2) MUTATED                                 0
  AMP PEAK 12(7Q31.2) WILD-TYPE                               1
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 12(7Q31.2) MUTATED                                               1
  AMP PEAK 12(7Q31.2) WILD-TYPE                                             3
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 12(7Q31.2) MUTATED                              1
  AMP PEAK 12(7Q31.2) WILD-TYPE                            6
D12V9, multiclass
                                                    clus
vv                                                   AMP PEAK 12(7Q31.2) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           34
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         138
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                   2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                               11
  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                                                 1
                                                    clus
vv                                                   AMP PEAK 12(7Q31.2) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             59
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           156
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  8
  LUNG CLEAR CELL ADENOCARCINOMA                                                 2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             3
  LUNG MUCINOUS ADENOCARCINOMA                                                   2
  LUNG PAPILLARY ADENOCARCINOMA                                                 12
  LUNG SIGNET RING ADENOCARCINOMA                                                1
  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"
D12V10, binary
                               cls
clus                              0   1
  AMP PEAK 12(7Q31.2) MUTATED    11 188
  AMP PEAK 12(7Q31.2) WILD-TYPE  10 253
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(7Q31.2) MUTATED     11  188
  AMP PEAK 12(7Q31.2) WILD-TYPE   10  253
     clus
vv    AMP PEAK 12(7Q31.2) MUTATED AMP PEAK 12(7Q31.2) WILD-TYPE
  NO                           11                            10
  YES                         188                           253
[1] 2 2
[1] FALSE
D12V11, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 12(7Q31.2) MUTATED   132   4   3   9
  AMP PEAK 12(7Q31.2) WILD-TYPE 186   7   1  10
D12V12, multiclass
    clus
vv   AMP PEAK 12(7Q31.2) MUTATED AMP PEAK 12(7Q31.2) WILD-TYPE
  R0                         132                           186
  R1                           4                             7
  R2                           3                             1
  RX                           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                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 12(7Q31.2) MUTATED                                  0     3
  AMP PEAK 12(7Q31.2) WILD-TYPE                                1     3
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 12(7Q31.2) MUTATED                          13   162
  AMP PEAK 12(7Q31.2) WILD-TYPE                        13   200
D12V13, multiclass
                                  clus
vv                                 AMP PEAK 12(7Q31.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 13
  WHITE                                                    162
                                  clus
vv                                 AMP PEAK 12(7Q31.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        3
  BLACK OR AFRICAN AMERICAN                                   13
  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"
D12V14, binary
                               cls
clus                              0   1
  AMP PEAK 12(7Q31.2) MUTATED     1 149
  AMP PEAK 12(7Q31.2) WILD-TYPE   6 183
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(7Q31.2) MUTATED      1  149
  AMP PEAK 12(7Q31.2) WILD-TYPE    6  183
                        clus
vv                       AMP PEAK 12(7Q31.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                         149
                        clus
vv                       AMP PEAK 12(7Q31.2) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           183
[1] 2 2
[1] FALSE

Clustering(13) Variable = AMP PEAK 13(8P11.23) MUTATION ANALYSIS
D13V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 13(8P11.23) MUTATED    89  22
  AMP PEAK 13(8P11.23) WILD-TYPE 232  60
  AMP PEAK 13(8P11.23) MUTATED AMP PEAK 13(8P11.23) WILD-TYPE 
                           111                            292 
  AMP PEAK 13(8P11.23) MUTATED AMP PEAK 13(8P11.23) WILD-TYPE 
                            22                             60 
$`AMP PEAK 13(8P11.23) MUTATED`
TCGA-05-4389 TCGA-05-4390 TCGA-05-4398 TCGA-05-4405 TCGA-05-4417 TCGA-05-4420 
        1369         1126         1431          610          455          912 
TCGA-05-4424 TCGA-05-4432 TCGA-05-5425 TCGA-05-5428 TCGA-35-4122 TCGA-35-5375 
         913          761          882          670          225          264 
TCGA-38-4625 TCGA-38-4628 TCGA-38-4629 TCGA-44-3918 TCGA-44-3919 TCGA-44-6147 
        1952         1492          864         1036          190          845 
TCGA-44-6774 TCGA-44-6778 TCGA-44-7660 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 
         658         1864          592         1970          882          535 
TCGA-44-8117 TCGA-44-A47B TCGA-44-A47F TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 
         385          287          337          157         1700          445 
TCGA-50-5051 TCGA-50-5072 TCGA-50-5931 TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 
         455          246          267          567          764          686 
TCGA-50-7109 TCGA-53-7624 TCGA-55-1592 TCGA-55-5899 TCGA-55-6642 TCGA-55-6969 
         255         1986          701           87          993         1239 
TCGA-55-6971 TCGA-55-7570 TCGA-55-7724 TCGA-55-7903 TCGA-55-7907 TCGA-55-8092 
          25            6         1958           19           16           26 
TCGA-55-8096 TCGA-55-8206 TCGA-55-8507 TCGA-55-8514 TCGA-55-8614 TCGA-55-8620 
          47           46            8          202          536           66 
TCGA-55-A494 TCGA-62-8398 TCGA-62-A471 TCGA-64-1676 TCGA-64-1680 TCGA-64-5779 
           5         1970         1246         1728         1126          864 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 TCGA-69-8255 
         690          414          230          184           89          129 
TCGA-73-4658 TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-75-6214 
        1600          467           40          164           38         1970 
TCGA-75-7027 TCGA-75-7031 TCGA-78-7145 TCGA-78-7148 TCGA-78-7149 TCGA-78-7155 
        1956         1965         1973         1944         1093         1957 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7220 TCGA-78-7535 TCGA-78-7542 TCGA-80-5607 
        1963         1221         1965         1972         1952         1965 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7954 TCGA-86-7955 TCGA-86-8279 TCGA-86-8585 
        1959           11         1963          508          482           35 
TCGA-86-8674 TCGA-86-A4D0 TCGA-91-6831 TCGA-91-6840 TCGA-91-7771 TCGA-91-8499 
         405           30          310          372          492           36 
TCGA-93-7347 TCGA-95-7043 TCGA-95-7948 TCGA-97-7547 TCGA-97-7553 TCGA-97-8172 
         297            2          476         1965         1332          182 
TCGA-97-8552 TCGA-97-A4M2 TCGA-99-8032 TCGA-99-8033 TCGA-L9-A444 TCGA-MP-A4T2 
         115          197           44          170            6         1951 
TCGA-MP-A4TA TCGA-MP-A4TE TCGA-MP-A4TH 
        1951         1970          142 

$`AMP PEAK 13(8P11.23) WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4403 TCGA-05-4410 
        1523          607          426         1947          578         1958 
TCGA-05-4415 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 
        1997          365          669          791          791          761 
TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
         730          457          151           30           62           14 
TCGA-35-4123 TCGA-38-4626 TCGA-38-4627 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
         182         1962         1147         1073          354         1357 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 
         448         1971          133         1324         1429          400 
TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
        1367          741         1280         1301           97          246 
TCGA-44-3396 TCGA-44-3398 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 
        1130         1163          722         1013          863          383 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6148 TCGA-44-6775 TCGA-44-6776 
         723          328          302          704          705         1938 
TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
        1942         1978          444          366          218          557 
TCGA-44-7672 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47G 
         719           99          260          486          466          351 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
         415           76         1932         1081         1421          428 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
         999          268          896          369          890          522 
TCGA-49-6761 TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
         354         2174         2146          785          944         1499 
TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5942 TCGA-50-6597 
         282         1091         2370          653          883         1015 
TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1595 
         105         1971          424          280         1178         1479 
TCGA-55-1596 TCGA-55-6543 TCGA-55-6712 TCGA-55-6972 TCGA-55-6980 TCGA-55-6983 
        1375            2           24         1475           67         1826 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
        1233         2151         1170           18           35          121 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
           4           95           40           39           39           34 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
          24           54          197           21            3           31 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
           5           33           21          100            6           43 
TCGA-55-8094 TCGA-55-8097 TCGA-55-8205 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 
           4           15           33           66          216           44 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
          23           29           11           15          228            9 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8621 
           3          146           15           48           49          106 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
          33           42           29           48         1952            1 
TCGA-55-A493 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 
          28           47          162         1216         1289         2696 
TCGA-62-8402 TCGA-62-A46U TCGA-62-A46V TCGA-62-A472 TCGA-64-1677 TCGA-64-1678 
        1445         2067         2199          910          628         1189 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5781 
        1686         1968         1959           62         1305         1559 
TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 
         866           31          610          573          427          385 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7765 
         174          141          422          202          186          165 
TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-A59K TCGA-71-6725 
          70          382          100           77          214           61 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4670 TCGA-73-7498 TCGA-73-7499 
         711          912          800          131          621          519 
TCGA-75-7025 TCGA-78-7146 TCGA-78-7147 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
        1967         1988         1950         1963         1202          760 
TCGA-78-7154 TCGA-78-7156 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        1948         1961          678          215         1940         1950 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
        1934         1937         1949         1944          327          881 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
         994         1949         1971         1981         1954         1964 
TCGA-80-5608 TCGA-83-5908 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        1972          824          630          422         1968          591 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
         745           10         1963           13           24          479 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8281 TCGA-86-8358 TCGA-86-8359 
         489          476           16         1955           19           26 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-A456 
          45           34           18           15          455           10 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 
          14           39          323         1940           60           79 
TCGA-91-6836 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 
         417          842          224           35          197          174 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7567 
          44          218          127          186           34          568 
TCGA-95-7944 TCGA-95-7947 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7552 TCGA-97-7554 
         377          477          121          964         1932          775 
TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 
         181           22          107         1965           87          147 
TCGA-97-8179 TCGA-97-8547 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
          15          148          271          392          427          459 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
         154          114          287          282          238          578 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
         435          116          285          622          353         1946 
TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TC 
        1967         1954         1954         1957         1980         1944 
TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
        1970         1955         1971         1490 

  AMP PEAK 13(8P11.23) MUTATED AMP PEAK 13(8P11.23) WILD-TYPE 
                             2                              1 
  AMP PEAK 13(8P11.23) MUTATED AMP PEAK 13(8P11.23) WILD-TYPE 
                          1986                           2696 
  AMP PEAK 13(8P11.23) MUTATED AMP PEAK 13(8P11.23) WILD-TYPE 
                         536.0                          431.5 
[1] "2.0 - 1986.0 (536.0)" "1.0 - 2696.0 (431.5)"
[1] "hr=" "1"  
D13V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 13(8P11.23) MUTATED         2       33       40        11        14
  AMP PEAK 13(8P11.23) WILD-TYPE       2       80       91        32        55
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 13(8P11.23) MUTATED           16          3        6
  AMP PEAK 13(8P11.23) WILD-TYPE         51          8       17
D13V3, multiclass
            clus
vv           AMP PEAK 13(8P11.23) MUTATED AMP PEAK 13(8P11.23) WILD-TYPE
  STAGE I                               2                              2
  STAGE IA                             33                             80
  STAGE IB                             40                             91
  STAGE IIA                            11                             32
  STAGE IIB                            14                             55
  STAGE IIIA                           16                             51
  STAGE IIIB                            3                              8
  STAGE IV                              6                             17
[1] 8 2
[1] TRUE
[1] "dimension of 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(8P11.23) MUTATED    39  73   7   4
  AMP PEAK 13(8P11.23) WILD-TYPE 104 186  33  14
D13V4, multiclass
    clus
vv   AMP PEAK 13(8P11.23) MUTATED AMP PEAK 13(8P11.23) WILD-TYPE
  T1                           39                            104
  T2                           73                            186
  T3                            7                             33
  T4                            4                             14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1 N2+N3
  AMP PEAK 13(8P11.23) MUTATED    82  23    17
  AMP PEAK 13(8P11.23) WILD-TYPE 213  62    55
D13V5, multiclass
       clus
vv      AMP PEAK 13(8P11.23) MUTATED AMP PEAK 13(8P11.23) WILD-TYPE
  N0                              82                            213
  N1                              23                             62
  N2+N3                           17                             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"
                                vv
clus                              M0  M1 M1A M1B  MX
  AMP PEAK 13(8P11.23) MUTATED    85   5   0   1  34
  AMP PEAK 13(8P11.23) WILD-TYPE 232  13   1   2  85
D13V6, multiclass
     clus
vv    AMP PEAK 13(8P11.23) MUTATED AMP PEAK 13(8P11.23) WILD-TYPE
  M0                            85                            232
  M1                             5                             13
  M1A                            0                              1
  M1B                            1                              2
  MX                            34                             85
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V7, binary
                                cls
clus                               0   1
  AMP PEAK 13(8P11.23) MUTATED    58  67
  AMP PEAK 13(8P11.23) WILD-TYPE 190 147
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(8P11.23) MUTATED     58   67
  AMP PEAK 13(8P11.23) WILD-TYPE  190  147
        clus
vv       AMP PEAK 13(8P11.23) MUTATED AMP PEAK 13(8P11.23) WILD-TYPE
  FEMALE                           58                            190
  MALE                             67                            147
[1] 2 2
[1] FALSE
D13V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 13(8P11.23) MUTATED                            5
  AMP PEAK 13(8P11.23) WILD-TYPE                          8
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 13(8P11.23) MUTATED                                  31
  AMP PEAK 13(8P11.23) WILD-TYPE                                62
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 13(8P11.23) MUTATED                                                   76
  AMP PEAK 13(8P11.23) WILD-TYPE                                                218
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 13(8P11.23) MUTATED                                            0
  AMP PEAK 13(8P11.23) WILD-TYPE                                          4
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 13(8P11.23) MUTATED                                               4
  AMP PEAK 13(8P11.23) WILD-TYPE                                            15
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 13(8P11.23) MUTATED                                0
  AMP PEAK 13(8P11.23) WILD-TYPE                              2
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 13(8P11.23) MUTATED                                    1
  AMP PEAK 13(8P11.23) WILD-TYPE                                  3
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 13(8P11.23) MUTATED                              0
  AMP PEAK 13(8P11.23) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 13(8P11.23) MUTATED                               5
  AMP PEAK 13(8P11.23) WILD-TYPE                            14
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 13(8P11.23) MUTATED                                 0
  AMP PEAK 13(8P11.23) WILD-TYPE                               1
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 13(8P11.23) MUTATED                                               2
  AMP PEAK 13(8P11.23) WILD-TYPE                                             2
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 13(8P11.23) MUTATED                              1
  AMP PEAK 13(8P11.23) WILD-TYPE                            6
D13V9, multiclass
                                                    clus
vv                                                   AMP PEAK 13(8P11.23) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            31
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           76
  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                                               0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 2
  MUCINOUS (COLLOID) CARCINOMA                                                  1
                                                    clus
vv                                                   AMP PEAK 13(8P11.23) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              62
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            218
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  15
  LUNG CLEAR CELL ADENOCARCINOMA                                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              3
  LUNG MUCINOUS ADENOCARCINOMA                                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                                  14
  LUNG SIGNET RING ADENOCARCINOMA                                                 1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                   2
  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"
D13V10, binary
                                cls
clus                               0   1
  AMP PEAK 13(8P11.23) MUTATED     7 118
  AMP PEAK 13(8P11.23) WILD-TYPE  14 323
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(8P11.23) MUTATED      7  118
  AMP PEAK 13(8P11.23) WILD-TYPE   14  323
     clus
vv    AMP PEAK 13(8P11.23) MUTATED AMP PEAK 13(8P11.23) WILD-TYPE
  NO                             7                             14
  YES                          118                            323
[1] 2 2
[1] FALSE
D13V11, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 13(8P11.23) MUTATED    84   5   1   3
  AMP PEAK 13(8P11.23) WILD-TYPE 234   6   3  16
D13V12, multiclass
    clus
vv   AMP PEAK 13(8P11.23) MUTATED AMP PEAK 13(8P11.23) WILD-TYPE
  R0                           84                            234
  R1                            5                              6
  R2                            1                              3
  RX                            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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 13(8P11.23) MUTATED                                  1     0
  AMP PEAK 13(8P11.23) WILD-TYPE                                0     6
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 13(8P11.23) MUTATED                           5   102
  AMP PEAK 13(8P11.23) WILD-TYPE                        21   260
D13V13, multiclass
                                  clus
vv                                 AMP PEAK 13(8P11.23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   5
  WHITE                                                     102
                                  clus
vv                                 AMP PEAK 13(8P11.23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         6
  BLACK OR AFRICAN AMERICAN                                    21
  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"
D13V14, binary
                                cls
clus                               0   1
  AMP PEAK 13(8P11.23) MUTATED     3  86
  AMP PEAK 13(8P11.23) WILD-TYPE   4 246
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(8P11.23) MUTATED      3   86
  AMP PEAK 13(8P11.23) WILD-TYPE    4  246
                        clus
vv                       AMP PEAK 13(8P11.23) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           86
                        clus
vv                       AMP PEAK 13(8P11.23) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            246
[1] 2 2
[1] FALSE

Clustering(14) Variable = AMP PEAK 14(8P11.21) MUTATION ANALYSIS
D14V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 14(8P11.21) MUTATED   109  30
  AMP PEAK 14(8P11.21) WILD-TYPE 212  52
  AMP PEAK 14(8P11.21) MUTATED AMP PEAK 14(8P11.21) WILD-TYPE 
                           139                            264 
  AMP PEAK 14(8P11.21) MUTATED AMP PEAK 14(8P11.21) WILD-TYPE 
                            30                             52 
$`AMP PEAK 14(8P11.21) MUTATED`
TCGA-05-4389 TCGA-05-4390 TCGA-05-4398 TCGA-05-4405 TCGA-05-4417 TCGA-05-4420 
        1369         1126         1431          610          455          912 
TCGA-05-4424 TCGA-05-4432 TCGA-05-5428 TCGA-35-4122 TCGA-35-5375 TCGA-38-4625 
         913          761          670          225          264         1952 
TCGA-38-4628 TCGA-38-4629 TCGA-44-3918 TCGA-44-6147 TCGA-44-6774 TCGA-44-6778 
        1492          864         1036          845          658         1864 
TCGA-44-7660 TCGA-44-7662 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 
         592          218         1970          882          535           99 
TCGA-44-A47B TCGA-44-A47F TCGA-49-4510 TCGA-49-4512 TCGA-50-5051 TCGA-50-5066 
         287          337          896          157          455          944 
TCGA-50-5072 TCGA-50-5931 TCGA-50-5933 TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 
         246          267         2370          567          764          686 
TCGA-50-7109 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-5899 TCGA-55-6642 TCGA-55-6969 
         255          280          701           87          993         1239 
TCGA-55-6971 TCGA-55-7570 TCGA-55-7724 TCGA-55-7903 TCGA-55-7907 TCGA-55-8092 
          25            6         1958           19           16           26 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8205 TCGA-55-8206 TCGA-55-8301 TCGA-55-8507 
           4           47           33           46           44            8 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A491 
         202          536           48           66           42         1952 
TCGA-55-A493 TCGA-55-A494 TCGA-62-8395 TCGA-62-8398 TCGA-62-A471 TCGA-64-1676 
          28            5         1216         1970         1246         1728 
TCGA-64-1680 TCGA-64-5775 TCGA-64-5779 TCGA-67-3771 TCGA-69-7760 TCGA-69-7763 
        1126           62          864          610          202          690 
TCGA-69-7764 TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 TCGA-69-8255 TCGA-73-4658 
         414          230          184           89          129         1600 
TCGA-73-4659 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-75-6214 TCGA-75-7027 
         711           40          164           38         1970         1956 
TCGA-75-7031 TCGA-78-7145 TCGA-78-7148 TCGA-78-7149 TCGA-78-7153 TCGA-78-7155 
        1965         1973         1944         1093          760         1957 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7542 
        1963         1221         1965         1972         1949         1952 
TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 TCGA-86-6851 TCGA-86-7701 TCGA-86-7954 
        1954         1964         1965         1959           11         1963 
TCGA-86-7955 TCGA-86-8279 TCGA-86-8585 TCGA-86-8669 TCGA-86-8673 TCGA-86-8674 
         508          482           35           34          455          405 
TCGA-86-A4D0 TCGA-86-A4P7 TCGA-91-6828 TCGA-91-6831 TCGA-91-6836 TCGA-91-6840 
          30           14          323          310          417          372 
TCGA-91-6848 TCGA-91-8499 TCGA-91-A4BC TCGA-93-7347 TCGA-93-8067 TCGA-95-7043 
         224           36           44          297          186            2 
TCGA-95-7948 TCGA-97-7547 TCGA-97-7553 TCGA-97-7554 TCGA-97-8171 TCGA-97-8172 
         476         1965         1332          775          107          182 
TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M2 TCGA-99-8032 TCGA-99-8033 TCGA-L9-A444 
          15          115          197           44          170            6 
TCGA-MN-A4N5 TCGA-MP-A4T2 TCGA-MP-A4TA TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
         353         1951         1951         1970         1970          142 
TCGA-MP-A4TK 
        1971 

$`AMP PEAK 14(8P11.21) WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4403 TCGA-05-4410 
        1523          607          426         1947          578         1958 
TCGA-05-4415 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 
        1997          365          669          791          791          761 
TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 
         730          457          151          882           30           62 
TCGA-35-3615 TCGA-35-4123 TCGA-38-4626 TCGA-38-4627 TCGA-38-4630 TCGA-38-4631 
          14          182         1962         1147         1073          354 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 
        1357          448         1971          133         1324         1429 
TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 
         400         1367          741         1280         1301           97 
TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
         246         1130         1163          190          722         1013 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6148 
         863          383          723          328          302          704 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 TCGA-44-7661 
         705         1938         1942         1978          444          366 
TCGA-44-7667 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
         557          719          385          260          486          466 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 
         351          415           76         1932         1081         1421 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
         428          999          268         1700          445          369 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 
         890          522          354         2174         2146          785 
TCGA-50-5068 TCGA-50-5930 TCGA-50-5932 TCGA-50-5935 TCGA-50-5942 TCGA-50-6597 
        1499          282         1091          653          883         1015 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-55-1594 TCGA-55-1595 
         105         1986         1971          424         1178         1479 
TCGA-55-1596 TCGA-55-6543 TCGA-55-6712 TCGA-55-6972 TCGA-55-6980 TCGA-55-6983 
        1375            2           24         1475           67         1826 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
        1233         2151         1170           18           35          121 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
           4           95           40           39           39           34 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
          24           54          197           21            3           31 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
           5           33           21          100            6           43 
TCGA-55-8097 TCGA-55-8207 TCGA-55-8299 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
          15           66          216           23           29           11 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8615 
          15          228            9            3          146           15 
TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Z TCGA-55-A490 TCGA-55-A492 
          49          106           33           29           48            1 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8397 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46U 
          47          162         1289         2696         1445         2067 
TCGA-62-A46V TCGA-62-A472 TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 
        2199          910          628         1189         1686         1968 
TCGA-64-5774 TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3772 
        1959         1305         1559          866           31          573 
TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7761 
         427          385          174          141          422          186 
TCGA-69-7765 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-A59K 
         165           70          382          100           77          214 
TCGA-71-6725 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-7498 
          61          912          800          467          131          621 
TCGA-73-7499 TCGA-75-7025 TCGA-78-7146 TCGA-78-7147 TCGA-78-7150 TCGA-78-7152 
         519         1967         1988         1950         1963         1202 
TCGA-78-7154 TCGA-78-7156 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        1948         1961          678          215         1940         1950 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7633 
        1934         1937         1944          327          881          994 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-80-5608 TCGA-83-5908 TCGA-86-7711 
        1949         1971         1981         1972          824          630 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
         422         1968          591          745           10         1963 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 
          13           24          479          489          476           16 
TCGA-86-8281 TCGA-86-8358 TCGA-86-8359 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 
        1955           19           26           45           18           15 
TCGA-86-A456 TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 TCGA-91-6847 
          10           39         1940           60           79          842 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD TCGA-93-7348 
          35          492          197          174          218          127 
TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-A4VK TCGA-97-7546 
          34          568          377          477          121          964 
TCGA-97-7552 TCGA-97-7937 TCGA-97-7941 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 
        1932          181           22         1965           87          147 
TCGA-97-8547 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-J2-8192 
         148          271          392          427          459          154 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
         114          287          282          238          578          435 
TCGA-L9-A443 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T4 
         116          285          622         1946         1967         1954 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TC TCGA-MP-A4TI TCGA-MP-A5C7 
        1954         1957         1980         1944         1955         1490 

  AMP PEAK 14(8P11.21) MUTATED AMP PEAK 14(8P11.21) WILD-TYPE 
                             2                              1 
  AMP PEAK 14(8P11.21) MUTATED AMP PEAK 14(8P11.21) WILD-TYPE 
                          2370                           2696 
  AMP PEAK 14(8P11.21) MUTATED AMP PEAK 14(8P11.21) WILD-TYPE 
                           482                            458 
[1] "2.0 - 2370.0 (482.0)" "1.0 - 2696.0 (458.0)"
[1] "hr=" "1.1"
D14V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 14(8P11.21) MUTATED         2       38       53        15        18
  AMP PEAK 14(8P11.21) WILD-TYPE       2       75       78        28        51
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 14(8P11.21) MUTATED           22          5        8
  AMP PEAK 14(8P11.21) WILD-TYPE         45          6       15
D14V3, multiclass
            clus
vv           AMP PEAK 14(8P11.21) MUTATED AMP PEAK 14(8P11.21) WILD-TYPE
  STAGE I                               2                              2
  STAGE IA                             38                             75
  STAGE IB                             53                             78
  STAGE IIA                            15                             28
  STAGE IIB                            18                             51
  STAGE IIIA                           22                             45
  STAGE IIIB                            5                              6
  STAGE IV                              8                             15
[1] 8 2
[1] TRUE
[1] "dimension of 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(8P11.21) MUTATED    44  98  10   7
  AMP PEAK 14(8P11.21) WILD-TYPE  99 161  30  11
D14V4, multiclass
    clus
vv   AMP PEAK 14(8P11.21) MUTATED AMP PEAK 14(8P11.21) WILD-TYPE
  T1                           44                             99
  T2                           98                            161
  T3                           10                             30
  T4                            7                             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1 N2+N3
  AMP PEAK 14(8P11.21) MUTATED   108  24    26
  AMP PEAK 14(8P11.21) WILD-TYPE 187  61    46
D14V5, multiclass
       clus
vv      AMP PEAK 14(8P11.21) MUTATED AMP PEAK 14(8P11.21) WILD-TYPE
  N0                             108                            187
  N1                              24                             61
  N2+N3                           26                             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"
                                vv
clus                              M0  M1 M1A M1B  MX
  AMP PEAK 14(8P11.21) MUTATED   110   5   1   2  43
  AMP PEAK 14(8P11.21) WILD-TYPE 207  13   0   1  76
D14V6, multiclass
     clus
vv    AMP PEAK 14(8P11.21) MUTATED AMP PEAK 14(8P11.21) WILD-TYPE
  M0                           110                            207
  M1                             5                             13
  M1A                            1                              0
  M1B                            2                              1
  MX                            43                             76
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V7, binary
                                cls
clus                               0   1
  AMP PEAK 14(8P11.21) MUTATED    71  90
  AMP PEAK 14(8P11.21) WILD-TYPE 177 124
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(8P11.21) MUTATED     71   90
  AMP PEAK 14(8P11.21) WILD-TYPE  177  124
        clus
vv       AMP PEAK 14(8P11.21) MUTATED AMP PEAK 14(8P11.21) WILD-TYPE
  FEMALE                           71                            177
  MALE                             90                            124
[1] 2 2
[1] FALSE
D14V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 14(8P11.21) MUTATED                            8
  AMP PEAK 14(8P11.21) WILD-TYPE                          5
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 14(8P11.21) MUTATED                                  34
  AMP PEAK 14(8P11.21) WILD-TYPE                                59
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 14(8P11.21) MUTATED                                                  104
  AMP PEAK 14(8P11.21) WILD-TYPE                                                190
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 14(8P11.21) MUTATED                                            0
  AMP PEAK 14(8P11.21) WILD-TYPE                                          4
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 14(8P11.21) MUTATED                                               5
  AMP PEAK 14(8P11.21) WILD-TYPE                                            14
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 14(8P11.21) MUTATED                                0
  AMP PEAK 14(8P11.21) WILD-TYPE                              2
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 14(8P11.21) MUTATED                                    0
  AMP PEAK 14(8P11.21) WILD-TYPE                                  4
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 14(8P11.21) MUTATED                              0
  AMP PEAK 14(8P11.21) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 14(8P11.21) MUTATED                               6
  AMP PEAK 14(8P11.21) WILD-TYPE                            13
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 14(8P11.21) MUTATED                                 1
  AMP PEAK 14(8P11.21) WILD-TYPE                               0
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 14(8P11.21) MUTATED                                               3
  AMP PEAK 14(8P11.21) WILD-TYPE                                             1
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 14(8P11.21) MUTATED                              0
  AMP PEAK 14(8P11.21) WILD-TYPE                            7
D14V9, multiclass
                                                    clus
vv                                                   AMP PEAK 14(8P11.21) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            34
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          104
  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                                                 6
  LUNG SIGNET RING ADENOCARCINOMA                                               1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 3
  MUCINOUS (COLLOID) CARCINOMA                                                  0
                                                    clus
vv                                                   AMP PEAK 14(8P11.21) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              59
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            190
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  14
  LUNG CLEAR CELL ADENOCARCINOMA                                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              4
  LUNG MUCINOUS ADENOCARCINOMA                                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                                  13
  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"
D14V10, binary
                                cls
clus                               0   1
  AMP PEAK 14(8P11.21) MUTATED     9 152
  AMP PEAK 14(8P11.21) WILD-TYPE  12 289
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(8P11.21) MUTATED      9  152
  AMP PEAK 14(8P11.21) WILD-TYPE   12  289
     clus
vv    AMP PEAK 14(8P11.21) MUTATED AMP PEAK 14(8P11.21) WILD-TYPE
  NO                             9                             12
  YES                          152                            289
[1] 2 2
[1] FALSE
D14V11, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 14(8P11.21) MUTATED   109   5   1   6
  AMP PEAK 14(8P11.21) WILD-TYPE 209   6   3  13
D14V12, multiclass
    clus
vv   AMP PEAK 14(8P11.21) MUTATED AMP PEAK 14(8P11.21) WILD-TYPE
  R0                          109                            209
  R1                            5                              6
  R2                            1                              3
  RX                            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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 14(8P11.21) MUTATED                                  0     2
  AMP PEAK 14(8P11.21) WILD-TYPE                                1     4
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 14(8P11.21) MUTATED                           8   126
  AMP PEAK 14(8P11.21) WILD-TYPE                        18   236
D14V13, multiclass
                                  clus
vv                                 AMP PEAK 14(8P11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   8
  WHITE                                                     126
                                  clus
vv                                 AMP PEAK 14(8P11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    18
  WHITE                                                       236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V14, binary
                                cls
clus                               0   1
  AMP PEAK 14(8P11.21) MUTATED     3 112
  AMP PEAK 14(8P11.21) WILD-TYPE   4 220
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(8P11.21) MUTATED      3  112
  AMP PEAK 14(8P11.21) WILD-TYPE    4  220
                        clus
vv                       AMP PEAK 14(8P11.21) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          112
                        clus
vv                       AMP PEAK 14(8P11.21) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            220
[1] 2 2
[1] FALSE

Clustering(15) Variable = AMP PEAK 15(8Q11.1) MUTATION ANALYSIS
D15V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 15(8Q11.1) MUTATED   146  41
  AMP PEAK 15(8Q11.1) WILD-TYPE 175  41
  AMP PEAK 15(8Q11.1) MUTATED AMP PEAK 15(8Q11.1) WILD-TYPE 
                          187                           216 
  AMP PEAK 15(8Q11.1) MUTATED AMP PEAK 15(8Q11.1) WILD-TYPE 
                           41                            41 
$`AMP PEAK 15(8Q11.1) MUTATED`
TCGA-05-4389 TCGA-05-4390 TCGA-05-4398 TCGA-05-4405 TCGA-05-4417 TCGA-05-4420 
        1369         1126         1431          610          455          912 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4432 TCGA-05-5420 TCGA-05-5428 TCGA-35-4122 
         913          669          761          457          670          225 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4628 TCGA-38-4629 TCGA-38-4631 
         182          264         1952         1492          864          354 
TCGA-38-4632 TCGA-38-6178 TCGA-44-2656 TCGA-44-2668 TCGA-44-3918 TCGA-44-3919 
        1357          448         1429          246         1036          190 
TCGA-44-5644 TCGA-44-6147 TCGA-44-6774 TCGA-44-6777 TCGA-44-6778 TCGA-44-7660 
         863          845          658         1942         1864          592 
TCGA-44-7662 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8119 
         218         1970          882          535          719           99 
TCGA-44-8120 TCGA-44-A47B TCGA-44-A4SU TCGA-49-4501 TCGA-49-4510 TCGA-49-4512 
         260          287           76         1421          896          157 
TCGA-49-6761 TCGA-50-5049 TCGA-50-5051 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
         354         2146          455          944         1499          246 
TCGA-50-5931 TCGA-50-5933 TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 TCGA-50-7109 
         267         2370          567          764          686          255 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 
         424          280          701         1479         1375           87 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6985 
         993           24         1239           25         1475         1233 
TCGA-55-7724 TCGA-55-7903 TCGA-55-7907 TCGA-55-7914 TCGA-55-7994 TCGA-55-8092 
        1958           19           16            3           31           26 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8301 
           4           47           15           33           46           44 
TCGA-55-8507 TCGA-55-8511 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
           8            9          202          536           15           48 
TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A493 
          66           42           29           48         1952           28 
TCGA-55-A494 TCGA-55-A4DG TCGA-62-8398 TCGA-62-8402 TCGA-62-A471 TCGA-62-A472 
           5          162         1970         1445         1246          910 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1680 TCGA-64-5775 TCGA-64-5779 TCGA-67-3771 
        1728          628         1126           62          864          610 
TCGA-67-6217 TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 
         422          690          414          230          184           89 
TCGA-69-8255 TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4670 TCGA-73-4675 
         129           61         1600          711          131           40 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-75-6214 TCGA-75-7027 
         164           38          621          519         1970         1956 
TCGA-75-7031 TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7153 
        1965         1988         1944         1093         1963          760 
TCGA-78-7155 TCGA-78-7158 TCGA-78-7159 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
        1957         1963         1221         1965         1972         1949 
TCGA-78-7539 TCGA-78-7542 TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 
         327         1952         1954         1964         1965         1972 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8074 
        1959           11         1963          508          745           24 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 TCGA-86-8669 TCGA-86-8673 
         482           16           26           35           34          455 
TCGA-86-8674 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-91-6828 TCGA-91-6831 TCGA-91-6836 
         405           30           14          323          310          417 
TCGA-91-6840 TCGA-91-6847 TCGA-91-A4BC TCGA-93-7347 TCGA-93-8067 TCGA-95-7039 
         372          842           44          297          186           34 
TCGA-95-7948 TCGA-97-7547 TCGA-97-7553 TCGA-97-7554 TCGA-97-8171 TCGA-97-8172 
         476         1965         1332          775          107          182 
TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M2 TCGA-99-8025 TCGA-99-8032 TCGA-99-8033 
          15          115          197          427           44          170 
TCGA-J2-8194 TCGA-L4-A4E5 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N4 TCGA-MN-A4N5 
         114          578          116            6          622          353 
TCGA-MP-A4T2 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
        1951         1951         1944         1970         1970          142 
TCGA-MP-A4TK 
        1971 

$`AMP PEAK 15(8Q11.1) WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4403 TCGA-05-4410 
        1523          607          426         1947          578         1958 
TCGA-05-4415 TCGA-05-4422 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4433 
        1997          365          791          791          761          730 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-38-4626 
         151          882           30           62           14         1962 
TCGA-38-4627 TCGA-38-4630 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2657 
        1147         1073         1971          133         1324          400 
TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-3396 
        1367          741         1280         1301           97         1130 
TCGA-44-3398 TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
        1163          722         1013          383          723          328 
TCGA-44-6146 TCGA-44-6148 TCGA-44-6775 TCGA-44-6776 TCGA-44-6779 TCGA-44-7659 
         302          704          705         1938         1978          444 
TCGA-44-7661 TCGA-44-7667 TCGA-44-8117 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47F 
         366          557          385          486          466          337 
TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 
         351          415         1932         1081          428          999 
TCGA-49-4507 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
         268         1700          445          369          890          522 
TCGA-50-5045 TCGA-50-5055 TCGA-50-5930 TCGA-50-5932 TCGA-50-5935 TCGA-50-5942 
        2174          785          282         1091          653          883 
TCGA-50-6597 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-55-1594 TCGA-55-6543 
        1015          105         1986         1971         1178            2 
TCGA-55-6980 TCGA-55-6983 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 
          67         1826         2151         1170           18           35 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7725 
         121            6            4           95           40           39 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7910 TCGA-55-7911 
          39           34           24           54          197           21 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
           5           33           21          100            6           43 
TCGA-55-8207 TCGA-55-8299 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 
          66          216           23           29           11           15 
TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
         228            3          146           49          106           33 
TCGA-55-A492 TCGA-55-A4DF TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 TCGA-62-A46U 
           1           47         1216         1289         2696         2067 
TCGA-62-A46V TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 
        2199         1189         1686         1968         1959         1305 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 
        1559          866           31          573          427          385 
TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7765 TCGA-69-7978 
         174          141          202          186          165           70 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-A59K TCGA-73-4662 TCGA-73-4666 
         382          100           77          214          912          800 
TCGA-73-4668 TCGA-75-7025 TCGA-78-7145 TCGA-78-7147 TCGA-78-7152 TCGA-78-7154 
         467         1967         1973         1950         1202         1948 
TCGA-78-7156 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
        1961          678          215         1940         1950         1934 
TCGA-78-7167 TCGA-78-7537 TCGA-78-7540 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
        1937         1944          881          994         1949         1971 
TCGA-78-8655 TCGA-83-5908 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        1981          824          630          422         1968          591 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
          10         1963           13          479          489          476 
TCGA-86-8281 TCGA-86-8358 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-A456 
        1955           19           45           18           15           10 
TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 TCGA-91-6848 TCGA-91-6849 
          39         1940           60           79          224           35 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7348 
         492          197          174           36          218          127 
TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-A4VK TCGA-97-7546 
           2          568          377          477          121          964 
TCGA-97-7552 TCGA-97-7937 TCGA-97-7941 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 
        1932          181           22         1965           87          147 
TCGA-97-8547 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8028 TCGA-J2-8192 TCGA-J2-A4AD 
         148          271          392          459          154          287 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-MN-A4N1 TCGA-MP-A4SV TCGA-MP-A4SW 
         282          238          435          285         1946         1967 
TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TI TCGA-MP-A5C7 
        1954         1954         1957         1980         1955         1490 

  AMP PEAK 15(8Q11.1) MUTATED AMP PEAK 15(8Q11.1) WILD-TYPE 
                            3                             1 
  AMP PEAK 15(8Q11.1) MUTATED AMP PEAK 15(8Q11.1) WILD-TYPE 
                         2370                          2696 
  AMP PEAK 15(8Q11.1) MUTATED AMP PEAK 15(8Q11.1) WILD-TYPE 
                          482                           452 
[1] "3.0 - 2370.0 (482.0)" "1.0 - 2696.0 (452.0)"
[1] "hr=" "1.3"
D15V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 15(8Q11.1) MUTATED         3       48       66        22        24
  AMP PEAK 15(8Q11.1) WILD-TYPE       1       65       65        21        45
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 15(8Q11.1) MUTATED           31          7       11
  AMP PEAK 15(8Q11.1) WILD-TYPE         36          4       12
D15V3, multiclass
            clus
vv           AMP PEAK 15(8Q11.1) MUTATED AMP PEAK 15(8Q11.1) WILD-TYPE
  STAGE I                              3                             1
  STAGE IA                            48                            65
  STAGE IB                            66                            65
  STAGE IIA                           22                            21
  STAGE IIB                           24                            45
  STAGE IIIA                          31                            36
  STAGE IIIB                           7                             4
  STAGE IV                            11                            12
[1] 8 2
[1] TRUE
[1] "dimension of 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(8Q11.1) MUTATED    61 129  14   7
  AMP PEAK 15(8Q11.1) WILD-TYPE  82 130  26  11
D15V4, multiclass
    clus
vv   AMP PEAK 15(8Q11.1) MUTATED AMP PEAK 15(8Q11.1) WILD-TYPE
  T1                          61                            82
  T2                         129                           130
  T3                          14                            26
  T4                           7                            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 15(8Q11.1) MUTATED   139  33    36
  AMP PEAK 15(8Q11.1) WILD-TYPE 156  52    36
D15V5, multiclass
       clus
vv      AMP PEAK 15(8Q11.1) MUTATED AMP PEAK 15(8Q11.1) WILD-TYPE
  N0                            139                           156
  N1                             33                            52
  N2+N3                          36                            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"
                               vv
clus                             M0  M1 M1A M1B  MX
  AMP PEAK 15(8Q11.1) MUTATED   143   8   1   2  56
  AMP PEAK 15(8Q11.1) WILD-TYPE 174  10   0   1  63
D15V6, multiclass
     clus
vv    AMP PEAK 15(8Q11.1) MUTATED AMP PEAK 15(8Q11.1) WILD-TYPE
  M0                          143                           174
  M1                            8                            10
  M1A                           1                             0
  M1B                           2                             1
  MX                           56                            63
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V7, binary
                               cls
clus                              0   1
  AMP PEAK 15(8Q11.1) MUTATED   107 105
  AMP PEAK 15(8Q11.1) WILD-TYPE 141 109
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(8Q11.1) MUTATED    107  105
  AMP PEAK 15(8Q11.1) WILD-TYPE  141  109
        clus
vv       AMP PEAK 15(8Q11.1) MUTATED AMP PEAK 15(8Q11.1) WILD-TYPE
  FEMALE                         107                           141
  MALE                           105                           109
[1] 2 2
[1] FALSE
D15V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 15(8Q11.1) MUTATED                            8
  AMP PEAK 15(8Q11.1) WILD-TYPE                          5
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 15(8Q11.1) MUTATED                                  41
  AMP PEAK 15(8Q11.1) WILD-TYPE                                52
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 15(8Q11.1) MUTATED                                                  143
  AMP PEAK 15(8Q11.1) WILD-TYPE                                                151
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 15(8Q11.1) MUTATED                                            0
  AMP PEAK 15(8Q11.1) WILD-TYPE                                          4
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 15(8Q11.1) MUTATED                                               8
  AMP PEAK 15(8Q11.1) WILD-TYPE                                            11
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 15(8Q11.1) MUTATED                                1
  AMP PEAK 15(8Q11.1) WILD-TYPE                              1
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 15(8Q11.1) MUTATED                                    0
  AMP PEAK 15(8Q11.1) WILD-TYPE                                  4
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 15(8Q11.1) MUTATED                              0
  AMP PEAK 15(8Q11.1) WILD-TYPE                            2
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 15(8Q11.1) MUTATED                               7
  AMP PEAK 15(8Q11.1) WILD-TYPE                            12
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 15(8Q11.1) MUTATED                                 1
  AMP PEAK 15(8Q11.1) WILD-TYPE                               0
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 15(8Q11.1) MUTATED                                               3
  AMP PEAK 15(8Q11.1) WILD-TYPE                                             1
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 15(8Q11.1) MUTATED                              0
  AMP PEAK 15(8Q11.1) WILD-TYPE                            7
D15V9, multiclass
                                                    clus
vv                                                   AMP PEAK 15(8Q11.1) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           41
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         143
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                   0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                8
  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                                3
  MUCINOUS (COLLOID) CARCINOMA                                                 0
                                                    clus
vv                                                   AMP PEAK 15(8Q11.1) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             52
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           151
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 11
  LUNG CLEAR CELL ADENOCARCINOMA                                                 1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             4
  LUNG MUCINOUS ADENOCARCINOMA                                                   2
  LUNG PAPILLARY ADENOCARCINOMA                                                 12
  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"
D15V10, binary
                               cls
clus                              0   1
  AMP PEAK 15(8Q11.1) MUTATED    11 201
  AMP PEAK 15(8Q11.1) WILD-TYPE  10 240
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(8Q11.1) MUTATED     11  201
  AMP PEAK 15(8Q11.1) WILD-TYPE   10  240
     clus
vv    AMP PEAK 15(8Q11.1) MUTATED AMP PEAK 15(8Q11.1) WILD-TYPE
  NO                           11                            10
  YES                         201                           240
[1] 2 2
[1] FALSE
D15V11, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 15(8Q11.1) MUTATED   149   6   1   7
  AMP PEAK 15(8Q11.1) WILD-TYPE 169   5   3  12
D15V12, multiclass
    clus
vv   AMP PEAK 15(8Q11.1) MUTATED AMP PEAK 15(8Q11.1) WILD-TYPE
  R0                         149                           169
  R1                           6                             5
  R2                           1                             3
  RX                           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                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 15(8Q11.1) MUTATED                                  0     5
  AMP PEAK 15(8Q11.1) WILD-TYPE                                1     1
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 15(8Q11.1) MUTATED                          10   169
  AMP PEAK 15(8Q11.1) WILD-TYPE                        16   193
D15V13, multiclass
                                  clus
vv                                 AMP PEAK 15(8Q11.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      5
  BLACK OR AFRICAN AMERICAN                                 10
  WHITE                                                    169
                                  clus
vv                                 AMP PEAK 15(8Q11.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                   16
  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"
D15V14, binary
                               cls
clus                              0   1
  AMP PEAK 15(8Q11.1) MUTATED     3 154
  AMP PEAK 15(8Q11.1) WILD-TYPE   4 178
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(8Q11.1) MUTATED      3  154
  AMP PEAK 15(8Q11.1) WILD-TYPE    4  178
                        clus
vv                       AMP PEAK 15(8Q11.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                         154
                        clus
vv                       AMP PEAK 15(8Q11.1) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           178
[1] 2 2
[1] FALSE

Clustering(16) Variable = AMP PEAK 16(8Q24.21) MUTATION ANALYSIS
D16V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 16(8Q24.21) MUTATED   194  59
  AMP PEAK 16(8Q24.21) WILD-TYPE 127  23
  AMP PEAK 16(8Q24.21) MUTATED AMP PEAK 16(8Q24.21) WILD-TYPE 
                           253                            150 
  AMP PEAK 16(8Q24.21) MUTATED AMP PEAK 16(8Q24.21) WILD-TYPE 
                            59                             23 
$`AMP PEAK 16(8Q24.21) MUTATED`
TCGA-05-4249 TCGA-05-4389 TCGA-05-4390 TCGA-05-4398 TCGA-05-4405 TCGA-05-4410 
        1523         1369         1126         1431          610         1958 
TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4432 
         455          912          365          913          669          761 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5428 TCGA-35-4122 TCGA-35-5375 TCGA-38-4625 
         457          151          670          225          264         1952 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-44-2656 
        1492          864          354         1357          448         1429 
TCGA-44-2657 TCGA-44-2662 TCGA-44-2665 TCGA-44-2668 TCGA-44-3396 TCGA-44-3918 
         400         1280         1301          246         1130         1036 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5644 TCGA-44-6144 TCGA-44-6147 TCGA-44-6774 
         190          722          863          723          845          658 
TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7661 TCGA-44-7662 
         705         1942         1864         1978          366          218 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8119 
         557         1970          882          535          719           99 
TCGA-44-8120 TCGA-44-A47B TCGA-44-A47F TCGA-44-A4SU TCGA-49-4486 TCGA-49-4501 
         260          287          337           76         1932         1421 
TCGA-49-4505 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-6745 TCGA-49-6761 
         428          268          896          157          522          354 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 
        2146          455          944         1499          246          267 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 TCGA-50-6597 
        1091         2370          567          764          686         1015 
TCGA-50-7109 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-1596 
         255          424          280          701         1479         1375 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6971 
          87            2          993           24         1239           25 
TCGA-55-6972 TCGA-55-6985 TCGA-55-6986 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        1475         1233         2151           95           40         1958 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 TCGA-55-7914 
          39           39           19           16           21            3 
TCGA-55-7994 TCGA-55-8085 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
          31           33          100           26            4           47 
TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8301 TCGA-55-8302 TCGA-55-8507 
          15           33           46           44           23            8 
TCGA-55-8511 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 
           9          202          536           15           48           66 
TCGA-55-8621 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A493 
         106           42           29           48         1952           28 
TCGA-55-A494 TCGA-55-A4DG TCGA-62-8395 TCGA-62-8398 TCGA-62-8402 TCGA-62-A471 
           5          162         1216         1970         1445         1246 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-1680 TCGA-64-5774 
         910         1728          628         1189         1126         1959 
TCGA-64-5775 TCGA-64-5779 TCGA-67-3770 TCGA-67-3771 TCGA-67-6217 TCGA-69-7760 
          62          864           31          610          422          202 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 TCGA-69-8255 
         690          414          230          184           89          129 
TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4668 
         214           61         1600          711          912          467 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
         131           40          164           38          621          519 
TCGA-75-6214 TCGA-75-7027 TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
        1970         1956         1965         1973         1988         1950 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
        1944         1093         1202          760         1948         1957 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7161 TCGA-78-7162 TCGA-78-7166 TCGA-78-7167 
        1963         1221          215         1940         1934         1937 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 TCGA-78-7542 TCGA-78-8660 
        1965         1972         1949          327         1952         1954 
TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 
        1964         1965         1972          824         1959           11 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
         630          422         1968         1963          508          745 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
          13           24          482           16           19           26 
TCGA-86-8585 TCGA-86-8669 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
          35           34           15          455          405           10 
TCGA-86-A4D0 TCGA-86-A4P7 TCGA-91-6828 TCGA-91-6831 TCGA-91-6836 TCGA-91-6840 
          30           14          323          310          417          372 
TCGA-91-6847 TCGA-91-7771 TCGA-91-8499 TCGA-93-7347 TCGA-93-8067 TCGA-95-7043 
         842          492           36          297          186            2 
TCGA-95-7567 TCGA-95-7948 TCGA-97-7547 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
         568          476         1965         1332          775          181 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 
         107          182           15          148          115          197 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8194 TCGA-J2-A4AD 
         427          459           44          170          114          287 
TCGA-J2-A4AE TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
         282          116            6          285          622          353 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 
        1946         1967         1951         1954         1954         1957 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        1951         1944         1970         1970          142         1955 
TCGA-MP-A4TK 
        1971 

$`AMP PEAK 16(8Q24.21) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4403 TCGA-05-4415 TCGA-05-4426 
         607          426         1947          578         1997          791 
TCGA-05-4427 TCGA-05-4430 TCGA-05-4433 TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 
         791          761          730          882           30           62 
TCGA-35-3615 TCGA-35-4123 TCGA-38-4626 TCGA-38-4627 TCGA-38-4630 TCGA-38-7271 
          14          182         1962         1147         1073         1971 
TCGA-38-A44F TCGA-44-2655 TCGA-44-2659 TCGA-44-2661 TCGA-44-2666 TCGA-44-3398 
         133         1324         1367          741           97         1163 
TCGA-44-5643 TCGA-44-5645 TCGA-44-6145 TCGA-44-6146 TCGA-44-6148 TCGA-44-6776 
        1013          383          328          302          704         1938 
TCGA-44-7659 TCGA-44-7660 TCGA-44-8117 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47G 
         444          592          385          486          466          351 
TCGA-44-A4SS TCGA-49-4494 TCGA-49-4506 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
         415         1081          999         1700          445          369 
TCGA-49-6744 TCGA-50-5045 TCGA-50-5055 TCGA-50-5930 TCGA-50-5935 TCGA-50-5942 
         890         2174          785          282          653          883 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-55-1594 TCGA-55-6980 TCGA-55-6983 
         105         1986         1971         1178           67         1826 
TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1170           18           35          121            6            4 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7910 TCGA-55-7995 TCGA-55-8087 
          34           24           54          197            5           21 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8207 TCGA-55-8299 TCGA-55-8505 TCGA-55-8506 
           6           43           66          216           29           11 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8619 TCGA-55-A48X 
          15          228            3          146           49           33 
TCGA-55-A492 TCGA-55-A4DF TCGA-62-8397 TCGA-62-8399 TCGA-62-A46U TCGA-62-A46V 
           1           47         1289         2696         2067         2199 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 
        1686         1968         1305         1559          866          573 
TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-69-7761 TCGA-69-7765 
         427          385          174          141          186          165 
TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-73-4666 TCGA-75-7025 
          70          382          100           77          800         1967 
TCGA-78-7150 TCGA-78-7156 TCGA-78-7160 TCGA-78-7163 TCGA-78-7537 TCGA-78-7540 
        1963         1961          678         1950         1944          881 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-86-7953 TCGA-86-8055 
         994         1949         1971         1981          591           10 
TCGA-86-8056 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8281 TCGA-86-8668 
        1963          479          489          476         1955           45 
TCGA-86-8671 TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 TCGA-91-6848 
          18           39         1940           60           79          224 
TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7348 
          35          197          174           44          218          127 
TCGA-95-7039 TCGA-95-7944 TCGA-95-7947 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7552 
          34          377          477          121          964         1932 
TCGA-97-7941 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 TCGA-97-A4M7 TCGA-99-7458 
          22         1965           87          147          271          392 
TCGA-J2-8192 TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MP-A4T9 TCGA-MP-A5C7 
         154          238          578          435         1980         1490 

  AMP PEAK 16(8Q24.21) MUTATED AMP PEAK 16(8Q24.21) WILD-TYPE 
                             2                              1 
  AMP PEAK 16(8Q24.21) MUTATED AMP PEAK 16(8Q24.21) WILD-TYPE 
                          2370                           2696 
  AMP PEAK 16(8Q24.21) MUTATED AMP PEAK 16(8Q24.21) WILD-TYPE 
                           492                            431 
[1] "2.0 - 2370.0 (492.0)" "1.0 - 2696.0 (431.0)"
[1] "hr=" "1.7"
D16V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 16(8Q24.21) MUTATED         2       67       89        26        43
  AMP PEAK 16(8Q24.21) WILD-TYPE       2       46       42        17        26
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 16(8Q24.21) MUTATED           43          8       16
  AMP PEAK 16(8Q24.21) WILD-TYPE         24          3        7
D16V3, multiclass
            clus
vv           AMP PEAK 16(8Q24.21) MUTATED AMP PEAK 16(8Q24.21) WILD-TYPE
  STAGE I                               2                              2
  STAGE IA                             67                             46
  STAGE IB                             89                             42
  STAGE IIA                            26                             17
  STAGE IIB                            43                             26
  STAGE IIIA                           43                             24
  STAGE IIIB                            8                              3
  STAGE IV                             16                              7
[1] 8 2
[1] TRUE
[1] "dimension of 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(8Q24.21) MUTATED    79 178  25  10
  AMP PEAK 16(8Q24.21) WILD-TYPE  64  81  15   8
D16V4, multiclass
    clus
vv   AMP PEAK 16(8Q24.21) MUTATED AMP PEAK 16(8Q24.21) WILD-TYPE
  T1                           79                             64
  T2                          178                             81
  T3                           25                             15
  T4                           10                              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 16(8Q24.21) MUTATED   189  51    48
  AMP PEAK 16(8Q24.21) WILD-TYPE 106  34    24
D16V5, multiclass
       clus
vv      AMP PEAK 16(8Q24.21) MUTATED AMP PEAK 16(8Q24.21) WILD-TYPE
  N0                             189                            106
  N1                              51                             34
  N2+N3                           48                             24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  AMP PEAK 16(8Q24.21) MUTATED   205  13   1   2  71
  AMP PEAK 16(8Q24.21) WILD-TYPE 112   5   0   1  48
D16V6, multiclass
     clus
vv    AMP PEAK 16(8Q24.21) MUTATED AMP PEAK 16(8Q24.21) WILD-TYPE
  M0                           205                            112
  M1                            13                              5
  M1A                            1                              0
  M1B                            2                              1
  MX                            71                             48
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V7, binary
                                cls
clus                               0   1
  AMP PEAK 16(8Q24.21) MUTATED   155 139
  AMP PEAK 16(8Q24.21) WILD-TYPE  93  75
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(8Q24.21) MUTATED    155  139
  AMP PEAK 16(8Q24.21) WILD-TYPE   93   75
        clus
vv       AMP PEAK 16(8Q24.21) MUTATED AMP PEAK 16(8Q24.21) WILD-TYPE
  FEMALE                          155                             93
  MALE                            139                             75
[1] 2 2
[1] FALSE
D16V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 16(8Q24.21) MUTATED                            9
  AMP PEAK 16(8Q24.21) WILD-TYPE                          4
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 16(8Q24.21) MUTATED                                  54
  AMP PEAK 16(8Q24.21) WILD-TYPE                                39
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 16(8Q24.21) MUTATED                                                  199
  AMP PEAK 16(8Q24.21) WILD-TYPE                                                 95
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 16(8Q24.21) MUTATED                                            1
  AMP PEAK 16(8Q24.21) WILD-TYPE                                          3
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 16(8Q24.21) MUTATED                                              11
  AMP PEAK 16(8Q24.21) WILD-TYPE                                             8
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 16(8Q24.21) MUTATED                                1
  AMP PEAK 16(8Q24.21) WILD-TYPE                              1
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 16(8Q24.21) MUTATED                                    3
  AMP PEAK 16(8Q24.21) WILD-TYPE                                  1
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 16(8Q24.21) MUTATED                              0
  AMP PEAK 16(8Q24.21) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 16(8Q24.21) MUTATED                              12
  AMP PEAK 16(8Q24.21) WILD-TYPE                             7
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 16(8Q24.21) MUTATED                                 1
  AMP PEAK 16(8Q24.21) WILD-TYPE                               0
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 16(8Q24.21) MUTATED                                               3
  AMP PEAK 16(8Q24.21) WILD-TYPE                                             1
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 16(8Q24.21) MUTATED                              0
  AMP PEAK 16(8Q24.21) WILD-TYPE                            7
D16V9, multiclass
                                                    clus
vv                                                   AMP PEAK 16(8Q24.21) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            54
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          199
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                11
  LUNG CLEAR CELL ADENOCARCINOMA                                                1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            3
  LUNG MUCINOUS ADENOCARCINOMA                                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                                12
  LUNG SIGNET RING ADENOCARCINOMA                                               1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 3
  MUCINOUS (COLLOID) CARCINOMA                                                  0
                                                    clus
vv                                                   AMP PEAK 16(8Q24.21) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              39
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             95
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                   8
  LUNG CLEAR CELL ADENOCARCINOMA                                                  1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              1
  LUNG MUCINOUS ADENOCARCINOMA                                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                                   7
  LUNG SIGNET RING ADENOCARCINOMA                                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                   1
  MUCINOUS (COLLOID) CARCINOMA                                                    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"
D16V10, binary
                                cls
clus                               0   1
  AMP PEAK 16(8Q24.21) MUTATED    14 280
  AMP PEAK 16(8Q24.21) WILD-TYPE   7 161
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(8Q24.21) MUTATED     14  280
  AMP PEAK 16(8Q24.21) WILD-TYPE    7  161
     clus
vv    AMP PEAK 16(8Q24.21) MUTATED AMP PEAK 16(8Q24.21) WILD-TYPE
  NO                            14                              7
  YES                          280                            161
[1] 2 2
[1] FALSE
D16V11, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 16(8Q24.21) MUTATED   203   9   4  12
  AMP PEAK 16(8Q24.21) WILD-TYPE 115   2   0   7
D16V12, multiclass
    clus
vv   AMP PEAK 16(8Q24.21) MUTATED AMP PEAK 16(8Q24.21) WILD-TYPE
  R0                          203                            115
  R1                            9                              2
  R2                            4                              0
  RX                           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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 16(8Q24.21) MUTATED                                  1     6
  AMP PEAK 16(8Q24.21) WILD-TYPE                                0     0
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 16(8Q24.21) MUTATED                          15   229
  AMP PEAK 16(8Q24.21) WILD-TYPE                        11   133
D16V13, multiclass
                                  clus
vv                                 AMP PEAK 16(8Q24.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       6
  BLACK OR AFRICAN AMERICAN                                  15
  WHITE                                                     229
                                  clus
vv                                 AMP PEAK 16(8Q24.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         0
  BLACK OR AFRICAN AMERICAN                                    11
  WHITE                                                       133
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V14, binary
                                cls
clus                               0   1
  AMP PEAK 16(8Q24.21) MUTATED     5 202
  AMP PEAK 16(8Q24.21) WILD-TYPE   2 130
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(8Q24.21) MUTATED      5  202
  AMP PEAK 16(8Q24.21) WILD-TYPE    2  130
                        clus
vv                       AMP PEAK 16(8Q24.21) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          202
                        clus
vv                       AMP PEAK 16(8Q24.21) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            130
[1] 2 2
[1] FALSE

Clustering(17) Variable = AMP PEAK 17(10P15.1) MUTATION ANALYSIS
D17V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 17(10P15.1) MUTATED    94  21
  AMP PEAK 17(10P15.1) WILD-TYPE 227  61
  AMP PEAK 17(10P15.1) MUTATED AMP PEAK 17(10P15.1) WILD-TYPE 
                           115                            288 
  AMP PEAK 17(10P15.1) MUTATED AMP PEAK 17(10P15.1) WILD-TYPE 
                            21                             61 
$`AMP PEAK 17(10P15.1) MUTATED`
TCGA-05-4382 TCGA-05-4389 TCGA-05-4390 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 
         607         1369         1126          610         1958         1997 
TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4427 TCGA-05-4430 
         455          912          365          913          791          761 
TCGA-05-4432 TCGA-05-5420 TCGA-05-5425 TCGA-35-4122 TCGA-38-4625 TCGA-38-4629 
         761          457          882          225         1952          864 
TCGA-38-4631 TCGA-38-4632 TCGA-44-3396 TCGA-44-3918 TCGA-44-6144 TCGA-44-6145 
         354         1357         1130         1036          723          328 
TCGA-44-6778 TCGA-44-7660 TCGA-44-7662 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
        1864          592          218          535          719          385 
TCGA-44-8120 TCGA-49-4514 TCGA-50-5049 TCGA-50-5051 TCGA-50-5068 TCGA-50-5933 
         260         1700         2146          455         1499         2370 
TCGA-50-5944 TCGA-50-5946 TCGA-50-7109 TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ 
         764          686          255         1986          424          280 
TCGA-55-1596 TCGA-55-6969 TCGA-55-6972 TCGA-55-7574 TCGA-55-7727 TCGA-55-7910 
        1375         1239         1475           95           34          197 
TCGA-55-8085 TCGA-55-8092 TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8511 
          33           26           44           23           11            9 
TCGA-55-8615 TCGA-55-8620 TCGA-55-A491 TCGA-55-A4DG TCGA-62-8398 TCGA-62-8399 
          15           66         1952          162         1970         2696 
TCGA-64-1678 TCGA-67-3771 TCGA-69-7763 TCGA-69-7979 TCGA-71-6725 TCGA-73-4658 
        1189          610          690           89           61         1600 
TCGA-73-4662 TCGA-73-4668 TCGA-73-4670 TCGA-73-4677 TCGA-75-6214 TCGA-75-7027 
         912          467          131           38         1970         1956 
TCGA-78-7149 TCGA-78-7154 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7539 
        1093         1948         1221          678          215          327 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8660 TCGA-78-8662 TCGA-80-5608 TCGA-86-7701 
        1952          994         1954         1964         1972           11 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7955 TCGA-86-8585 TCGA-86-8672 TCGA-86-8673 
         630          422          508           35           15          455 
TCGA-86-A456 TCGA-86-A4D0 TCGA-91-6829 TCGA-91-6836 TCGA-91-7771 TCGA-93-8067 
          10           30         1940          417          492          186 
TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
           2          568          377         1332          775          181 
TCGA-97-8179 TCGA-99-8025 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
          15          427          114          116            6          285 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4TE 
         622          353         1954         1954         1957         1970 
TCGA-MP-A4TF 
        1970 

$`AMP PEAK 17(10P15.1) WILD-TYPE`
TCGA-05-4249 TCGA-05-4384 TCGA-05-4396 TCGA-05-4398 TCGA-05-4403 TCGA-05-4425 
        1523          426         1947         1431          578          669 
TCGA-05-4426 TCGA-05-4433 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
         791          730          151          670           30           62 
TCGA-35-3615 TCGA-35-4123 TCGA-35-5375 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
          14          182          264         1962         1147         1492 
TCGA-38-4630 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 
        1073          448         1971          133         1324         1429 
TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 
         400         1367          741         1280         1301           97 
TCGA-44-2668 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
         246         1163          190          722         1013          863 
TCGA-44-5645 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
         383          302          845          704          658          705 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 TCGA-44-7661 TCGA-44-7667 
        1938         1942         1978          444          366          557 
TCGA-44-7669 TCGA-44-7670 TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
        1970          882           99          486          466          287 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 
         337          351          415           76         1932         1081 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
        1421          428          999          268          896          157 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-50-5045 
         445          369          890          522          354         2174 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
         785          944          246          282          267         1091 
TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 TCGA-50-6597 TCGA-50-8460 TCGA-53-7626 
         653          567          883         1015          105         1971 
TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
         701         1178         1479           87            2          993 
TCGA-55-6712 TCGA-55-6971 TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 
          24           25           67         1826         1233         2151 
TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1170           18           35          121            6            4 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 TCGA-55-7815 
          40         1958           39           39           24           54 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
          19           16           21            3           31            5 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8094 TCGA-55-8096 
          21          100            6           43            4           47 
TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8505 
          15           33           46           66          216           29 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
           8           15          228            3          146          202 
TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
         536           48           49          106           33           42 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
          29           48            1           28            5           47 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8402 TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 
        1216         1289         1445         2067         2199         1246 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 
         910         1728          628         1686         1126         1968 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
        1959           62         1305          864         1559          866 
TCGA-67-3770 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 
          31          573          427          385          174          141 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
         422          202          186          414          165          230 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
         184           70          382          100           77          129 
TCGA-69-A59K TCGA-73-4659 TCGA-73-4666 TCGA-73-4675 TCGA-73-4676 TCGA-73-7498 
         214          711          800           40          164          621 
TCGA-73-7499 TCGA-75-7025 TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
         519         1967         1965         1973         1988         1950 
TCGA-78-7148 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7155 TCGA-78-7156 
        1944         1963         1202          760         1957         1961 
TCGA-78-7158 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        1963         1940         1950         1934         1937         1965 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 TCGA-78-8640 TCGA-78-8648 
        1972         1949         1944          881         1949         1971 
TCGA-78-8655 TCGA-80-5607 TCGA-83-5908 TCGA-86-6851 TCGA-86-7714 TCGA-86-7953 
        1981         1965          824         1959         1968          591 
TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
        1963          745           10         1963           13           24 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8281 
         479          489          476          482           16         1955 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8674 
          19           26           45           34           18          405 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
          14           39          323           60          310           79 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 
         372          842          224           35          197          174 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-95-7039 
          36           44          218          297          127           34 
TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
         477          476          121          964         1965         1932 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 
          22          107          182         1965           87          147 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8028 
         148          115          197          271          392          459 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
          44          170          154          287          282          238 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T9 
         578          435         1946         1967         1951         1980 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
        1951         1944          142         1955         1971         1490 

  AMP PEAK 17(10P15.1) MUTATED AMP PEAK 17(10P15.1) WILD-TYPE 
                             2                              1 
  AMP PEAK 17(10P15.1) MUTATED AMP PEAK 17(10P15.1) WILD-TYPE 
                          2696                           2199 
  AMP PEAK 17(10P15.1) MUTATED AMP PEAK 17(10P15.1) WILD-TYPE 
                         610.0                          426.5 
[1] "2.0 - 2696.0 (610.0)" "1.0 - 2199.0 (426.5)"
[1] "hr=" "1.5"
D17V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 17(10P15.1) MUTATED         1       31       40        11        19
  AMP PEAK 17(10P15.1) WILD-TYPE       3       82       91        32        50
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 17(10P15.1) MUTATED           15          5        8
  AMP PEAK 17(10P15.1) WILD-TYPE         52          6       15
D17V3, multiclass
            clus
vv           AMP PEAK 17(10P15.1) MUTATED AMP PEAK 17(10P15.1) WILD-TYPE
  STAGE I                               1                              3
  STAGE IA                             31                             82
  STAGE IB                             40                             91
  STAGE IIA                            11                             32
  STAGE IIB                            19                             50
  STAGE IIIA                           15                             52
  STAGE IIIB                            5                              6
  STAGE IV                              8                             15
[1] 8 2
[1] TRUE
[1] "dimension of 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(10P15.1) MUTATED    31  80  12   6
  AMP PEAK 17(10P15.1) WILD-TYPE 112 179  28  12
D17V4, multiclass
    clus
vv   AMP PEAK 17(10P15.1) MUTATED AMP PEAK 17(10P15.1) WILD-TYPE
  T1                           31                            112
  T2                           80                            179
  T3                           12                             28
  T4                            6                             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 17(10P15.1) MUTATED    95  15    19
  AMP PEAK 17(10P15.1) WILD-TYPE 200  70    53
D17V5, multiclass
       clus
vv      AMP PEAK 17(10P15.1) MUTATED AMP PEAK 17(10P15.1) WILD-TYPE
  N0                              95                            200
  N1                              15                             70
  N2+N3                           19                             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"
                                vv
clus                              M0  M1 M1A M1B  MX
  AMP PEAK 17(10P15.1) MUTATED    92   7   0   1  30
  AMP PEAK 17(10P15.1) WILD-TYPE 225  11   1   2  89
D17V6, multiclass
     clus
vv    AMP PEAK 17(10P15.1) MUTATED AMP PEAK 17(10P15.1) WILD-TYPE
  M0                            92                            225
  M1                             7                             11
  M1A                            0                              1
  M1B                            1                              2
  MX                            30                             89
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V7, binary
                                cls
clus                               0   1
  AMP PEAK 17(10P15.1) MUTATED    53  77
  AMP PEAK 17(10P15.1) WILD-TYPE 195 137
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(10P15.1) MUTATED     53   77
  AMP PEAK 17(10P15.1) WILD-TYPE  195  137
        clus
vv       AMP PEAK 17(10P15.1) MUTATED AMP PEAK 17(10P15.1) WILD-TYPE
  FEMALE                           53                            195
  MALE                             77                            137
[1] 2 2
[1] FALSE
D17V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 17(10P15.1) MUTATED                            5
  AMP PEAK 17(10P15.1) WILD-TYPE                          8
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 17(10P15.1) MUTATED                                  28
  AMP PEAK 17(10P15.1) WILD-TYPE                                65
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 17(10P15.1) MUTATED                                                   79
  AMP PEAK 17(10P15.1) WILD-TYPE                                                215
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 17(10P15.1) MUTATED                                            0
  AMP PEAK 17(10P15.1) WILD-TYPE                                          4
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 17(10P15.1) MUTATED                                               4
  AMP PEAK 17(10P15.1) WILD-TYPE                                            15
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 17(10P15.1) MUTATED                                0
  AMP PEAK 17(10P15.1) WILD-TYPE                              2
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 17(10P15.1) MUTATED                                    2
  AMP PEAK 17(10P15.1) WILD-TYPE                                  2
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 17(10P15.1) MUTATED                              0
  AMP PEAK 17(10P15.1) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 17(10P15.1) MUTATED                               9
  AMP PEAK 17(10P15.1) WILD-TYPE                            10
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 17(10P15.1) MUTATED                                 0
  AMP PEAK 17(10P15.1) WILD-TYPE                               1
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 17(10P15.1) MUTATED                                               2
  AMP PEAK 17(10P15.1) WILD-TYPE                                             2
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 17(10P15.1) MUTATED                              1
  AMP PEAK 17(10P15.1) WILD-TYPE                            6
D17V9, multiclass
                                                    clus
vv                                                   AMP PEAK 17(10P15.1) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            28
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           79
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 4
  LUNG CLEAR CELL ADENOCARCINOMA                                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            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 17(10P15.1) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              65
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            215
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  15
  LUNG CLEAR CELL ADENOCARCINOMA                                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              2
  LUNG MUCINOUS ADENOCARCINOMA                                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                                  10
  LUNG SIGNET RING ADENOCARCINOMA                                                 1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                   2
  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"
D17V10, binary
                                cls
clus                               0   1
  AMP PEAK 17(10P15.1) MUTATED     3 127
  AMP PEAK 17(10P15.1) WILD-TYPE  18 314
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(10P15.1) MUTATED      3  127
  AMP PEAK 17(10P15.1) WILD-TYPE   18  314
     clus
vv    AMP PEAK 17(10P15.1) MUTATED AMP PEAK 17(10P15.1) WILD-TYPE
  NO                             3                             18
  YES                          127                            314
[1] 2 2
[1] FALSE
D17V11, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 17(10P15.1) MUTATED    89   4   0   8
  AMP PEAK 17(10P15.1) WILD-TYPE 229   7   4  11
D17V12, multiclass
    clus
vv   AMP PEAK 17(10P15.1) MUTATED AMP PEAK 17(10P15.1) WILD-TYPE
  R0                           89                            229
  R1                            4                              7
  R2                            0                              4
  RX                            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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 17(10P15.1) MUTATED                                  1     4
  AMP PEAK 17(10P15.1) WILD-TYPE                                0     2
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 17(10P15.1) MUTATED                           8    90
  AMP PEAK 17(10P15.1) WILD-TYPE                        18   272
D17V13, multiclass
                                  clus
vv                                 AMP PEAK 17(10P15.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                   8
  WHITE                                                      90
                                  clus
vv                                 AMP PEAK 17(10P15.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         2
  BLACK OR AFRICAN AMERICAN                                    18
  WHITE                                                       272
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V14, binary
                                cls
clus                               0   1
  AMP PEAK 17(10P15.1) MUTATED     3  83
  AMP PEAK 17(10P15.1) WILD-TYPE   4 249
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(10P15.1) MUTATED      3   83
  AMP PEAK 17(10P15.1) WILD-TYPE    4  249
                        clus
vv                       AMP PEAK 17(10P15.1) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           83
                        clus
vv                       AMP PEAK 17(10P15.1) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            249
[1] 2 2
[1] FALSE

Clustering(18) Variable = AMP PEAK 18(11Q13.3) MUTATION ANALYSIS
D18V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 18(11Q13.3) MUTATED   111  33
  AMP PEAK 18(11Q13.3) WILD-TYPE 210  49
  AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE 
                           144                            259 
  AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE 
                            33                             49 
$`AMP PEAK 18(11Q13.3) MUTATED`
TCGA-05-4389 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4425 
        1369         1958         1997          455          912          669 
TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5429 TCGA-38-4628 
         761          730          457          151           30         1492 
TCGA-38-4629 TCGA-38-4632 TCGA-44-2656 TCGA-44-2659 TCGA-44-2662 TCGA-44-3918 
         864         1357         1429         1367         1280         1036 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6774 TCGA-44-6775 TCGA-44-6778 TCGA-44-6779 
         863          383          658          705         1864         1978 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7669 TCGA-44-8117 TCGA-44-8119 
         592          366          218         1970          385           99 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-49-4494 TCGA-49-4512 TCGA-50-5932 
         486          466          287         1081          157         1091 
TCGA-50-5933 TCGA-50-5941 TCGA-50-5946 TCGA-50-6597 TCGA-53-7624 TCGA-53-7813 
        2370          567          686         1015         1986          424 
TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 
         701         1178         1479         1375           87            2 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6971 TCGA-55-7576 TCGA-55-7910 TCGA-55-7994 
         993           24           25           40          197           31 
TCGA-55-7995 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8205 TCGA-55-8506 
           5           26            4           47           33           11 
TCGA-55-8507 TCGA-55-8510 TCGA-55-8511 TCGA-55-8514 TCGA-55-8615 TCGA-55-8616 
           8          228            9          202           15           48 
TCGA-55-A490 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8399 TCGA-62-8402 TCGA-64-1676 
          48            5          162         2696         1445         1728 
TCGA-64-1677 TCGA-64-1678 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5779 
         628         1189         1968         1959           62          864 
TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-6215 TCGA-69-7973 TCGA-69-7974 
         866           31          610          174          230          184 
TCGA-69-7979 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4662 
          89          129          214           61         1600          912 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4676 TCGA-78-7147 TCGA-78-7148 TCGA-78-7154 
         800          467          164         1950         1944         1948 
TCGA-78-7155 TCGA-78-7159 TCGA-78-7161 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 
        1957         1221          215         1950         1937         1965 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 TCGA-78-7542 TCGA-78-8655 TCGA-78-8662 
        1972         1949          327         1952         1981         1964 
TCGA-80-5608 TCGA-86-6851 TCGA-86-7701 TCGA-86-7953 TCGA-86-7955 TCGA-86-8054 
        1972         1959           11          591          508          745 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-A4D0 
         476          482           16           19           26           30 
TCGA-91-6829 TCGA-91-6831 TCGA-91-6836 TCGA-91-6840 TCGA-91-6848 TCGA-91-A4BC 
        1940          310          417          372          224           44 
TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-97-7553 TCGA-97-7937 
         127          186           34            2         1332          181 
TCGA-97-8174 TCGA-97-8177 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD TCGA-L9-A443 
        1965          147           44          170          287          116 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TI 
           6          285          622         1951         1944         1955 

$`AMP PEAK 18(11Q13.3) WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4390 TCGA-05-4396 TCGA-05-4398 
        1523          607          426         1126         1947         1431 
TCGA-05-4403 TCGA-05-4405 TCGA-05-4422 TCGA-05-4424 TCGA-05-4426 TCGA-05-4427 
         578          610          365          913          791          791 
TCGA-05-4430 TCGA-05-5425 TCGA-05-5428 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 
         761          882          670           62           14          225 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4630 
         182          264         1952         1962         1147         1073 
TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2657 
         354          448         1971          133         1324          400 
TCGA-44-2661 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 
         741         1301           97          246         1130         1163 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
         190          722         1013          723          328          302 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6776 TCGA-44-6777 TCGA-44-7659 TCGA-44-7667 
         845          704         1938         1942          444          557 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8120 TCGA-44-A47F TCGA-44-A47G 
         882          535          719          260          337          351 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
         415           76         1932         1421          428          999 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
         268          896         1700          445          369          890 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
         522          354         2174         2146          455          785 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5935 
         944         1499          246          282          267          653 
TCGA-50-5942 TCGA-50-5944 TCGA-50-7109 TCGA-50-8460 TCGA-53-7626 TCGA-53-A4EZ 
         883          764          255          105         1971          280 
TCGA-55-6969 TCGA-55-6972 TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 
        1239         1475           67         1826         1233         2151 
TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1170           18           35          121            6            4 
TCGA-55-7574 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
          95         1958           39           39           34           24 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 TCGA-55-7914 TCGA-55-8085 
          54           19           16           21            3           33 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8097 TCGA-55-8206 
          21          100            6           43           15           46 
TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8508 
          66          216           44           23           29           15 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
           3          146          536           49           66          106 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
          33           42           29         1952            1           28 
TCGA-55-A4DF TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-A46U TCGA-62-A46V 
          47         1216         1289         1970         2067         2199 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1679 TCGA-64-1680 TCGA-64-5778 TCGA-64-5781 
        1246          910         1686         1126         1305         1559 
TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
         573          427          385          141          422          202 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7978 TCGA-69-7980 
         186          690          414          165           70          382 
TCGA-69-8253 TCGA-69-8254 TCGA-73-4659 TCGA-73-4670 TCGA-73-4675 TCGA-73-4677 
         100           77          711          131           40           38 
TCGA-73-7498 TCGA-73-7499 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 
         621          519         1970         1967         1956         1965 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
        1973         1988         1093         1963         1202          760 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 TCGA-78-7162 TCGA-78-7166 TCGA-78-7537 
        1961         1963          678         1940         1934         1944 
TCGA-78-7540 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8660 TCGA-80-5607 
         881          994         1949         1971         1954         1965 
TCGA-83-5908 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7954 TCGA-86-8055 
         824          630          422         1968         1963           10 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8281 
        1963           13           24          479          489         1955 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
          35           45           34           18           15          455 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 
         405           10           14           39          323           60 
TCGA-91-6835 TCGA-91-6847 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
          79          842           35          492          197          174 
TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
          36          218          297          568          377          477 
TCGA-95-7948 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7554 
         476          121          964         1965         1932          775 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 TCGA-97-8179 TCGA-97-8547 
          22          107          182           87           15          148 
TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
         115          197          271          392          427          459 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
         154          114          282          238          578          435 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 
         353         1946         1967         1951         1954         1954 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TK 
        1957         1980         1970         1970          142         1971 
TCGA-MP-A5C7 
        1490 

  AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE 
                             2                              1 
  AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE 
                          2696                           2199 
  AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE 
                           484                            448 
[1] "2.0 - 2696.0 (484.0)" "1.0 - 2199.0 (448.0)"
[1] "hr=" "1.1"
D18V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 18(11Q13.3) MUTATED         0       33       46        15        26
  AMP PEAK 18(11Q13.3) WILD-TYPE       4       80       85        28        43
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 18(11Q13.3) MUTATED           24          4       10
  AMP PEAK 18(11Q13.3) WILD-TYPE         43          7       13
D18V3, multiclass
            clus
vv           AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE
  STAGE I                               0                              4
  STAGE IA                             33                             80
  STAGE IB                             46                             85
  STAGE IIA                            15                             28
  STAGE IIB                            26                             43
  STAGE IIIA                           24                             43
  STAGE IIIB                            4                              7
  STAGE IV                             10                             13
[1] 8 2
[1] TRUE
[1] "dimension of 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(11Q13.3) MUTATED    40  97  14   5
  AMP PEAK 18(11Q13.3) WILD-TYPE 103 162  26  13
D18V4, multiclass
    clus
vv   AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE
  T1                           40                            103
  T2                           97                            162
  T3                           14                             26
  T4                            5                             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 18(11Q13.3) MUTATED   102  25    27
  AMP PEAK 18(11Q13.3) WILD-TYPE 193  60    45
D18V5, multiclass
       clus
vv      AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE
  N0                             102                            193
  N1                              25                             60
  N2+N3                           27                             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"
                                vv
clus                              M0  M1 M1A M1B  MX
  AMP PEAK 18(11Q13.3) MUTATED   102   9   0   1  44
  AMP PEAK 18(11Q13.3) WILD-TYPE 215   9   1   2  75
D18V6, multiclass
     clus
vv    AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE
  M0                           102                            215
  M1                             9                              9
  M1A                            0                              1
  M1B                            1                              2
  MX                            44                             75
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V7, binary
                                cls
clus                               0   1
  AMP PEAK 18(11Q13.3) MUTATED    82  76
  AMP PEAK 18(11Q13.3) WILD-TYPE 166 138
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(11Q13.3) MUTATED     82   76
  AMP PEAK 18(11Q13.3) WILD-TYPE  166  138
        clus
vv       AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE
  FEMALE                           82                            166
  MALE                             76                            138
[1] 2 2
[1] FALSE
D18V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 18(11Q13.3) MUTATED                            4
  AMP PEAK 18(11Q13.3) WILD-TYPE                          9
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 18(11Q13.3) MUTATED                                  29
  AMP PEAK 18(11Q13.3) WILD-TYPE                                64
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 18(11Q13.3) MUTATED                                                  111
  AMP PEAK 18(11Q13.3) WILD-TYPE                                                183
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 18(11Q13.3) MUTATED                                            1
  AMP PEAK 18(11Q13.3) WILD-TYPE                                          3
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 18(11Q13.3) MUTATED                                               4
  AMP PEAK 18(11Q13.3) WILD-TYPE                                            15
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 18(11Q13.3) MUTATED                                1
  AMP PEAK 18(11Q13.3) WILD-TYPE                              1
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 18(11Q13.3) MUTATED                                    2
  AMP PEAK 18(11Q13.3) WILD-TYPE                                  2
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 18(11Q13.3) MUTATED                              0
  AMP PEAK 18(11Q13.3) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 18(11Q13.3) MUTATED                               4
  AMP PEAK 18(11Q13.3) WILD-TYPE                            15
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 18(11Q13.3) MUTATED                                 1
  AMP PEAK 18(11Q13.3) WILD-TYPE                               0
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 18(11Q13.3) MUTATED                                               1
  AMP PEAK 18(11Q13.3) WILD-TYPE                                             3
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 18(11Q13.3) MUTATED                              0
  AMP PEAK 18(11Q13.3) WILD-TYPE                            7
D18V9, multiclass
                                                    clus
vv                                                   AMP PEAK 18(11Q13.3) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            29
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          111
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 4
  LUNG CLEAR CELL ADENOCARCINOMA                                                1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            2
  LUNG MUCINOUS ADENOCARCINOMA                                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                                 4
  LUNG SIGNET RING ADENOCARCINOMA                                               1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 1
  MUCINOUS (COLLOID) CARCINOMA                                                  0
                                                    clus
vv                                                   AMP PEAK 18(11Q13.3) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              64
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            183
  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                                                  15
  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"
D18V10, binary
                                cls
clus                               0   1
  AMP PEAK 18(11Q13.3) MUTATED     8 150
  AMP PEAK 18(11Q13.3) WILD-TYPE  13 291
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(11Q13.3) MUTATED      8  150
  AMP PEAK 18(11Q13.3) WILD-TYPE   13  291
     clus
vv    AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE
  NO                             8                             13
  YES                          150                            291
[1] 2 2
[1] FALSE
D18V11, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 18(11Q13.3) MUTATED   107   3   1   8
  AMP PEAK 18(11Q13.3) WILD-TYPE 211   8   3  11
D18V12, multiclass
    clus
vv   AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE
  R0                          107                            211
  R1                            3                              8
  R2                            1                              3
  RX                            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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 18(11Q13.3) MUTATED                                  1     4
  AMP PEAK 18(11Q13.3) WILD-TYPE                                0     2
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 18(11Q13.3) MUTATED                          11   123
  AMP PEAK 18(11Q13.3) WILD-TYPE                        15   239
D18V13, multiclass
                                  clus
vv                                 AMP PEAK 18(11Q13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  11
  WHITE                                                     123
                                  clus
vv                                 AMP PEAK 18(11Q13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         2
  BLACK OR AFRICAN AMERICAN                                    15
  WHITE                                                       239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V14, binary
                                cls
clus                               0   1
  AMP PEAK 18(11Q13.3) MUTATED     3 113
  AMP PEAK 18(11Q13.3) WILD-TYPE   4 219
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(11Q13.3) MUTATED      3  113
  AMP PEAK 18(11Q13.3) WILD-TYPE    4  219
                        clus
vv                       AMP PEAK 18(11Q13.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          113
                        clus
vv                       AMP PEAK 18(11Q13.3) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            219
[1] 2 2
[1] FALSE

Clustering(19) Variable = AMP PEAK 19(12P12.1) MUTATION ANALYSIS
D19V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 19(12P12.1) MUTATED   110  32
  AMP PEAK 19(12P12.1) WILD-TYPE 211  50
  AMP PEAK 19(12P12.1) MUTATED AMP PEAK 19(12P12.1) WILD-TYPE 
                           142                            261 
  AMP PEAK 19(12P12.1) MUTATED AMP PEAK 19(12P12.1) WILD-TYPE 
                            32                             50 
$`AMP PEAK 19(12P12.1) MUTATED`
TCGA-05-4382 TCGA-05-4389 TCGA-05-4390 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 
         607         1369         1126         1997          455          912 
TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 TCGA-05-5428 TCGA-35-4122 TCGA-35-5375 
         761          730          457          670          225          264 
TCGA-38-4625 TCGA-38-4628 TCGA-38-4632 TCGA-44-2657 TCGA-44-2668 TCGA-44-5643 
        1952         1492         1357          400          246         1013 
TCGA-44-5644 TCGA-44-6779 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
         863         1978          592          366          218          557 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7672 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
        1970          882          719          486          466          287 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-6742 TCGA-49-6745 TCGA-50-5045 
         268          896          157          445          522         2174 
TCGA-50-5072 TCGA-50-5931 TCGA-50-5935 TCGA-50-5941 TCGA-50-5944 TCGA-50-6597 
         246          267          653          567          764         1015 
TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-6642 TCGA-55-6712 
         701         1178         1479         1375          993           24 
TCGA-55-6971 TCGA-55-6980 TCGA-55-6985 TCGA-55-6987 TCGA-55-7283 TCGA-55-7284 
          25           67         1233         1170           35          121 
TCGA-55-7576 TCGA-55-7726 TCGA-55-7728 TCGA-55-7815 TCGA-55-7907 TCGA-55-7910 
          40           39           24           54           16          197 
TCGA-55-7911 TCGA-55-7995 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
          21            5          100           26            4           47 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8615 TCGA-55-A490 
          23           29            8           15           15           48 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-62-8398 TCGA-62-8402 TCGA-62-A471 
          28            5           47         1970         1445         1246 
TCGA-64-1678 TCGA-64-1681 TCGA-64-5775 TCGA-67-3774 TCGA-69-7973 TCGA-69-7974 
        1189         1968           62          385          230          184 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8255 TCGA-69-A59K TCGA-73-4662 TCGA-73-4666 
          89          382          129          214          912          800 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-75-7027 TCGA-78-7145 TCGA-78-7146 
         467          131           40         1956         1973         1988 
TCGA-78-7148 TCGA-78-7154 TCGA-78-7155 TCGA-78-7159 TCGA-78-7161 TCGA-78-7167 
        1944         1948         1957         1221          215         1937 
TCGA-78-7220 TCGA-78-8655 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-7713 
        1965         1981          824         1959           11          422 
TCGA-86-7953 TCGA-86-7954 TCGA-86-8278 TCGA-86-8280 TCGA-86-8669 TCGA-86-8673 
         591         1963          476           16           34          455 
TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6829 TCGA-91-6835 TCGA-91-6836 TCGA-91-6847 
          30          323         1940           79          417          842 
TCGA-91-6848 TCGA-91-7771 TCGA-91-8499 TCGA-93-8067 TCGA-95-7567 TCGA-95-7944 
         224          492           36          186          568          377 
TCGA-97-7554 TCGA-97-8552 TCGA-97-A4M7 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
         775          115          271          459           44          170 
TCGA-L9-A443 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4T7 
         116          285          622          353         1946         1954 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TK 
        1970         1970         1955         1971 

$`AMP PEAK 19(12P12.1) WILD-TYPE`
TCGA-05-4249 TCGA-05-4384 TCGA-05-4396 TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 
        1523          426         1947         1431          578          610 
TCGA-05-4410 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 
        1958          365          913          669          791          791 
TCGA-05-4430 TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
         761          151          882           30           62           14 
TCGA-35-4123 TCGA-38-4626 TCGA-38-4627 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
         182         1962         1147          864         1073          354 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2659 
         448         1971          133         1324         1429         1367 
TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-3396 TCGA-44-3398 
         741         1280         1301           97         1130         1163 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
        1036          190          722          383          723          328 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
         302          845          704          658          705         1938 
TCGA-44-6777 TCGA-44-6778 TCGA-44-7659 TCGA-44-7671 TCGA-44-8117 TCGA-44-8119 
        1942         1864          444          535          385           99 
TCGA-44-8120 TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
         260          337          351          415           76         1932 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4514 TCGA-49-6743 
        1081         1421          428          999         1700          369 
TCGA-49-6744 TCGA-49-6761 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
         890          354         2146          455          785          944 
TCGA-50-5068 TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 TCGA-50-5942 TCGA-50-5946 
        1499          282         1091         2370          883          686 
TCGA-50-7109 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
         255          105         1986         1971          424          280 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6969 TCGA-55-6972 TCGA-55-6983 TCGA-55-6986 
          87            2         1239         1475         1826         2151 
TCGA-55-7281 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7724 TCGA-55-7725 
          18            6            4           95         1958           39 
TCGA-55-7727 TCGA-55-7903 TCGA-55-7914 TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 
          34           19            3           31           33           21 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
           6           43           15           33           46           66 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8506 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
         216           44           11          228            9            3 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
         146          202          536           48           49           66 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 
         106           33           42           29         1952            1 
TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 TCGA-62-A46U TCGA-62-A46V 
         162         1216         1289         2696         2067         2199 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1680 TCGA-64-5774 
         910         1728          628         1686         1126         1959 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 
        1305          864         1559          866           31          610 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
         573          427          174          141          422          202 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7978 TCGA-69-8253 
         186          690          414          165           70          100 
TCGA-69-8254 TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4676 TCGA-73-4677 
          77           61         1600          711          164           38 
TCGA-73-7498 TCGA-73-7499 TCGA-75-6214 TCGA-75-7025 TCGA-75-7031 TCGA-78-7147 
         621          519         1970         1967         1965         1950 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7156 TCGA-78-7158 
        1093         1963         1202          760         1961         1963 
TCGA-78-7160 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7535 TCGA-78-7536 
         678         1940         1950         1934         1972         1949 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
        1944          327          881         1952          994         1949 
TCGA-78-8648 TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 TCGA-86-7711 
        1971         1954         1964         1965         1972          630 
TCGA-86-7714 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
        1968          508          745           10         1963           13 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8279 TCGA-86-8281 TCGA-86-8358 
          24          479          489          482         1955           19 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 
          26           35           45           18           15          405 
TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6830 TCGA-91-6831 TCGA-91-6840 
          10           14           39           60          310          372 
TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
          35          197          174           44          218          297 
TCGA-93-7348 TCGA-95-7039 TCGA-95-7043 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK 
         127           34            2          477          476          121 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 TCGA-97-7941 
         964         1965         1932         1332          181           22 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 
         107          182         1965           87          147           15 
TCGA-97-8547 TCGA-97-A4M2 TCGA-99-7458 TCGA-99-8025 TCGA-J2-8192 TCGA-J2-8194 
         148          197          392          427          154          114 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A444 
         287          282          238          578          435            6 
TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
        1967         1951         1954         1957         1980         1951 
TCGA-MP-A4TC TCGA-MP-A4TH TCGA-MP-A5C7 
        1944          142         1490 

  AMP PEAK 19(12P12.1) MUTATED AMP PEAK 19(12P12.1) WILD-TYPE 
                             4                              1 
  AMP PEAK 19(12P12.1) MUTATED AMP PEAK 19(12P12.1) WILD-TYPE 
                          2174                           2696 
  AMP PEAK 19(12P12.1) MUTATED AMP PEAK 19(12P12.1) WILD-TYPE 
                           458                            477 
[1] "4.0 - 2174.0 (458.0)" "1.0 - 2696.0 (477.0)"
[1] "hr=" "1.2"
D19V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 19(12P12.1) MUTATED         2       36       43        19        22
  AMP PEAK 19(12P12.1) WILD-TYPE       2       77       88        24        47
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 19(12P12.1) MUTATED           29          2       11
  AMP PEAK 19(12P12.1) WILD-TYPE         38          9       12
D19V3, multiclass
            clus
vv           AMP PEAK 19(12P12.1) MUTATED AMP PEAK 19(12P12.1) WILD-TYPE
  STAGE I                               2                              2
  STAGE IA                             36                             77
  STAGE IB                             43                             88
  STAGE IIA                            19                             24
  STAGE IIB                            22                             47
  STAGE IIIA                           29                             38
  STAGE IIIB                            2                              9
  STAGE IV                             11                             12
[1] 8 2
[1] TRUE
[1] "dimension of 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(12P12.1) MUTATED    43 100  15   5
  AMP PEAK 19(12P12.1) WILD-TYPE 100 159  25  13
D19V4, multiclass
    clus
vv   AMP PEAK 19(12P12.1) MUTATED AMP PEAK 19(12P12.1) WILD-TYPE
  T1                           43                            100
  T2                          100                            159
  T3                           15                             25
  T4                            5                             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 19(12P12.1) MUTATED   101  32    27
  AMP PEAK 19(12P12.1) WILD-TYPE 194  53    45
D19V5, multiclass
       clus
vv      AMP PEAK 19(12P12.1) MUTATED AMP PEAK 19(12P12.1) WILD-TYPE
  N0                             101                            194
  N1                              32                             53
  N2+N3                           27                             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"
                                vv
clus                              M0  M1 M1A M1B  MX
  AMP PEAK 19(12P12.1) MUTATED   107  10   0   1  45
  AMP PEAK 19(12P12.1) WILD-TYPE 210   8   1   2  74
D19V6, multiclass
     clus
vv    AMP PEAK 19(12P12.1) MUTATED AMP PEAK 19(12P12.1) WILD-TYPE
  M0                           107                            210
  M1                            10                              8
  M1A                            0                              1
  M1B                            1                              2
  MX                            45                             74
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V7, binary
                                cls
clus                               0   1
  AMP PEAK 19(12P12.1) MUTATED    85  79
  AMP PEAK 19(12P12.1) WILD-TYPE 163 135
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(12P12.1) MUTATED     85   79
  AMP PEAK 19(12P12.1) WILD-TYPE  163  135
        clus
vv       AMP PEAK 19(12P12.1) MUTATED AMP PEAK 19(12P12.1) WILD-TYPE
  FEMALE                           85                            163
  MALE                             79                            135
[1] 2 2
[1] FALSE
D19V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 19(12P12.1) MUTATED                            3
  AMP PEAK 19(12P12.1) WILD-TYPE                         10
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 19(12P12.1) MUTATED                                  28
  AMP PEAK 19(12P12.1) WILD-TYPE                                65
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 19(12P12.1) MUTATED                                                  116
  AMP PEAK 19(12P12.1) WILD-TYPE                                                178
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 19(12P12.1) MUTATED                                            0
  AMP PEAK 19(12P12.1) WILD-TYPE                                          4
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 19(12P12.1) MUTATED                                               8
  AMP PEAK 19(12P12.1) WILD-TYPE                                            11
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 19(12P12.1) MUTATED                                1
  AMP PEAK 19(12P12.1) WILD-TYPE                              1
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 19(12P12.1) MUTATED                                    1
  AMP PEAK 19(12P12.1) WILD-TYPE                                  3
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 19(12P12.1) MUTATED                              0
  AMP PEAK 19(12P12.1) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 19(12P12.1) MUTATED                               3
  AMP PEAK 19(12P12.1) WILD-TYPE                            16
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 19(12P12.1) MUTATED                                 0
  AMP PEAK 19(12P12.1) WILD-TYPE                               1
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 19(12P12.1) MUTATED                                               1
  AMP PEAK 19(12P12.1) WILD-TYPE                                             3
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 19(12P12.1) MUTATED                              3
  AMP PEAK 19(12P12.1) WILD-TYPE                            4
D19V9, multiclass
                                                    clus
vv                                                   AMP PEAK 19(12P12.1) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            28
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          116
  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                                                 3
  LUNG SIGNET RING ADENOCARCINOMA                                               0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 1
  MUCINOUS (COLLOID) CARCINOMA                                                  3
                                                    clus
vv                                                   AMP PEAK 19(12P12.1) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              65
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            178
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  11
  LUNG CLEAR CELL ADENOCARCINOMA                                                  1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              3
  LUNG MUCINOUS ADENOCARCINOMA                                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                                  16
  LUNG SIGNET RING ADENOCARCINOMA                                                 1
  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"
D19V10, binary
                                cls
clus                               0   1
  AMP PEAK 19(12P12.1) MUTATED     8 156
  AMP PEAK 19(12P12.1) WILD-TYPE  13 285
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(12P12.1) MUTATED      8  156
  AMP PEAK 19(12P12.1) WILD-TYPE   13  285
     clus
vv    AMP PEAK 19(12P12.1) MUTATED AMP PEAK 19(12P12.1) WILD-TYPE
  NO                             8                             13
  YES                          156                            285
[1] 2 2
[1] FALSE
D19V11, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 19(12P12.1) MUTATED   114   3   4   6
  AMP PEAK 19(12P12.1) WILD-TYPE 204   8   0  13
D19V12, multiclass
    clus
vv   AMP PEAK 19(12P12.1) MUTATED AMP PEAK 19(12P12.1) WILD-TYPE
  R0                          114                            204
  R1                            3                              8
  R2                            4                              0
  RX                            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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 19(12P12.1) MUTATED                                  1     3
  AMP PEAK 19(12P12.1) WILD-TYPE                                0     3
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 19(12P12.1) MUTATED                          12   122
  AMP PEAK 19(12P12.1) WILD-TYPE                        14   240
D19V13, multiclass
                                  clus
vv                                 AMP PEAK 19(12P12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  12
  WHITE                                                     122
                                  clus
vv                                 AMP PEAK 19(12P12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         3
  BLACK OR AFRICAN AMERICAN                                    14
  WHITE                                                       240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V14, binary
                                cls
clus                               0   1
  AMP PEAK 19(12P12.1) MUTATED     2 114
  AMP PEAK 19(12P12.1) WILD-TYPE   5 218
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(12P12.1) MUTATED      2  114
  AMP PEAK 19(12P12.1) WILD-TYPE    5  218
                        clus
vv                       AMP PEAK 19(12P12.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          114
                        clus
vv                       AMP PEAK 19(12P12.1) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            218
[1] 2 2
[1] FALSE

Clustering(20) Variable = AMP PEAK 20(12Q14.1) MUTATION ANALYSIS
D20V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 20(12Q14.1) MUTATED   104  28
  AMP PEAK 20(12Q14.1) WILD-TYPE 217  54
  AMP PEAK 20(12Q14.1) MUTATED AMP PEAK 20(12Q14.1) WILD-TYPE 
                           132                            271 
  AMP PEAK 20(12Q14.1) MUTATED AMP PEAK 20(12Q14.1) WILD-TYPE 
                            28                             54 
$`AMP PEAK 20(12Q14.1) MUTATED`
TCGA-05-4389 TCGA-05-4390 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4430 
        1369         1126         1997          455          912          761 
TCGA-05-4432 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-35-4122 TCGA-35-5375 
         761          457          151          882          225          264 
TCGA-38-4628 TCGA-38-4631 TCGA-44-2656 TCGA-44-2657 TCGA-44-2668 TCGA-44-3918 
        1492          354         1429          400          246         1036 
TCGA-44-5644 TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 TCGA-44-7667 TCGA-44-7669 
         863         1864         1978          592          557         1970 
TCGA-44-7670 TCGA-44-7672 TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
         882          719           99          486          466          287 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4514 TCGA-49-6742 TCGA-49-6745 TCGA-50-5045 
         268          896         1700          445          522         2174 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5072 TCGA-50-5931 TCGA-50-5944 TCGA-50-5946 
         455          785          246          267          764          686 
TCGA-50-6597 TCGA-53-7624 TCGA-53-7813 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 
        1015         1986          424         1178         1479         1375 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6971 TCGA-55-6980 TCGA-55-6987 TCGA-55-7284 
         993           24           25           67         1170          121 
TCGA-55-7726 TCGA-55-7728 TCGA-55-7815 TCGA-55-7907 TCGA-55-7910 TCGA-55-7995 
          39           24           54           16          197            5 
TCGA-55-8089 TCGA-55-8096 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 
         100           47           23           29            8           15 
TCGA-55-8615 TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-62-8398 
          15           48           28            5           47         1970 
TCGA-62-8402 TCGA-62-A46V TCGA-62-A471 TCGA-64-1678 TCGA-64-1681 TCGA-64-5775 
        1445         2199         1246         1189         1968           62 
TCGA-64-5779 TCGA-67-3774 TCGA-69-7760 TCGA-69-7973 TCGA-69-7980 TCGA-69-8255 
         864          385          202          230          382          129 
TCGA-69-A59K TCGA-73-4666 TCGA-73-4670 TCGA-73-4675 TCGA-75-7027 TCGA-78-7145 
         214          800          131           40         1956         1973 
TCGA-78-7146 TCGA-78-7148 TCGA-78-7161 TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 
        1988         1944          215         1937         1965         1949 
TCGA-78-8655 TCGA-86-7701 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
        1981           11          422          591         1963          508 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8669 
         476          482           19           26           35           34 
TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6836 TCGA-91-6840 TCGA-91-6848 TCGA-91-6849 
          30          323          417          372          224           35 
TCGA-91-7771 TCGA-93-8067 TCGA-95-7567 TCGA-95-7944 TCGA-97-8177 TCGA-97-8552 
         492          186          568          377          147          115 
TCGA-97-A4M7 TCGA-99-8032 TCGA-99-8033 TCGA-L9-A443 TCGA-MN-A4N1 TCGA-MN-A4N4 
         271           44          170          116          285          622 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4T7 TCGA-MP-A4TE TCGA-MP-A4TI TCGA-MP-A4TK 
         353         1946         1954         1970         1955         1971 

$`AMP PEAK 20(12Q14.1) WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4398 TCGA-05-4403 
        1523          607          426         1947         1431          578 
TCGA-05-4405 TCGA-05-4410 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
         610         1958          365          913          669          791 
TCGA-05-4427 TCGA-05-4433 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
         791          730          670           30           62           14 
TCGA-35-4123 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4629 TCGA-38-4630 
         182         1952         1962         1147          864         1073 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2659 
        1357          448         1971          133         1324         1367 
TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-3396 TCGA-44-3398 
         741         1280         1301           97         1130         1163 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
         190          722         1013          383          723          328 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
         302          845          704          658          705         1938 
TCGA-44-6777 TCGA-44-7659 TCGA-44-7661 TCGA-44-7662 TCGA-44-7671 TCGA-44-8117 
        1942          444          366          218          535          385 
TCGA-44-8120 TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
         260          337          351          415           76         1932 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4512 TCGA-49-6743 
        1081         1421          428          999          157          369 
TCGA-49-6744 TCGA-49-6761 TCGA-50-5049 TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 
         890          354         2146          944         1499          282 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 TCGA-50-7109 
        1091         2370          653          567          883          255 
TCGA-50-8460 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-5899 TCGA-55-6543 
         105         1971          280          701           87            2 
TCGA-55-6969 TCGA-55-6972 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 TCGA-55-7281 
        1239         1475         1826         1233         2151           18 
TCGA-55-7283 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
          35            6            4           95           40         1958 
TCGA-55-7725 TCGA-55-7727 TCGA-55-7903 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
          39           34           19           21            3           31 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
          33           21            6           43           26            4 
TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 
          15           33           46           66          216           44 
TCGA-55-8506 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
          11          228            9            3          146          202 
TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
         536           48           49           66          106           33 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DG TCGA-62-8395 
          42           29         1952            1          162         1216 
TCGA-62-8397 TCGA-62-8399 TCGA-62-A46U TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
        1289         2696         2067          910         1728          628 
TCGA-64-1679 TCGA-64-1680 TCGA-64-5774 TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 
        1686         1126         1959         1305         1559          866 
TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
          31          610          573          427          174          141 
TCGA-67-6217 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 
         422          186          690          414          165          184 
TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-71-6725 TCGA-73-4658 
          70           89          100           77           61         1600 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4668 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
         711          912          467          164           38          621 
TCGA-73-7499 TCGA-75-6214 TCGA-75-7025 TCGA-75-7031 TCGA-78-7147 TCGA-78-7149 
         519         1970         1967         1965         1950         1093 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
        1963         1202          760         1948         1957         1961 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
        1963         1221          678         1940         1950         1934 
TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        1972         1944          327          881         1952          994 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 
        1949         1971         1954         1964         1965         1972 
TCGA-83-5908 TCGA-86-6851 TCGA-86-7711 TCGA-86-7714 TCGA-86-8054 TCGA-86-8055 
         824         1959          630         1968          745           10 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8280 
        1963           13           24          479          489           16 
TCGA-86-8281 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
        1955           45           18           15          455          405 
TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
          10           14           39         1940           60          310 
TCGA-91-6835 TCGA-91-6847 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
          79          842          197          174           36           44 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-95-7039 TCGA-95-7043 TCGA-95-7947 
         218          297          127           34            2          477 
TCGA-95-7948 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
         476          121          964         1965         1932         1332 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
         775          181           22          107          182         1965 
TCGA-97-8175 TCGA-97-8179 TCGA-97-8547 TCGA-97-A4M2 TCGA-99-7458 TCGA-99-8025 
          87           15          148          197          392          427 
TCGA-99-8028 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
         459          154          114          287          282          238 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A444 TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 
         578          435            6         1967         1951         1954 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TF TCGA-MP-A4TH 
        1957         1980         1951         1944         1970          142 
TCGA-MP-A5C7 
        1490 

  AMP PEAK 20(12Q14.1) MUTATED AMP PEAK 20(12Q14.1) WILD-TYPE 
                             5                              1 
  AMP PEAK 20(12Q14.1) MUTATED AMP PEAK 20(12Q14.1) WILD-TYPE 
                          2199                           2696 
  AMP PEAK 20(12Q14.1) MUTATED AMP PEAK 20(12Q14.1) WILD-TYPE 
                           450                            479 
[1] "5.0 - 2199.0 (450.0)" "1.0 - 2696.0 (479.0)"
[1] "hr=" "1"  
D20V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 20(12Q14.1) MUTATED         2       31       40        17        24
  AMP PEAK 20(12Q14.1) WILD-TYPE       2       82       91        26        45
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 20(12Q14.1) MUTATED           25          3       10
  AMP PEAK 20(12Q14.1) WILD-TYPE         42          8       13
D20V3, multiclass
            clus
vv           AMP PEAK 20(12Q14.1) MUTATED AMP PEAK 20(12Q14.1) WILD-TYPE
  STAGE I                               2                              2
  STAGE IA                             31                             82
  STAGE IB                             40                             91
  STAGE IIA                            17                             26
  STAGE IIB                            24                             45
  STAGE IIIA                           25                             42
  STAGE IIIB                            3                              8
  STAGE IV                             10                             13
[1] 8 2
[1] TRUE
[1] "dimension of 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(12Q14.1) MUTATED    38  93  14   6
  AMP PEAK 20(12Q14.1) WILD-TYPE 105 166  26  12
D20V4, multiclass
    clus
vv   AMP PEAK 20(12Q14.1) MUTATED AMP PEAK 20(12Q14.1) WILD-TYPE
  T1                           38                            105
  T2                           93                            166
  T3                           14                             26
  T4                            6                             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 20(12Q14.1) MUTATED    94  31    24
  AMP PEAK 20(12Q14.1) WILD-TYPE 201  54    48
D20V5, multiclass
       clus
vv      AMP PEAK 20(12Q14.1) MUTATED AMP PEAK 20(12Q14.1) WILD-TYPE
  N0                              94                            201
  N1                              31                             54
  N2+N3                           24                             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"
                                vv
clus                              M0  M1 M1A M1B  MX
  AMP PEAK 20(12Q14.1) MUTATED   104  10   0   0  37
  AMP PEAK 20(12Q14.1) WILD-TYPE 213   8   1   3  82
D20V6, multiclass
     clus
vv    AMP PEAK 20(12Q14.1) MUTATED AMP PEAK 20(12Q14.1) WILD-TYPE
  M0                           104                            213
  M1                            10                              8
  M1A                            0                              1
  M1B                            0                              3
  MX                            37                             82
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V7, binary
                                cls
clus                               0   1
  AMP PEAK 20(12Q14.1) MUTATED    73  79
  AMP PEAK 20(12Q14.1) WILD-TYPE 175 135
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(12Q14.1) MUTATED     73   79
  AMP PEAK 20(12Q14.1) WILD-TYPE  175  135
        clus
vv       AMP PEAK 20(12Q14.1) MUTATED AMP PEAK 20(12Q14.1) WILD-TYPE
  FEMALE                           73                            175
  MALE                             79                            135
[1] 2 2
[1] FALSE
D20V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 20(12Q14.1) MUTATED                            4
  AMP PEAK 20(12Q14.1) WILD-TYPE                          9
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 20(12Q14.1) MUTATED                                  28
  AMP PEAK 20(12Q14.1) WILD-TYPE                                65
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 20(12Q14.1) MUTATED                                                  106
  AMP PEAK 20(12Q14.1) WILD-TYPE                                                188
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 20(12Q14.1) MUTATED                                            0
  AMP PEAK 20(12Q14.1) WILD-TYPE                                          4
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 20(12Q14.1) MUTATED                                               5
  AMP PEAK 20(12Q14.1) WILD-TYPE                                            14
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 20(12Q14.1) MUTATED                                1
  AMP PEAK 20(12Q14.1) WILD-TYPE                              1
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 20(12Q14.1) MUTATED                                    0
  AMP PEAK 20(12Q14.1) WILD-TYPE                                  4
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 20(12Q14.1) MUTATED                              0
  AMP PEAK 20(12Q14.1) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 20(12Q14.1) MUTATED                               3
  AMP PEAK 20(12Q14.1) WILD-TYPE                            16
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 20(12Q14.1) MUTATED                                 0
  AMP PEAK 20(12Q14.1) WILD-TYPE                               1
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 20(12Q14.1) MUTATED                                               2
  AMP PEAK 20(12Q14.1) WILD-TYPE                                             2
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 20(12Q14.1) MUTATED                              3
  AMP PEAK 20(12Q14.1) WILD-TYPE                            4
D20V9, multiclass
                                                    clus
vv                                                   AMP PEAK 20(12Q14.1) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            28
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          106
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 5
  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                                 2
  MUCINOUS (COLLOID) CARCINOMA                                                  3
                                                    clus
vv                                                   AMP PEAK 20(12Q14.1) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              65
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            188
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  14
  LUNG CLEAR CELL ADENOCARCINOMA                                                  1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              4
  LUNG MUCINOUS ADENOCARCINOMA                                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                                  16
  LUNG SIGNET RING ADENOCARCINOMA                                                 1
  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"
D20V10, binary
                                cls
clus                               0   1
  AMP PEAK 20(12Q14.1) MUTATED     7 145
  AMP PEAK 20(12Q14.1) WILD-TYPE  14 296
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(12Q14.1) MUTATED      7  145
  AMP PEAK 20(12Q14.1) WILD-TYPE   14  296
     clus
vv    AMP PEAK 20(12Q14.1) MUTATED AMP PEAK 20(12Q14.1) WILD-TYPE
  NO                             7                             14
  YES                          145                            296
[1] 2 2
[1] FALSE
D20V11, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 20(12Q14.1) MUTATED   106   2   3   7
  AMP PEAK 20(12Q14.1) WILD-TYPE 212   9   1  12
D20V12, multiclass
    clus
vv   AMP PEAK 20(12Q14.1) MUTATED AMP PEAK 20(12Q14.1) WILD-TYPE
  R0                          106                            212
  R1                            2                              9
  R2                            3                              1
  RX                            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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 20(12Q14.1) MUTATED                                  0     3
  AMP PEAK 20(12Q14.1) WILD-TYPE                                1     3
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 20(12Q14.1) MUTATED                          10   113
  AMP PEAK 20(12Q14.1) WILD-TYPE                        16   249
D20V13, multiclass
                                  clus
vv                                 AMP PEAK 20(12Q14.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  10
  WHITE                                                     113
                                  clus
vv                                 AMP PEAK 20(12Q14.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         3
  BLACK OR AFRICAN AMERICAN                                    16
  WHITE                                                       249
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V14, binary
                                cls
clus                               0   1
  AMP PEAK 20(12Q14.1) MUTATED     3 101
  AMP PEAK 20(12Q14.1) WILD-TYPE   4 231
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(12Q14.1) MUTATED      3  101
  AMP PEAK 20(12Q14.1) WILD-TYPE    4  231
                        clus
vv                       AMP PEAK 20(12Q14.1) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          101
                        clus
vv                       AMP PEAK 20(12Q14.1) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            231
[1] 2 2
[1] FALSE

Clustering(21) Variable = AMP PEAK 21(12Q15) MUTATION ANALYSIS
D21V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 21(12Q15) MUTATED   104  28
  AMP PEAK 21(12Q15) WILD-TYPE 217  54
  AMP PEAK 21(12Q15) MUTATED AMP PEAK 21(12Q15) WILD-TYPE 
                         132                          271 
  AMP PEAK 21(12Q15) MUTATED AMP PEAK 21(12Q15) WILD-TYPE 
                          28                           54 
$`AMP PEAK 21(12Q15) MUTATED`
TCGA-05-4382 TCGA-05-4389 TCGA-05-4390 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 
         607         1369         1126         1997          455          912 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 TCGA-05-5425 TCGA-35-4122 
         761          761          730          457          882          225 
TCGA-35-5375 TCGA-38-4628 TCGA-38-4631 TCGA-44-2656 TCGA-44-3918 TCGA-44-5644 
         264         1492          354         1429         1036          863 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
        1864         1978          592          557         1970          882 
TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-49-4501 TCGA-49-4507 
          99          486          466          287         1421          268 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6744 TCGA-49-6745 
         896          157         1700          445          890          522 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5072 TCGA-50-5931 
        2174         2146          455          785          246          267 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6597 TCGA-53-7624 TCGA-53-7813 TCGA-55-1594 
         764          686         1015         1986          424         1178 
TCGA-55-1595 TCGA-55-1596 TCGA-55-6642 TCGA-55-6712 TCGA-55-6971 TCGA-55-6987 
        1479         1375          993           24           25         1170 
TCGA-55-7284 TCGA-55-7726 TCGA-55-7728 TCGA-55-7815 TCGA-55-7910 TCGA-55-7995 
         121           39           24           54          197            5 
TCGA-55-8085 TCGA-55-8089 TCGA-55-8090 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 
          33          100            6           23           29            8 
TCGA-55-8508 TCGA-55-8615 TCGA-55-A48Y TCGA-55-A490 TCGA-55-A491 TCGA-55-A493 
          15           15           42           48         1952           28 
TCGA-55-A494 TCGA-55-A4DF TCGA-62-8398 TCGA-62-8402 TCGA-62-A46V TCGA-62-A471 
           5           47         1970         1445         2199         1246 
TCGA-64-1678 TCGA-64-1681 TCGA-64-5779 TCGA-67-3774 TCGA-69-7760 TCGA-69-7973 
        1189         1968          864          385          202          230 
TCGA-69-7980 TCGA-69-8255 TCGA-69-A59K TCGA-73-4666 TCGA-73-4675 TCGA-75-7027 
         382          129          214          800           40         1956 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 TCGA-78-7161 TCGA-78-7167 TCGA-78-7220 
        1973         1988         1944          215         1937         1965 
TCGA-78-7536 TCGA-78-8655 TCGA-86-6851 TCGA-86-7701 TCGA-86-7713 TCGA-86-7953 
        1949         1981         1959           11          422          591 
TCGA-86-8074 TCGA-86-8278 TCGA-86-8279 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
          24          476          482           19           26           35 
TCGA-86-8669 TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6831 TCGA-91-6836 TCGA-91-6840 
          34           30          323          310          417          372 
TCGA-91-6848 TCGA-91-7771 TCGA-91-8499 TCGA-93-8067 TCGA-95-7567 TCGA-95-7944 
         224          492           36          186          568          377 
TCGA-95-7947 TCGA-97-8177 TCGA-97-8552 TCGA-97-A4M7 TCGA-99-8032 TCGA-99-8033 
         477          147          115          271           44          170 
TCGA-L9-A443 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T7 TCGA-MP-A4TE TCGA-MP-A4TI 
         116         1946         1967         1954         1970         1955 

$`AMP PEAK 21(12Q15) WILD-TYPE`
TCGA-05-4249 TCGA-05-4384 TCGA-05-4396 TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 
        1523          426         1947         1431          578          610 
TCGA-05-4410 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 
        1958          365          913          669          791          791 
TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4123 
         151          670           30           62           14          182 
TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4629 TCGA-38-4630 TCGA-38-4632 
        1952         1962         1147          864         1073         1357 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2657 TCGA-44-2659 
         448         1971          133         1324          400         1367 
TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 
         741         1280         1301           97          246         1130 
TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 
        1163          190          722         1013          383          723 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
         328          302          845          704          658          705 
TCGA-44-6776 TCGA-44-6777 TCGA-44-7659 TCGA-44-7661 TCGA-44-7662 TCGA-44-7671 
        1938         1942          444          366          218          535 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
         719          385          260          337          351          415 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-6743 
          76         1932         1081          428          999          369 
TCGA-49-6761 TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 
         354          944         1499          282         1091         2370 
TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 TCGA-50-7109 TCGA-50-8460 TCGA-53-7626 
         653          567          883          255          105         1971 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-5899 TCGA-55-6543 TCGA-55-6969 TCGA-55-6972 
         280          701           87            2         1239         1475 
TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 TCGA-55-7281 TCGA-55-7283 
          67         1826         1233         2151           18           35 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
           6            4           95           40         1958           39 
TCGA-55-7727 TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
          34           19           16           21            3           31 
TCGA-55-8087 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
          21           43           26            4           47           15 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8506 
          33           46           66          216           44           11 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
         228            9            3          146          202          536 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Z 
          48           49           66          106           33           29 
TCGA-55-A492 TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 TCGA-62-A46U 
           1          162         1216         1289         2696         2067 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1680 TCGA-64-5774 
         910         1728          628         1686         1126         1959 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 
          62         1305         1559          866           31          610 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7761 
         573          427          174          141          422          186 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
         690          414          165          184           70           89 
TCGA-69-8253 TCGA-69-8254 TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
         100           77           61         1600          711          912 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
         467          131          164           38          621          519 
TCGA-75-6214 TCGA-75-7025 TCGA-75-7031 TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 
        1970         1967         1965         1950         1093         1963 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
        1202          760         1948         1957         1961         1963 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7535 
        1221          678         1940         1950         1934         1972 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
        1944          327          881         1952          994         1949 
TCGA-78-8648 TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 
        1971         1954         1964         1965         1972          824 
TCGA-86-7711 TCGA-86-7714 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
         630         1968         1963          508          745           10 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 TCGA-86-8076 TCGA-86-8280 TCGA-86-8281 
        1963           13          479          489           16         1955 
TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
          45           18           15          455          405           10 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 TCGA-91-6847 
          14           39         1940           60           79          842 
TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
          35          197          174           44          218          297 
TCGA-93-7348 TCGA-95-7039 TCGA-95-7043 TCGA-95-7948 TCGA-95-A4VK TCGA-97-7546 
         127           34            2          476          121          964 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 
        1965         1932         1332          775          181           22 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8179 TCGA-97-8547 
         107          182         1965           87           15          148 
TCGA-97-A4M2 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-J2-8192 TCGA-J2-8194 
         197          392          427          459          154          114 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A444 
         287          282          238          578          435            6 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T8 
         285          622          353         1951         1954         1957 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TK 
        1980         1951         1944         1970          142         1971 
TCGA-MP-A5C7 
        1490 

  AMP PEAK 21(12Q15) MUTATED AMP PEAK 21(12Q15) WILD-TYPE 
                           5                            1 
  AMP PEAK 21(12Q15) MUTATED AMP PEAK 21(12Q15) WILD-TYPE 
                        2199                         2696 
  AMP PEAK 21(12Q15) MUTATED AMP PEAK 21(12Q15) WILD-TYPE 
                         471                          459 
[1] "5.0 - 2199.0 (471.0)" "1.0 - 2696.0 (459.0)"
[1] "hr=" "1.2"
D21V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 21(12Q15) MUTATED         2       34       40        19        23
  AMP PEAK 21(12Q15) WILD-TYPE       2       79       91        24        46
                              vv
clus                           STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 21(12Q15) MUTATED           25          3        9
  AMP PEAK 21(12Q15) WILD-TYPE         42          8       14
D21V3, multiclass
            clus
vv           AMP PEAK 21(12Q15) MUTATED AMP PEAK 21(12Q15) WILD-TYPE
  STAGE I                             2                            2
  STAGE IA                           34                           79
  STAGE IB                           40                           91
  STAGE IIA                          19                           24
  STAGE IIB                          23                           46
  STAGE IIIA                         25                           42
  STAGE IIIB                          3                            8
  STAGE IV                            9                           14
[1] 8 2
[1] TRUE
[1] "dimension of 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(12Q15) MUTATED    42  94  13   5
  AMP PEAK 21(12Q15) WILD-TYPE 101 165  27  13
D21V4, multiclass
    clus
vv   AMP PEAK 21(12Q15) MUTATED AMP PEAK 21(12Q15) WILD-TYPE
  T1                         42                          101
  T2                         94                          165
  T3                         13                           27
  T4                          5                           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 21(12Q15) MUTATED    96  32    25
  AMP PEAK 21(12Q15) WILD-TYPE 199  53    47
D21V5, multiclass
       clus
vv      AMP PEAK 21(12Q15) MUTATED AMP PEAK 21(12Q15) WILD-TYPE
  N0                            96                          199
  N1                            32                           53
  N2+N3                         25                           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"
                              vv
clus                            M0  M1 M1A M1B  MX
  AMP PEAK 21(12Q15) MUTATED   107   9   0   0  38
  AMP PEAK 21(12Q15) WILD-TYPE 210   9   1   3  81
D21V6, multiclass
     clus
vv    AMP PEAK 21(12Q15) MUTATED AMP PEAK 21(12Q15) WILD-TYPE
  M0                         107                          210
  M1                           9                            9
  M1A                          0                            1
  M1B                          0                            3
  MX                          38                           81
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V7, binary
                              cls
clus                             0   1
  AMP PEAK 21(12Q15) MUTATED    75  80
  AMP PEAK 21(12Q15) WILD-TYPE 173 134
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 21(12Q15) MUTATED     75   80
  AMP PEAK 21(12Q15) WILD-TYPE  173  134
        clus
vv       AMP PEAK 21(12Q15) MUTATED AMP PEAK 21(12Q15) WILD-TYPE
  FEMALE                         75                          173
  MALE                           80                          134
[1] 2 2
[1] FALSE
D21V8, continuous
                              vv
clus                           LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 21(12Q15) MUTATED                            4
  AMP PEAK 21(12Q15) WILD-TYPE                          9
                              vv
clus                           LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 21(12Q15) MUTATED                                  32
  AMP PEAK 21(12Q15) WILD-TYPE                                61
                              vv
clus                           LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 21(12Q15) MUTATED                                                  105
  AMP PEAK 21(12Q15) WILD-TYPE                                                189
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 21(12Q15) MUTATED                                            0
  AMP PEAK 21(12Q15) WILD-TYPE                                          4
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 21(12Q15) MUTATED                                               4
  AMP PEAK 21(12Q15) WILD-TYPE                                            15
                              vv
clus                           LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 21(12Q15) MUTATED                                1
  AMP PEAK 21(12Q15) WILD-TYPE                              1
                              vv
clus                           LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 21(12Q15) MUTATED                                    0
  AMP PEAK 21(12Q15) WILD-TYPE                                  4
                              vv
clus                           LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 21(12Q15) MUTATED                              0
  AMP PEAK 21(12Q15) WILD-TYPE                            2
                              vv
clus                           LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 21(12Q15) MUTATED                               4
  AMP PEAK 21(12Q15) WILD-TYPE                            15
                              vv
clus                           LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 21(12Q15) MUTATED                                 0
  AMP PEAK 21(12Q15) WILD-TYPE                               1
                              vv
clus                           LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 21(12Q15) MUTATED                                               2
  AMP PEAK 21(12Q15) WILD-TYPE                                             2
                              vv
clus                           MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 21(12Q15) MUTATED                              3
  AMP PEAK 21(12Q15) WILD-TYPE                            4
D21V9, multiclass
                                                    clus
vv                                                   AMP PEAK 21(12Q15) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                  4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                          32
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                        105
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                  0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                               4
  LUNG CLEAR CELL ADENOCARCINOMA                                              1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                          0
  LUNG MUCINOUS ADENOCARCINOMA                                                0
  LUNG PAPILLARY ADENOCARCINOMA                                               4
  LUNG SIGNET RING ADENOCARCINOMA                                             0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                               2
  MUCINOUS (COLLOID) CARCINOMA                                                3
                                                    clus
vv                                                   AMP PEAK 21(12Q15) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                    9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            61
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          189
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                15
  LUNG CLEAR CELL ADENOCARCINOMA                                                1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            4
  LUNG MUCINOUS ADENOCARCINOMA                                                  2
  LUNG PAPILLARY ADENOCARCINOMA                                                15
  LUNG SIGNET RING ADENOCARCINOMA                                               1
  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"
D21V10, binary
                              cls
clus                             0   1
  AMP PEAK 21(12Q15) MUTATED     8 147
  AMP PEAK 21(12Q15) WILD-TYPE  13 294
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 21(12Q15) MUTATED      8  147
  AMP PEAK 21(12Q15) WILD-TYPE   13  294
     clus
vv    AMP PEAK 21(12Q15) MUTATED AMP PEAK 21(12Q15) WILD-TYPE
  NO                           8                           13
  YES                        147                          294
[1] 2 2
[1] FALSE
D21V11, continuous
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 21(12Q15) MUTATED   107   3   3   6
  AMP PEAK 21(12Q15) WILD-TYPE 211   8   1  13
D21V12, multiclass
    clus
vv   AMP PEAK 21(12Q15) MUTATED AMP PEAK 21(12Q15) WILD-TYPE
  R0                        107                          211
  R1                          3                            8
  R2                          3                            1
  RX                          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                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 21(12Q15) MUTATED                                  0     3
  AMP PEAK 21(12Q15) WILD-TYPE                                1     3
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 21(12Q15) MUTATED                           8   117
  AMP PEAK 21(12Q15) WILD-TYPE                        18   245
D21V13, multiclass
                                  clus
vv                                 AMP PEAK 21(12Q15) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     3
  BLACK OR AFRICAN AMERICAN                                 8
  WHITE                                                   117
                                  clus
vv                                 AMP PEAK 21(12Q15) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  18
  WHITE                                                     245
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V14, binary
                              cls
clus                             0   1
  AMP PEAK 21(12Q15) MUTATED     3 102
  AMP PEAK 21(12Q15) WILD-TYPE   4 230
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 21(12Q15) MUTATED      3  102
  AMP PEAK 21(12Q15) WILD-TYPE    4  230
                        clus
vv                       AMP PEAK 21(12Q15) MUTATED
  HISPANIC OR LATINO                              3
  NOT HISPANIC OR LATINO                        102
                        clus
vv                       AMP PEAK 21(12Q15) WILD-TYPE
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          230
[1] 2 2
[1] FALSE

Clustering(22) Variable = AMP PEAK 22(13Q33.3) MUTATION ANALYSIS
D22V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 22(13Q33.3) MUTATED    51  15
  AMP PEAK 22(13Q33.3) WILD-TYPE 270  67
  AMP PEAK 22(13Q33.3) MUTATED AMP PEAK 22(13Q33.3) WILD-TYPE 
                            66                            337 
  AMP PEAK 22(13Q33.3) MUTATED AMP PEAK 22(13Q33.3) WILD-TYPE 
                            15                             67 
$`AMP PEAK 22(13Q33.3) MUTATED`
TCGA-05-4249 TCGA-05-4382 TCGA-05-5428 TCGA-38-4629 TCGA-38-4631 TCGA-44-2655 
        1523          607          670          864          354         1324 
TCGA-44-2659 TCGA-44-6775 TCGA-44-7660 TCGA-44-7670 TCGA-44-7671 TCGA-49-4501 
        1367          705          592          882          535         1421 
TCGA-49-6742 TCGA-49-6743 TCGA-50-5045 TCGA-50-5930 TCGA-50-5941 TCGA-53-7624 
         445          369         2174          282          567         1986 
TCGA-53-7626 TCGA-55-5899 TCGA-55-7281 TCGA-55-7726 TCGA-55-7907 TCGA-55-7910 
        1971           87           18           39           16          197 
TCGA-55-8089 TCGA-55-8094 TCGA-55-8205 TCGA-55-8507 TCGA-55-8508 TCGA-55-8511 
         100            4           33            8           15            9 
TCGA-55-8620 TCGA-55-A48Z TCGA-55-A490 TCGA-55-A492 TCGA-62-8402 TCGA-62-A46U 
          66           29           48            1         1445         2067 
TCGA-64-1680 TCGA-67-3771 TCGA-67-3772 TCGA-67-6215 TCGA-69-7979 TCGA-69-7980 
        1126          610          573          174           89          382 
TCGA-69-8253 TCGA-73-4677 TCGA-75-6214 TCGA-75-7027 TCGA-75-7031 TCGA-78-7149 
         100           38         1970         1956         1965         1093 
TCGA-78-7155 TCGA-78-7167 TCGA-78-7220 TCGA-78-7537 TCGA-86-6851 TCGA-86-7955 
        1957         1937         1965         1944         1959          508 
TCGA-86-8074 TCGA-86-8075 TCGA-91-6847 TCGA-95-7567 TCGA-97-7546 TCGA-97-7547 
          24          479          842          568          964         1965 
TCGA-97-8177 TCGA-J2-A4AE TCGA-L9-A444 TCGA-MN-A4N4 TCGA-MP-A4SW TCGA-MP-A4T7 
         147          282            6          622         1967         1954 

$`AMP PEAK 22(13Q33.3) WILD-TYPE`
TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 TCGA-05-4398 TCGA-05-4403 
         426         1369         1126         1947         1431          578 
TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 
         610         1958         1997          455          912          365 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
         913          669          791          791          761          761 
TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 
         730          457          151          882           30           62 
TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
          14          225          182          264         1952         1962 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
        1147         1492         1073         1357          448         1971 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 
         133         1429          400          741         1280         1301 
TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
          97          246         1130         1163         1036          190 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
         722         1013          863          383          723          328 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6776 TCGA-44-6777 
         302          845          704          658         1938         1942 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
        1864         1978          444          366          218          557 
TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 
        1970          719          385           99          260          486 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
         466          287          337          351          415           76 
TCGA-49-4486 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
        1932         1081          428          999          268          896 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-50-5049 
         157         1700          890          522          354         2146 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 
         455          785          944         1499          246          267 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        1091         2370          653          883          764          686 
TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
        1015          255          105          424          280          701 
TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
        1178         1479         1375            2          993           24 
TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 
        1239           25         1475           67         1826         1233 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        2151         1170           35          121            6            4 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7727 TCGA-55-7728 
          95           40         1958           39           34           24 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
          54           19           21            3           31            5 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8096 
          33           21            6           43           26           47 
TCGA-55-8097 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
          15           46           66          216           44           23 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
          29           11          228            3          146          202 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
         536           15           48           49          106           33 
TCGA-55-A48Y TCGA-55-A491 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
          42         1952           28            5           47          162 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-A46V TCGA-62-A471 
        1216         1289         1970         2696         2199         1246 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 
         910         1728          628         1189         1686         1968 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
        1959           62         1305          864         1559          866 
TCGA-67-3770 TCGA-67-3773 TCGA-67-3774 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
          31          427          385          141          422          202 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
         186          690          414          165          230          184 
TCGA-69-7978 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 
          70           77          129          214           61         1600 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
         711          912          800          467          131           40 
TCGA-73-4676 TCGA-73-7498 TCGA-73-7499 TCGA-75-7025 TCGA-78-7145 TCGA-78-7146 
         164          621          519         1967         1973         1988 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
        1950         1944         1963         1202          760         1948 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
        1961         1963         1221          678          215         1940 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 TCGA-78-7540 
        1950         1934         1972         1949          327          881 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
        1952          994         1949         1971         1981         1954 
TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 TCGA-86-7701 TCGA-86-7711 
        1964         1965         1972          824           11          630 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 
         422         1968          591         1963          745           10 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        1963           13          489          476          482           16 
TCGA-86-8281 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
        1955           19           26           35           45           34 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 
          18           15          455          405           10           30 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
          14           39          323         1940           60          310 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
          79          417          372          224           35          492 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
         197          174           36           44          218          297 
TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-95-7944 TCGA-95-7947 
         127          186           34            2          377          477 
TCGA-95-7948 TCGA-95-A4VK TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
         476          121         1932         1332          775          181 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8179 
          22          107          182         1965           87           15 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
         148          115          197          271          392          427 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
         459           44          170          154          114          287 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-MN-A4N1 TCGA-MN-A4N5 
         238          578          435          116          285          353 
TCGA-MP-A4SV TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
        1946         1951         1954         1957         1980         1951 
TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
        1944         1970         1970          142         1955         1971 
TCGA-MP-A5C7 
        1490 

  AMP PEAK 22(13Q33.3) MUTATED AMP PEAK 22(13Q33.3) WILD-TYPE 
                             1                              2 
  AMP PEAK 22(13Q33.3) MUTATED AMP PEAK 22(13Q33.3) WILD-TYPE 
                          2174                           2696 
  AMP PEAK 22(13Q33.3) MUTATED AMP PEAK 22(13Q33.3) WILD-TYPE 
                         570.5                          455.0 
[1] "1.0 - 2174.0 (570.5)" "2.0 - 2696.0 (455.0)"
[1] "hr=" "1.1"
D22V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 22(13Q33.3) MUTATED         1       16       22        10         9
  AMP PEAK 22(13Q33.3) WILD-TYPE       3       97      109        33        60
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 22(13Q33.3) MUTATED            7          3        8
  AMP PEAK 22(13Q33.3) WILD-TYPE         60          8       15
D22V3, multiclass
            clus
vv           AMP PEAK 22(13Q33.3) MUTATED AMP PEAK 22(13Q33.3) WILD-TYPE
  STAGE I                               1                              3
  STAGE IA                             16                             97
  STAGE IB                             22                            109
  STAGE IIA                            10                             33
  STAGE IIB                             9                             60
  STAGE IIIA                            7                             60
  STAGE IIIB                            3                              8
  STAGE IV                              8                             15
[1] 8 2
[1] TRUE
[1] "dimension of 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(13Q33.3) MUTATED    26  46   2   2
  AMP PEAK 22(13Q33.3) WILD-TYPE 117 213  38  16
D22V4, multiclass
    clus
vv   AMP PEAK 22(13Q33.3) MUTATED AMP PEAK 22(13Q33.3) WILD-TYPE
  T1                           26                            117
  T2                           46                            213
  T3                            2                             38
  T4                            2                             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 22(13Q33.3) MUTATED    48  18    10
  AMP PEAK 22(13Q33.3) WILD-TYPE 247  67    62
D22V5, multiclass
       clus
vv      AMP PEAK 22(13Q33.3) MUTATED AMP PEAK 22(13Q33.3) WILD-TYPE
  N0                              48                            247
  N1                              18                             67
  N2+N3                           10                             62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  AMP PEAK 22(13Q33.3) MUTATED    49   6   0   2  19
  AMP PEAK 22(13Q33.3) WILD-TYPE 268  12   1   1 100
D22V6, multiclass
     clus
vv    AMP PEAK 22(13Q33.3) MUTATED AMP PEAK 22(13Q33.3) WILD-TYPE
  M0                            49                            268
  M1                             6                             12
  M1A                            0                              1
  M1B                            2                              1
  MX                            19                            100
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V7, binary
                                cls
clus                               0   1
  AMP PEAK 22(13Q33.3) MUTATED    46  30
  AMP PEAK 22(13Q33.3) WILD-TYPE 202 184
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(13Q33.3) MUTATED     46   30
  AMP PEAK 22(13Q33.3) WILD-TYPE  202  184
        clus
vv       AMP PEAK 22(13Q33.3) MUTATED AMP PEAK 22(13Q33.3) WILD-TYPE
  FEMALE                           46                            202
  MALE                             30                            184
[1] 2 2
[1] FALSE
D22V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 22(13Q33.3) MUTATED                            3
  AMP PEAK 22(13Q33.3) WILD-TYPE                         10
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 22(13Q33.3) MUTATED                                  17
  AMP PEAK 22(13Q33.3) WILD-TYPE                                76
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 22(13Q33.3) MUTATED                                                   48
  AMP PEAK 22(13Q33.3) WILD-TYPE                                                246
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 22(13Q33.3) MUTATED                                            0
  AMP PEAK 22(13Q33.3) WILD-TYPE                                          4
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 22(13Q33.3) MUTATED                                               2
  AMP PEAK 22(13Q33.3) WILD-TYPE                                            17
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 22(13Q33.3) MUTATED                                1
  AMP PEAK 22(13Q33.3) WILD-TYPE                              1
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 22(13Q33.3) MUTATED                                    0
  AMP PEAK 22(13Q33.3) WILD-TYPE                                  4
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 22(13Q33.3) MUTATED                              0
  AMP PEAK 22(13Q33.3) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 22(13Q33.3) MUTATED                               3
  AMP PEAK 22(13Q33.3) WILD-TYPE                            16
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 22(13Q33.3) MUTATED                                 0
  AMP PEAK 22(13Q33.3) WILD-TYPE                               1
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 22(13Q33.3) MUTATED                                               0
  AMP PEAK 22(13Q33.3) WILD-TYPE                                             4
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 22(13Q33.3) MUTATED                              2
  AMP PEAK 22(13Q33.3) WILD-TYPE                            5
D22V9, multiclass
                                                    clus
vv                                                   AMP PEAK 22(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 22(13Q33.3) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              76
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            246
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  17
  LUNG CLEAR CELL ADENOCARCINOMA                                                  1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              4
  LUNG MUCINOUS ADENOCARCINOMA                                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                                  16
  LUNG SIGNET RING ADENOCARCINOMA                                                 1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                   4
  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"
D22V10, binary
                                cls
clus                               0   1
  AMP PEAK 22(13Q33.3) MUTATED     4  72
  AMP PEAK 22(13Q33.3) WILD-TYPE  17 369
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(13Q33.3) MUTATED      4   72
  AMP PEAK 22(13Q33.3) WILD-TYPE   17  369
     clus
vv    AMP PEAK 22(13Q33.3) MUTATED AMP PEAK 22(13Q33.3) WILD-TYPE
  NO                             4                             17
  YES                           72                            369
[1] 2 2
[1] FALSE
D22V11, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 22(13Q33.3) MUTATED    55   0   1   2
  AMP PEAK 22(13Q33.3) WILD-TYPE 263  11   3  17
D22V12, multiclass
    clus
vv   AMP PEAK 22(13Q33.3) MUTATED AMP PEAK 22(13Q33.3) WILD-TYPE
  R0                           55                            263
  R1                            0                             11
  R2                            1                              3
  RX                            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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 22(13Q33.3) MUTATED                                  0     0
  AMP PEAK 22(13Q33.3) WILD-TYPE                                1     6
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 22(13Q33.3) MUTATED                           6    60
  AMP PEAK 22(13Q33.3) WILD-TYPE                        20   302
D22V13, multiclass
                                  clus
vv                                 AMP PEAK 22(13Q33.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   6
  WHITE                                                      60
                                  clus
vv                                 AMP PEAK 22(13Q33.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         6
  BLACK OR AFRICAN AMERICAN                                    20
  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"
D22V14, binary
                                cls
clus                               0   1
  AMP PEAK 22(13Q33.3) MUTATED     3  53
  AMP PEAK 22(13Q33.3) WILD-TYPE   4 279
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(13Q33.3) MUTATED      3   53
  AMP PEAK 22(13Q33.3) WILD-TYPE    4  279
                        clus
vv                       AMP PEAK 22(13Q33.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           53
                        clus
vv                       AMP PEAK 22(13Q33.3) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            279
[1] 2 2
[1] FALSE

Clustering(23) Variable = AMP PEAK 23(14Q13.3) MUTATION ANALYSIS
D23V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 23(14Q13.3) MUTATED   143  40
  AMP PEAK 23(14Q13.3) WILD-TYPE 178  42
  AMP PEAK 23(14Q13.3) MUTATED AMP PEAK 23(14Q13.3) WILD-TYPE 
                           183                            220 
  AMP PEAK 23(14Q13.3) MUTATED AMP PEAK 23(14Q13.3) WILD-TYPE 
                            40                             42 
$`AMP PEAK 23(14Q13.3) MUTATED`
TCGA-05-4389 TCGA-05-4390 TCGA-05-4398 TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 
        1369         1126         1431          610         1997          455 
TCGA-05-4424 TCGA-05-4427 TCGA-05-4432 TCGA-05-5423 TCGA-05-5715 TCGA-35-4123 
         913          791          761          151           62          182 
TCGA-35-5375 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4632 
         264         1147         1492          864         1073         1357 
TCGA-44-2659 TCGA-44-2668 TCGA-44-3398 TCGA-44-3918 TCGA-44-4112 TCGA-44-6147 
        1367          246         1163         1036          722          845 
TCGA-44-6774 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 
         658         1864         1978          444          592          218 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7672 TCGA-44-8119 TCGA-44-A479 
         557         1970          882          719           99          486 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 
         466          287           76         1932         1081         1421 
TCGA-49-4512 TCGA-49-6761 TCGA-50-5045 TCGA-50-5935 TCGA-50-5941 TCGA-50-5946 
         157          354         2174          653          567          686 
TCGA-50-7109 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1595 TCGA-55-5899 
         255          424          280         1178         1479           87 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6971 TCGA-55-6983 TCGA-55-7281 
           2          993           24           25         1826           18 
TCGA-55-7724 TCGA-55-7727 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        1958           34           54           19           16          197 
TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 TCGA-55-8091 TCGA-55-8096 TCGA-55-8206 
           3            5           33           43           47           46 
TCGA-55-8207 TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 
          66           44           23           11            8          228 
TCGA-55-8511 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-A48Y 
           9          202          536           15           48           42 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8402 
          29           48           28           47          162         1445 
TCGA-62-A46U TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-5774 TCGA-64-5775 
        2067         1728          628         1189         1959           62 
TCGA-64-5779 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
         864          866           31          610          573          427 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7763 TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 
         422          202          690          230          184           89 
TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
         214           61         1600          711          912          800 
TCGA-73-4677 TCGA-73-7499 TCGA-75-7025 TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 
          38          519         1967         1965         1973         1988 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7155 TCGA-78-7159 TCGA-78-7161 TCGA-78-7167 
        1944         1093         1957         1221          215         1937 
TCGA-78-7536 TCGA-78-7539 TCGA-78-8640 TCGA-78-8660 TCGA-78-8662 TCGA-80-5608 
        1949          327         1949         1954         1964         1972 
TCGA-83-5908 TCGA-86-7701 TCGA-86-7713 TCGA-86-7953 TCGA-86-7955 TCGA-86-8054 
         824           11          422          591          508          745 
TCGA-86-8055 TCGA-86-8074 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
          10           24          476          482           16           19 
TCGA-86-8585 TCGA-86-8669 TCGA-86-8673 TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6829 
          35           34          455           30          323         1940 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
         310           79          417          372          842          224 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-93-8067 
         492          197          174           36           44          186 
TCGA-95-7567 TCGA-97-7546 TCGA-97-7554 TCGA-97-7937 TCGA-97-8171 TCGA-97-8179 
         568          964          775          181          107           15 
TCGA-99-7458 TCGA-99-8032 TCGA-J2-8192 TCGA-J2-A4AG TCGA-L9-A443 TCGA-L9-A444 
         392           44          154          238          116            6 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4T9 
         285          622         1946         1954         1957         1980 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TK 
        1970         1970         1971 

$`AMP PEAK 23(14Q13.3) WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4403 TCGA-05-4410 
        1523          607          426         1947          578         1958 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4433 
         912          365          669          791          761          730 
TCGA-05-5420 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-35-3615 TCGA-35-4122 
         457          882          670           30           14          225 
TCGA-38-4625 TCGA-38-4626 TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F 
        1952         1962          354          448         1971          133 
TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 
        1324         1429          400          741         1280         1301 
TCGA-44-2666 TCGA-44-3396 TCGA-44-3919 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 
          97         1130          190         1013          863          383 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6148 TCGA-44-6775 TCGA-44-6776 
         723          328          302          704          705         1938 
TCGA-44-6777 TCGA-44-7661 TCGA-44-7671 TCGA-44-8117 TCGA-44-8120 TCGA-44-A47F 
        1942          366          535          385          260          337 
TCGA-44-A47G TCGA-44-A4SS TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
         351          415          428          999          268          896 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-50-5049 
        1700          445          369          890          522         2146 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
         455          785          944         1499          246          282 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5942 TCGA-50-5944 TCGA-50-6597 
         267         1091         2370          883          764         1015 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-55-1592 TCGA-55-1596 TCGA-55-6969 
         105         1986         1971          701         1375         1239 
TCGA-55-6972 TCGA-55-6980 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7283 
        1475           67         1233         2151         1170           35 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7725 
         121            6            4           95           40           39 
TCGA-55-7726 TCGA-55-7728 TCGA-55-7911 TCGA-55-7994 TCGA-55-8087 TCGA-55-8089 
          39           24           21           31           21          100 
TCGA-55-8090 TCGA-55-8092 TCGA-55-8094 TCGA-55-8097 TCGA-55-8205 TCGA-55-8299 
           6           26            4           15           33          216 
TCGA-55-8505 TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 TCGA-55-8619 TCGA-55-8620 
          29           15            3          146           49           66 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A494 TCGA-62-8395 
         106           33         1952            1            5         1216 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 
        1289         1970         2696         2199         1246          910 
TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5778 TCGA-64-5781 TCGA-67-3774 
        1686         1126         1968         1305         1559          385 
TCGA-67-6215 TCGA-67-6216 TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 TCGA-69-7978 
         174          141          186          414          165           70 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-73-4668 TCGA-73-4670 
         382          100           77          129          467          131 
TCGA-73-4675 TCGA-73-4676 TCGA-73-7498 TCGA-75-6214 TCGA-75-7027 TCGA-78-7147 
          40          164          621         1970         1956         1950 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 
        1963         1202          760         1948         1961         1963 
TCGA-78-7160 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7220 TCGA-78-7535 
         678         1940         1950         1934         1965         1972 
TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 
        1944          881         1952          994         1971         1981 
TCGA-80-5607 TCGA-86-6851 TCGA-86-7711 TCGA-86-7714 TCGA-86-7954 TCGA-86-8056 
        1965         1959          630         1968         1963         1963 
TCGA-86-8073 TCGA-86-8075 TCGA-86-8076 TCGA-86-8281 TCGA-86-8359 TCGA-86-8668 
          13          479          489         1955           26           45 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 
          18           15          405           10           14           39 
TCGA-91-6830 TCGA-91-6849 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-95-7039 
          60           35          218          297          127           34 
TCGA-95-7043 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-97-7547 
           2          377          477          476          121         1965 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7941 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        1932         1332           22          182         1965           87 
TCGA-97-8177 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-8025 
         147          148          115          197          271          427 
TCGA-99-8028 TCGA-99-8033 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E5 
         459          170          114          287          282          578 
TCGA-L4-A4E6 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T7 TCGA-MP-A4TA 
         435          353         1967         1951         1954         1951 
TCGA-MP-A4TC TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A5C7 
        1944          142         1955         1490 

  AMP PEAK 23(14Q13.3) MUTATED AMP PEAK 23(14Q13.3) WILD-TYPE 
                             2                              1 
  AMP PEAK 23(14Q13.3) MUTATED AMP PEAK 23(14Q13.3) WILD-TYPE 
                          2174                           2696 
  AMP PEAK 23(14Q13.3) MUTATED AMP PEAK 23(14Q13.3) WILD-TYPE 
                         455.0                          471.5 
[1] "2.0 - 2174.0 (455.0)" "1.0 - 2696.0 (471.5)"
[1] "hr=" "1.4"
D23V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 23(14Q13.3) MUTATED         1       50       56        27        28
  AMP PEAK 23(14Q13.3) WILD-TYPE       3       63       75        16        41
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 23(14Q13.3) MUTATED           29          6        9
  AMP PEAK 23(14Q13.3) WILD-TYPE         38          5       14
D23V3, multiclass
            clus
vv           AMP PEAK 23(14Q13.3) MUTATED AMP PEAK 23(14Q13.3) WILD-TYPE
  STAGE I                               1                              3
  STAGE IA                             50                             63
  STAGE IB                             56                             75
  STAGE IIA                            27                             16
  STAGE IIB                            28                             41
  STAGE IIIA                           29                             38
  STAGE IIIB                            6                              5
  STAGE IV                              9                             14
[1] 8 2
[1] TRUE
[1] "dimension of 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(14Q13.3) MUTATED    63 121  14   8
  AMP PEAK 23(14Q13.3) WILD-TYPE  80 138  26  10
D23V4, multiclass
    clus
vv   AMP PEAK 23(14Q13.3) MUTATED AMP PEAK 23(14Q13.3) WILD-TYPE
  T1                           63                             80
  T2                          121                            138
  T3                           14                             26
  T4                            8                             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 23(14Q13.3) MUTATED   131  38    33
  AMP PEAK 23(14Q13.3) WILD-TYPE 164  47    39
D23V5, multiclass
       clus
vv      AMP PEAK 23(14Q13.3) MUTATED AMP PEAK 23(14Q13.3) WILD-TYPE
  N0                             131                            164
  N1                              38                             47
  N2+N3                           33                             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"
                                vv
clus                              M0  M1 M1A M1B  MX
  AMP PEAK 23(14Q13.3) MUTATED   129   8   1   0  68
  AMP PEAK 23(14Q13.3) WILD-TYPE 188  10   0   3  51
D23V6, multiclass
     clus
vv    AMP PEAK 23(14Q13.3) MUTATED AMP PEAK 23(14Q13.3) WILD-TYPE
  M0                           129                            188
  M1                             8                             10
  M1A                            1                              0
  M1B                            0                              3
  MX                            68                             51
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V7, binary
                                cls
clus                               0   1
  AMP PEAK 23(14Q13.3) MUTATED   112  94
  AMP PEAK 23(14Q13.3) WILD-TYPE 136 120
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(14Q13.3) MUTATED    112   94
  AMP PEAK 23(14Q13.3) WILD-TYPE  136  120
        clus
vv       AMP PEAK 23(14Q13.3) MUTATED AMP PEAK 23(14Q13.3) WILD-TYPE
  FEMALE                          112                            136
  MALE                             94                            120
[1] 2 2
[1] FALSE
D23V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 23(14Q13.3) MUTATED                            8
  AMP PEAK 23(14Q13.3) WILD-TYPE                          5
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 23(14Q13.3) MUTATED                                  31
  AMP PEAK 23(14Q13.3) WILD-TYPE                                62
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 23(14Q13.3) MUTATED                                                  147
  AMP PEAK 23(14Q13.3) WILD-TYPE                                                147
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 23(14Q13.3) MUTATED                                            1
  AMP PEAK 23(14Q13.3) WILD-TYPE                                          3
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 23(14Q13.3) MUTATED                                               6
  AMP PEAK 23(14Q13.3) WILD-TYPE                                            13
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 23(14Q13.3) MUTATED                                1
  AMP PEAK 23(14Q13.3) WILD-TYPE                              1
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 23(14Q13.3) MUTATED                                    2
  AMP PEAK 23(14Q13.3) WILD-TYPE                                  2
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 23(14Q13.3) MUTATED                              0
  AMP PEAK 23(14Q13.3) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 23(14Q13.3) MUTATED                               7
  AMP PEAK 23(14Q13.3) WILD-TYPE                            12
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 23(14Q13.3) MUTATED                                 0
  AMP PEAK 23(14Q13.3) WILD-TYPE                               1
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 23(14Q13.3) MUTATED                                               2
  AMP PEAK 23(14Q13.3) WILD-TYPE                                             2
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 23(14Q13.3) MUTATED                              1
  AMP PEAK 23(14Q13.3) WILD-TYPE                            6
D23V9, multiclass
                                                    clus
vv                                                   AMP PEAK 23(14Q13.3) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            31
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          147
  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                                                 7
  LUNG SIGNET RING ADENOCARCINOMA                                               0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 2
  MUCINOUS (COLLOID) CARCINOMA                                                  1
                                                    clus
vv                                                   AMP PEAK 23(14Q13.3) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              62
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            147
  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                                                  12
  LUNG SIGNET RING ADENOCARCINOMA                                                 1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                   2
  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"
D23V10, binary
                                cls
clus                               0   1
  AMP PEAK 23(14Q13.3) MUTATED     7 199
  AMP PEAK 23(14Q13.3) WILD-TYPE  14 242
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(14Q13.3) MUTATED      7  199
  AMP PEAK 23(14Q13.3) WILD-TYPE   14  242
     clus
vv    AMP PEAK 23(14Q13.3) MUTATED AMP PEAK 23(14Q13.3) WILD-TYPE
  NO                             7                             14
  YES                          199                            242
[1] 2 2
[1] FALSE
D23V11, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 23(14Q13.3) MUTATED   142   6   1   8
  AMP PEAK 23(14Q13.3) WILD-TYPE 176   5   3  11
D23V12, multiclass
    clus
vv   AMP PEAK 23(14Q13.3) MUTATED AMP PEAK 23(14Q13.3) WILD-TYPE
  R0                          142                            176
  R1                            6                              5
  R2                            1                              3
  RX                            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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 23(14Q13.3) MUTATED                                  0     4
  AMP PEAK 23(14Q13.3) WILD-TYPE                                1     2
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 23(14Q13.3) MUTATED                          11   164
  AMP PEAK 23(14Q13.3) WILD-TYPE                        15   198
D23V13, multiclass
                                  clus
vv                                 AMP PEAK 23(14Q13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  11
  WHITE                                                     164
                                  clus
vv                                 AMP PEAK 23(14Q13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         2
  BLACK OR AFRICAN AMERICAN                                    15
  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"
D23V14, binary
                                cls
clus                               0   1
  AMP PEAK 23(14Q13.3) MUTATED     2 153
  AMP PEAK 23(14Q13.3) WILD-TYPE   5 179
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(14Q13.3) MUTATED      2  153
  AMP PEAK 23(14Q13.3) WILD-TYPE    5  179
                        clus
vv                       AMP PEAK 23(14Q13.3) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          153
                        clus
vv                       AMP PEAK 23(14Q13.3) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            179
[1] 2 2
[1] FALSE

Clustering(24) Variable = AMP PEAK 24(16P11.2) MUTATION ANALYSIS
D24V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 24(16P11.2) MUTATED   107  27
  AMP PEAK 24(16P11.2) WILD-TYPE 214  55
  AMP PEAK 24(16P11.2) MUTATED AMP PEAK 24(16P11.2) WILD-TYPE 
                           134                            269 
  AMP PEAK 24(16P11.2) MUTATED AMP PEAK 24(16P11.2) WILD-TYPE 
                            27                             55 
$`AMP PEAK 24(16P11.2) MUTATED`
TCGA-05-4249 TCGA-05-4390 TCGA-05-4420 TCGA-05-5423 TCGA-35-4122 TCGA-35-5375 
        1523         1126          912          151          225          264 
TCGA-38-4625 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4631 TCGA-38-6178 
        1952         1147         1492          864          354          448 
TCGA-44-2659 TCGA-44-2662 TCGA-44-2665 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
        1367         1280         1301         1036          190          722 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6147 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 
         863          383          845          705         1942         1864 
TCGA-44-6779 TCGA-44-7662 TCGA-44-7670 TCGA-44-A47A TCGA-44-A47B TCGA-44-A4SU 
        1978          218          882          466          287           76 
TCGA-49-4505 TCGA-49-4507 TCGA-49-4512 TCGA-49-6744 TCGA-50-5933 TCGA-50-5935 
         428          268          157          890         2370          653 
TCGA-50-5941 TCGA-50-6597 TCGA-50-8460 TCGA-55-1592 TCGA-55-1594 TCGA-55-6712 
         567         1015          105          701         1178           24 
TCGA-55-6980 TCGA-55-7281 TCGA-55-7284 TCGA-55-7573 TCGA-55-7726 TCGA-55-7907 
          67           18          121            4           39           16 
TCGA-55-7910 TCGA-55-7995 TCGA-55-8091 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 
         197            5           43           26           47           15 
TCGA-55-8206 TCGA-55-8506 TCGA-55-8510 TCGA-55-8512 TCGA-55-8620 TCGA-55-A48Z 
          46           11          228            3           66           29 
TCGA-55-A490 TCGA-55-A493 TCGA-55-A4DG TCGA-62-8398 TCGA-62-A46V TCGA-64-1676 
          48           28          162         1970         2199         1728 
TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-67-3770 TCGA-67-3772 TCGA-67-6215 
        1686         1126         1968           31          573          174 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7764 TCGA-69-7973 TCGA-69-7978 TCGA-69-7980 
         422          202          414          230           70          382 
TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4668 TCGA-73-4675 TCGA-75-6214 
         214           61         1600          467           40         1970 
TCGA-75-7025 TCGA-78-7145 TCGA-78-7146 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        1967         1973         1988         1093         1963         1202 
TCGA-78-7154 TCGA-78-7156 TCGA-78-7159 TCGA-78-7161 TCGA-78-7163 TCGA-78-7535 
        1948         1961         1221          215         1950         1972 
TCGA-78-7536 TCGA-78-7542 TCGA-78-8640 TCGA-86-7701 TCGA-86-7713 TCGA-86-7953 
        1949         1952         1949           11          422          591 
TCGA-86-7955 TCGA-86-8055 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 
         508           10          476          482           16           26 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8673 TCGA-86-A456 TCGA-86-A4D0 
          35           45           34          455           10           30 
TCGA-91-6840 TCGA-91-8499 TCGA-93-7348 TCGA-95-7947 TCGA-95-A4VK TCGA-97-7546 
         372           36          127          477          121          964 
TCGA-97-7547 TCGA-97-7937 TCGA-97-7941 TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 
        1965          181           22          147           15          115 
TCGA-97-A4M7 TCGA-99-8025 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L9-A443 
         271          427          170          287          238          116 
TCGA-MN-A4N4 TCGA-MP-A4SW 
         622         1967 

$`AMP PEAK 24(16P11.2) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4396 TCGA-05-4398 TCGA-05-4403 
         607          426         1369         1947         1431          578 
TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 TCGA-05-4422 TCGA-05-4424 
         610         1958         1997          455          365          913 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
         669          791          791          761          761          730 
TCGA-05-5420 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
         457          882          670           30           62           14 
TCGA-35-4123 TCGA-38-4626 TCGA-38-4630 TCGA-38-4632 TCGA-38-7271 TCGA-38-A44F 
         182         1962         1073         1357         1971          133 
TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2666 TCGA-44-2668 
        1324         1429          400          741           97          246 
TCGA-44-3396 TCGA-44-3398 TCGA-44-5643 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
        1130         1163         1013          723          328          302 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6776 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
         704          658         1938          444          592          366 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
         557         1970          535          719          385           99 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 
         260          486          337          351          415         1932 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4506 TCGA-49-4510 TCGA-49-4514 TCGA-49-6742 
        1081         1421          999          896         1700          445 
TCGA-49-6743 TCGA-49-6745 TCGA-49-6761 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
         369          522          354         2174         2146          455 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
         785          944         1499          246          282          267 
TCGA-50-5932 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-7109 TCGA-53-7624 
        1091          883          764          686          255         1986 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 
        1971          424          280         1479         1375           87 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6983 
           2          993         1239           25         1475         1826 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 
        1233         2151         1170           35            6           95 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
          40         1958           39           34           24           54 
TCGA-55-7903 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 
          19           21            3           31           33           21 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8094 TCGA-55-8205 TCGA-55-8207 TCGA-55-8299 
         100            6            4           33           66          216 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8511 
          44           23           29            8           15            9 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
         146          202          536           15           48           49 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A491 TCGA-55-A492 TCGA-55-A494 
         106           33           42         1952            1            5 
TCGA-55-A4DF TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46U 
          47         1216         1289         2696         1445         2067 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1677 TCGA-64-1678 TCGA-64-5774 TCGA-64-5775 
        1246          910          628         1189         1959           62 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3773 
        1305          864         1559          866          610          427 
TCGA-67-3774 TCGA-67-6216 TCGA-69-7761 TCGA-69-7763 TCGA-69-7765 TCGA-69-7974 
         385          141          186          690          165          184 
TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-73-4659 TCGA-73-4662 
          89          100           77          129          711          912 
TCGA-73-4666 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
         800          131          164           38          621          519 
TCGA-75-7027 TCGA-75-7031 TCGA-78-7147 TCGA-78-7148 TCGA-78-7153 TCGA-78-7155 
        1956         1965         1950         1944          760         1957 
TCGA-78-7158 TCGA-78-7160 TCGA-78-7162 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        1963          678         1940         1934         1937         1965 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 
        1944          327          881          994         1971         1981 
TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 
        1954         1964         1965         1972          824         1959 
TCGA-86-7711 TCGA-86-7714 TCGA-86-7954 TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 
         630         1968         1963          745         1963           13 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8281 TCGA-86-8358 TCGA-86-8671 
          24          479          489         1955           19           18 
TCGA-86-8672 TCGA-86-8674 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
          15          405           14           39          323         1940 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6847 TCGA-91-6848 
          60          310           79          417          842          224 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD 
          35          492          197          174           44          218 
TCGA-93-7347 TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 
         297          186           34            2          568          377 
TCGA-95-7948 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-8171 TCGA-97-8172 
         476         1932         1332          775          107          182 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8547 TCGA-97-A4M2 TCGA-99-7458 TCGA-99-8028 
        1965           87          148          197          392          459 
TCGA-99-8032 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 
          44          154          114          282          578          435 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4T2 TCGA-MP-A4T4 
           6          285          353         1946         1951         1954 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TE 
        1954         1957         1980         1951         1944         1970 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
        1970          142         1955         1971         1490 

  AMP PEAK 24(16P11.2) MUTATED AMP PEAK 24(16P11.2) WILD-TYPE 
                             3                              1 
  AMP PEAK 24(16P11.2) MUTATED AMP PEAK 24(16P11.2) WILD-TYPE 
                          2370                           2696 
  AMP PEAK 24(16P11.2) MUTATED AMP PEAK 24(16P11.2) WILD-TYPE 
                         398.5                          535.0 
[1] "3.0 - 2370.0 (398.5)" "1.0 - 2696.0 (535.0)"
[1] "hr=" "1.1"
D24V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 24(16P11.2) MUTATED         2       41       38        14        19
  AMP PEAK 24(16P11.2) WILD-TYPE       2       72       93        29        50
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 24(16P11.2) MUTATED           22          4        8
  AMP PEAK 24(16P11.2) WILD-TYPE         45          7       15
D24V3, multiclass
            clus
vv           AMP PEAK 24(16P11.2) MUTATED AMP PEAK 24(16P11.2) WILD-TYPE
  STAGE I                               2                              2
  STAGE IA                             41                             72
  STAGE IB                             38                             93
  STAGE IIA                            14                             29
  STAGE IIB                            19                             50
  STAGE IIIA                           22                             45
  STAGE IIIB                            4                              7
  STAGE IV                              8                             15
[1] 8 2
[1] TRUE
[1] "dimension of 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(16P11.2) MUTATED    52  76  14   5
  AMP PEAK 24(16P11.2) WILD-TYPE  91 183  26  13
D24V4, multiclass
    clus
vv   AMP PEAK 24(16P11.2) MUTATED AMP PEAK 24(16P11.2) WILD-TYPE
  T1                           52                             91
  T2                           76                            183
  T3                           14                             26
  T4                            5                             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 24(16P11.2) MUTATED    91  27    25
  AMP PEAK 24(16P11.2) WILD-TYPE 204  58    47
D24V5, multiclass
       clus
vv      AMP PEAK 24(16P11.2) MUTATED AMP PEAK 24(16P11.2) WILD-TYPE
  N0                              91                            204
  N1                              27                             58
  N2+N3                           25                             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"
                                vv
clus                              M0  M1 M1A M1B  MX
  AMP PEAK 24(16P11.2) MUTATED   101   6   0   2  36
  AMP PEAK 24(16P11.2) WILD-TYPE 216  12   1   1  83
D24V6, multiclass
     clus
vv    AMP PEAK 24(16P11.2) MUTATED AMP PEAK 24(16P11.2) WILD-TYPE
  M0                           101                            216
  M1                             6                             12
  M1A                            0                              1
  M1B                            2                              1
  MX                            36                             83
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V7, binary
                                cls
clus                               0   1
  AMP PEAK 24(16P11.2) MUTATED    83  65
  AMP PEAK 24(16P11.2) WILD-TYPE 165 149
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(16P11.2) MUTATED     83   65
  AMP PEAK 24(16P11.2) WILD-TYPE  165  149
        clus
vv       AMP PEAK 24(16P11.2) MUTATED AMP PEAK 24(16P11.2) WILD-TYPE
  FEMALE                           83                            165
  MALE                             65                            149
[1] 2 2
[1] FALSE
D24V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 24(16P11.2) MUTATED                            4
  AMP PEAK 24(16P11.2) WILD-TYPE                          9
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 24(16P11.2) MUTATED                                  24
  AMP PEAK 24(16P11.2) WILD-TYPE                                69
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 24(16P11.2) MUTATED                                                  104
  AMP PEAK 24(16P11.2) WILD-TYPE                                                190
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 24(16P11.2) MUTATED                                            1
  AMP PEAK 24(16P11.2) WILD-TYPE                                          3
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 24(16P11.2) MUTATED                                               6
  AMP PEAK 24(16P11.2) WILD-TYPE                                            13
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 24(16P11.2) MUTATED                                0
  AMP PEAK 24(16P11.2) WILD-TYPE                              2
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 24(16P11.2) MUTATED                                    2
  AMP PEAK 24(16P11.2) WILD-TYPE                                  2
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 24(16P11.2) MUTATED                              0
  AMP PEAK 24(16P11.2) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 24(16P11.2) MUTATED                               6
  AMP PEAK 24(16P11.2) WILD-TYPE                            13
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 24(16P11.2) MUTATED                                 0
  AMP PEAK 24(16P11.2) WILD-TYPE                               1
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 24(16P11.2) MUTATED                                               1
  AMP PEAK 24(16P11.2) WILD-TYPE                                             3
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 24(16P11.2) MUTATED                              0
  AMP PEAK 24(16P11.2) WILD-TYPE                            7
D24V9, multiclass
                                                    clus
vv                                                   AMP PEAK 24(16P11.2) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            24
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          104
  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                                                 6
  LUNG SIGNET RING ADENOCARCINOMA                                               0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 1
  MUCINOUS (COLLOID) CARCINOMA                                                  0
                                                    clus
vv                                                   AMP PEAK 24(16P11.2) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              69
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            190
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  13
  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                                   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"
D24V10, binary
                                cls
clus                               0   1
  AMP PEAK 24(16P11.2) MUTATED     6 142
  AMP PEAK 24(16P11.2) WILD-TYPE  15 299
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(16P11.2) MUTATED      6  142
  AMP PEAK 24(16P11.2) WILD-TYPE   15  299
     clus
vv    AMP PEAK 24(16P11.2) MUTATED AMP PEAK 24(16P11.2) WILD-TYPE
  NO                             6                             15
  YES                          142                            299
[1] 2 2
[1] FALSE
D24V11, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 24(16P11.2) MUTATED   107   4   1   8
  AMP PEAK 24(16P11.2) WILD-TYPE 211   7   3  11
D24V12, multiclass
    clus
vv   AMP PEAK 24(16P11.2) MUTATED AMP PEAK 24(16P11.2) WILD-TYPE
  R0                          107                            211
  R1                            4                              7
  R2                            1                              3
  RX                            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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 24(16P11.2) MUTATED                                  1     2
  AMP PEAK 24(16P11.2) WILD-TYPE                                0     4
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 24(16P11.2) MUTATED                           5   125
  AMP PEAK 24(16P11.2) WILD-TYPE                        21   237
D24V13, multiclass
                                  clus
vv                                 AMP PEAK 24(16P11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   5
  WHITE                                                     125
                                  clus
vv                                 AMP PEAK 24(16P11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    21
  WHITE                                                       237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V14, binary
                                cls
clus                               0   1
  AMP PEAK 24(16P11.2) MUTATED     2 108
  AMP PEAK 24(16P11.2) WILD-TYPE   5 224
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(16P11.2) MUTATED      2  108
  AMP PEAK 24(16P11.2) WILD-TYPE    5  224
                        clus
vv                       AMP PEAK 24(16P11.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          108
                        clus
vv                       AMP PEAK 24(16P11.2) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            224
[1] 2 2
[1] FALSE

Clustering(25) Variable = AMP PEAK 25(17Q12) MUTATION ANALYSIS
D25V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 25(17Q12) MUTATED   144  37
  AMP PEAK 25(17Q12) WILD-TYPE 177  45
  AMP PEAK 25(17Q12) MUTATED AMP PEAK 25(17Q12) WILD-TYPE 
                         181                          222 
  AMP PEAK 25(17Q12) MUTATED AMP PEAK 25(17Q12) WILD-TYPE 
                          37                           45 
$`AMP PEAK 25(17Q12) MUTATED`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4389 TCGA-05-4398 TCGA-05-4410 TCGA-05-4415 
        1523          607         1369         1431         1958         1997 
TCGA-05-4417 TCGA-05-4424 TCGA-05-4425 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
         455          913          669          791          761          761 
TCGA-05-5715 TCGA-35-4122 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
          62          225         1492          864         1073          354 
TCGA-38-4632 TCGA-44-2662 TCGA-44-2668 TCGA-44-3396 TCGA-44-3919 TCGA-44-6144 
        1357         1280          246         1130          190          723 
TCGA-44-6148 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-7660 TCGA-44-7661 
         704          705         1942         1864          592          366 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7670 TCGA-44-8119 TCGA-44-8120 TCGA-44-A47B 
         218          557          882           99          260          287 
TCGA-44-A4SS TCGA-49-4501 TCGA-49-4505 TCGA-49-4507 TCGA-49-6742 TCGA-49-6743 
         415         1421          428          268          445          369 
TCGA-49-6744 TCGA-49-6745 TCGA-50-5049 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 
         890          522         2146          282          267         2370 
TCGA-50-5935 TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 TCGA-50-6597 TCGA-53-7813 
         653          567          764          686         1015          424 
TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6642 
         701         1178         1479         1375           87          993 
TCGA-55-6712 TCGA-55-7281 TCGA-55-7576 TCGA-55-7727 TCGA-55-7815 TCGA-55-7903 
          24           18           40           34           54           19 
TCGA-55-7907 TCGA-55-7911 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8089 
          16           21           31            5           33          100 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8205 TCGA-55-8207 TCGA-55-8302 TCGA-55-8507 
          26            4           33           66           23            8 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8514 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Z 
         228            9          202           48           66           29 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8398 TCGA-62-8402 
          48         1952            5          162         1970         1445 
TCGA-62-A471 TCGA-64-1676 TCGA-64-1677 TCGA-64-1680 TCGA-64-5774 TCGA-67-3770 
        1246         1728          628         1126         1959           31 
TCGA-67-3771 TCGA-67-3772 TCGA-67-6215 TCGA-69-7760 TCGA-69-7761 TCGA-69-7973 
         610          573          174          202          186          230 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 
         184           70          382          214           61         1600 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 TCGA-73-7499 
         912          800          467           40          164          519 
TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 TCGA-78-7154 
        1965         1973         1988         1950         1093         1948 
TCGA-78-7156 TCGA-78-7159 TCGA-78-7161 TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 
        1961         1221          215         1937         1965         1949 
TCGA-78-7539 TCGA-78-7633 TCGA-78-8640 TCGA-78-8660 TCGA-78-8662 TCGA-86-6851 
         327          994         1949         1954         1964         1959 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 
         630          422          591         1963          508           10 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 TCGA-86-8358 TCGA-86-8585 TCGA-86-8668 
          24          479          482           19           35           45 
TCGA-86-8669 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-91-6828 TCGA-91-6835 TCGA-91-6836 
          34           30           14          323           79          417 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 
         372          842          224          127          186           34 
TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-97-7553 TCGA-97-7554 
           2          568          377          477         1332          775 
TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-99-8025 
          87          147           15          148          115          427 
TCGA-99-8032 TCGA-J2-A4AD TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
          44          287          116            6          285          622 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TE 
         353         1946         1954         1957         1980         1970 
TCGA-MP-A4TK 
        1971 

$`AMP PEAK 25(17Q12) WILD-TYPE`
TCGA-05-4384 TCGA-05-4390 TCGA-05-4396 TCGA-05-4403 TCGA-05-4405 TCGA-05-4420 
         426         1126         1947          578          610          912 
TCGA-05-4422 TCGA-05-4426 TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 
         365          791          730          457          151          882 
TCGA-05-5428 TCGA-05-5429 TCGA-35-3615 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
         670           30           14          182          264         1952 
TCGA-38-4626 TCGA-38-4627 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 
        1962         1147          448         1971          133         1324 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2665 TCGA-44-2666 
        1429          400         1367          741         1301           97 
TCGA-44-3398 TCGA-44-3918 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 
        1163         1036          722         1013          863          383 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6774 TCGA-44-6776 TCGA-44-6779 
         328          302          845          658         1938         1978 
TCGA-44-7659 TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-A479 
         444         1970          535          719          385          486 
TCGA-44-A47A TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 
         466          337          351           76         1932         1081 
TCGA-49-4506 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6761 TCGA-50-5045 
         999          896          157         1700          354         2174 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5932 
         455          785          944         1499          246         1091 
TCGA-50-5942 TCGA-50-7109 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ 
         883          255          105         1986         1971          280 
TCGA-55-6543 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 TCGA-55-6983 
           2         1239           25         1475           67         1826 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
        1233         2151         1170           35          121            6 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 
           4           95         1958           39           39           24 
TCGA-55-7910 TCGA-55-7914 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8096 
         197            3           21            6           43           47 
TCGA-55-8097 TCGA-55-8206 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 
          15           46          216           44           29           11 
TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-8615 TCGA-55-8619 
          15            3          146          536           15           49 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A492 TCGA-55-A493 TCGA-55-A4DF 
         106           33           42            1           28           47 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 TCGA-62-A46U TCGA-62-A46V TCGA-62-A472 
        1216         1289         2696         2067         2199          910 
TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
        1189         1686         1968           62         1305          864 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3773 TCGA-67-3774 TCGA-67-6216 TCGA-67-6217 
        1559          866          427          385          141          422 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 
         690          414          165           89          100           77 
TCGA-69-8255 TCGA-73-4659 TCGA-73-4670 TCGA-73-4677 TCGA-73-7498 TCGA-75-6214 
         129          711          131           38          621         1970 
TCGA-75-7025 TCGA-75-7027 TCGA-78-7148 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
        1967         1956         1944         1963         1202          760 
TCGA-78-7155 TCGA-78-7158 TCGA-78-7160 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
        1957         1963          678         1940         1950         1934 
TCGA-78-7535 TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-8648 TCGA-78-8655 
        1972         1944          881         1952         1971         1981 
TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 TCGA-86-7701 TCGA-86-7714 TCGA-86-8054 
        1965         1972          824           11         1968          745 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8281 
        1963           13          489          476           16         1955 
TCGA-86-8359 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
          26           18           15          455          405           10 
TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6849 TCGA-91-7771 
          39         1940           60          310           35          492 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
         197          174           36           44          218          297 
TCGA-95-7948 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7937 
         476          121          964         1965         1932          181 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-A4M2 TCGA-97-A4M7 
          22          107          182         1965          197          271 
TCGA-99-7458 TCGA-99-8028 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE 
         392          459          170          154          114          282 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T7 
         238          578          435         1967         1951         1954 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A5C7 
        1951         1944         1970          142         1955         1490 

  AMP PEAK 25(17Q12) MUTATED AMP PEAK 25(17Q12) WILD-TYPE 
                           2                            1 
  AMP PEAK 25(17Q12) MUTATED AMP PEAK 25(17Q12) WILD-TYPE 
                        2370                         2696 
  AMP PEAK 25(17Q12) MUTATED AMP PEAK 25(17Q12) WILD-TYPE 
                         445                          476 
[1] "2.0 - 2370.0 (445.0)" "1.0 - 2696.0 (476.0)"
[1] "hr=" "1.3"
D25V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 25(17Q12) MUTATED         2       47       59        19        29
  AMP PEAK 25(17Q12) WILD-TYPE       2       66       72        24        40
                              vv
clus                           STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 25(17Q12) MUTATED           33          8       12
  AMP PEAK 25(17Q12) WILD-TYPE         34          3       11
D25V3, multiclass
            clus
vv           AMP PEAK 25(17Q12) MUTATED AMP PEAK 25(17Q12) WILD-TYPE
  STAGE I                             2                            2
  STAGE IA                           47                           66
  STAGE IB                           59                           72
  STAGE IIA                          19                           24
  STAGE IIB                          29                           40
  STAGE IIIA                         33                           34
  STAGE IIIB                          8                            3
  STAGE IV                           12                           11
[1] 8 2
[1] TRUE
[1] "dimension of 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(17Q12) MUTATED    57 124  18   9
  AMP PEAK 25(17Q12) WILD-TYPE  86 135  22   9
D25V4, multiclass
    clus
vv   AMP PEAK 25(17Q12) MUTATED AMP PEAK 25(17Q12) WILD-TYPE
  T1                         57                           86
  T2                        124                          135
  T3                         18                           22
  T4                          9                            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 25(17Q12) MUTATED   129  39    38
  AMP PEAK 25(17Q12) WILD-TYPE 166  46    34
D25V5, multiclass
       clus
vv      AMP PEAK 25(17Q12) MUTATED AMP PEAK 25(17Q12) WILD-TYPE
  N0                           129                          166
  N1                            39                           46
  N2+N3                         38                           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"
                              vv
clus                            M0  M1 M1A M1B  MX
  AMP PEAK 25(17Q12) MUTATED   147  10   0   2  50
  AMP PEAK 25(17Q12) WILD-TYPE 170   8   1   1  69
D25V6, multiclass
     clus
vv    AMP PEAK 25(17Q12) MUTATED AMP PEAK 25(17Q12) WILD-TYPE
  M0                         147                          170
  M1                          10                            8
  M1A                          0                            1
  M1B                          2                            1
  MX                          50                           69
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V7, binary
                              cls
clus                             0   1
  AMP PEAK 25(17Q12) MUTATED   107 102
  AMP PEAK 25(17Q12) WILD-TYPE 141 112
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 25(17Q12) MUTATED    107  102
  AMP PEAK 25(17Q12) WILD-TYPE  141  112
        clus
vv       AMP PEAK 25(17Q12) MUTATED AMP PEAK 25(17Q12) WILD-TYPE
  FEMALE                        107                          141
  MALE                          102                          112
[1] 2 2
[1] FALSE
D25V8, continuous
                              vv
clus                           LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 25(17Q12) MUTATED                            6
  AMP PEAK 25(17Q12) WILD-TYPE                          7
                              vv
clus                           LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 25(17Q12) MUTATED                                  45
  AMP PEAK 25(17Q12) WILD-TYPE                                48
                              vv
clus                           LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 25(17Q12) MUTATED                                                  137
  AMP PEAK 25(17Q12) WILD-TYPE                                                157
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 25(17Q12) MUTATED                                            1
  AMP PEAK 25(17Q12) WILD-TYPE                                          3
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 25(17Q12) MUTATED                                               5
  AMP PEAK 25(17Q12) WILD-TYPE                                            14
                              vv
clus                           LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 25(17Q12) MUTATED                                2
  AMP PEAK 25(17Q12) WILD-TYPE                              0
                              vv
clus                           LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 25(17Q12) MUTATED                                    2
  AMP PEAK 25(17Q12) WILD-TYPE                                  2
                              vv
clus                           LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 25(17Q12) MUTATED                              1
  AMP PEAK 25(17Q12) WILD-TYPE                            1
                              vv
clus                           LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 25(17Q12) MUTATED                               6
  AMP PEAK 25(17Q12) WILD-TYPE                            13
                              vv
clus                           LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 25(17Q12) MUTATED                                 0
  AMP PEAK 25(17Q12) WILD-TYPE                               1
                              vv
clus                           LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 25(17Q12) MUTATED                                               3
  AMP PEAK 25(17Q12) WILD-TYPE                                             1
                              vv
clus                           MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 25(17Q12) MUTATED                              1
  AMP PEAK 25(17Q12) WILD-TYPE                            6
D25V9, multiclass
                                                    clus
vv                                                   AMP PEAK 25(17Q12) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                  6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                          45
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                        137
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                  1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                               5
  LUNG CLEAR CELL ADENOCARCINOMA                                              2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                          2
  LUNG MUCINOUS ADENOCARCINOMA                                                1
  LUNG PAPILLARY ADENOCARCINOMA                                               6
  LUNG SIGNET RING ADENOCARCINOMA                                             0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                               3
  MUCINOUS (COLLOID) CARCINOMA                                                1
                                                    clus
vv                                                   AMP PEAK 25(17Q12) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                    7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            48
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          157
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                14
  LUNG CLEAR CELL ADENOCARCINOMA                                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            2
  LUNG MUCINOUS ADENOCARCINOMA                                                  1
  LUNG PAPILLARY ADENOCARCINOMA                                                13
  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"
D25V10, binary
                              cls
clus                             0   1
  AMP PEAK 25(17Q12) MUTATED    12 197
  AMP PEAK 25(17Q12) WILD-TYPE   9 244
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 25(17Q12) MUTATED     12  197
  AMP PEAK 25(17Q12) WILD-TYPE    9  244
     clus
vv    AMP PEAK 25(17Q12) MUTATED AMP PEAK 25(17Q12) WILD-TYPE
  NO                          12                            9
  YES                        197                          244
[1] 2 2
[1] FALSE
D25V11, continuous
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 25(17Q12) MUTATED   139   5   2  14
  AMP PEAK 25(17Q12) WILD-TYPE 179   6   2   5
D25V12, multiclass
    clus
vv   AMP PEAK 25(17Q12) MUTATED AMP PEAK 25(17Q12) WILD-TYPE
  R0                        139                          179
  R1                          5                            6
  R2                          2                            2
  RX                         14                            5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 25(17Q12) MUTATED                                  1     4
  AMP PEAK 25(17Q12) WILD-TYPE                                0     2
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 25(17Q12) MUTATED                          10   163
  AMP PEAK 25(17Q12) WILD-TYPE                        16   199
D25V13, multiclass
                                  clus
vv                                 AMP PEAK 25(17Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          1
  ASIAN                                                     4
  BLACK OR AFRICAN AMERICAN                                10
  WHITE                                                   163
                                  clus
vv                                 AMP PEAK 25(17Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  16
  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"
D25V14, binary
                              cls
clus                             0   1
  AMP PEAK 25(17Q12) MUTATED     3 145
  AMP PEAK 25(17Q12) WILD-TYPE   4 187
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 25(17Q12) MUTATED      3  145
  AMP PEAK 25(17Q12) WILD-TYPE    4  187
                        clus
vv                       AMP PEAK 25(17Q12) MUTATED
  HISPANIC OR LATINO                              3
  NOT HISPANIC OR LATINO                        145
                        clus
vv                       AMP PEAK 25(17Q12) WILD-TYPE
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          187
[1] 2 2
[1] FALSE

Clustering(26) Variable = AMP PEAK 26(17Q23.1) MUTATION ANALYSIS
D26V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 26(17Q23.1) MUTATED   158  38
  AMP PEAK 26(17Q23.1) WILD-TYPE 163  44
  AMP PEAK 26(17Q23.1) MUTATED AMP PEAK 26(17Q23.1) WILD-TYPE 
                           196                            207 
  AMP PEAK 26(17Q23.1) MUTATED AMP PEAK 26(17Q23.1) WILD-TYPE 
                            38                             44 
$`AMP PEAK 26(17Q23.1) MUTATED`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4389 TCGA-05-4398 TCGA-05-4410 TCGA-05-4415 
        1523          607         1369         1431         1958         1997 
TCGA-05-4417 TCGA-05-4420 TCGA-05-4424 TCGA-05-4425 TCGA-05-4427 TCGA-05-4430 
         455          912          913          669          791          761 
TCGA-05-4432 TCGA-35-4122 TCGA-38-4628 TCGA-38-4629 TCGA-38-4631 TCGA-38-4632 
         761          225         1492          864          354         1357 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2662 TCGA-44-2668 TCGA-44-3396 TCGA-44-3918 
        1429          400         1280          246         1130         1036 
TCGA-44-3919 TCGA-44-6144 TCGA-44-6148 TCGA-44-6775 TCGA-44-6777 TCGA-44-6779 
         190          723          704          705         1942         1978 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7670 TCGA-44-8117 
         592          366          218          557          882          385 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-49-4501 
          99          260          486          466          287         1421 
TCGA-49-4505 TCGA-49-4507 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
         428          268          445          369          890          522 
TCGA-49-6761 TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5935 
         354         1499          282          267         2370          653 
TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 TCGA-50-6597 TCGA-53-7624 TCGA-53-7813 
         567          764          686         1015         1986          424 
TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-5899 TCGA-55-6642 TCGA-55-6712 
         701         1178         1479           87          993           24 
TCGA-55-6971 TCGA-55-7281 TCGA-55-7283 TCGA-55-7576 TCGA-55-7727 TCGA-55-7815 
          25           18           35           40           34           54 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 TCGA-55-7994 TCGA-55-7995 TCGA-55-8089 
          19           16           21           31            5          100 
TCGA-55-8094 TCGA-55-8205 TCGA-55-8207 TCGA-55-8302 TCGA-55-8506 TCGA-55-8507 
           4           33           66           23           11            8 
TCGA-55-8510 TCGA-55-8514 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Z TCGA-55-A490 
         228          202           48           66           29           48 
TCGA-55-A491 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8398 TCGA-62-8402 TCGA-62-A46U 
        1952            5          162         1970         1445         2067 
TCGA-62-A471 TCGA-64-1676 TCGA-64-1677 TCGA-64-1680 TCGA-64-5774 TCGA-64-5815 
        1246         1728          628         1126         1959          866 
TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-6215 TCGA-67-6217 TCGA-69-7760 
          31          610          573          174          422          202 
TCGA-69-7764 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8255 
         414          230          184           70          382          129 
TCGA-71-6725 TCGA-73-4658 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4675 
          61         1600          912          800          467           40 
TCGA-73-4676 TCGA-73-7499 TCGA-75-6214 TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 
         164          519         1970         1965         1973         1988 
TCGA-78-7147 TCGA-78-7149 TCGA-78-7154 TCGA-78-7159 TCGA-78-7161 TCGA-78-7167 
        1950         1093         1948         1221          215         1937 
TCGA-78-7220 TCGA-78-7539 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8655 
        1965          327         1952          994         1949         1981 
TCGA-78-8660 TCGA-78-8662 TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 
        1954         1964         1959          630          422          591 
TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 
         508           10         1963           24          479          482 
TCGA-86-8358 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8672 TCGA-86-8673 
          19           35           45           34           15          455 
TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-91-6828 TCGA-91-6835 TCGA-91-6836 
          10           30           14          323           79          417 
TCGA-91-6847 TCGA-91-6848 TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 
         842          224          127          186           34            2 
TCGA-95-7567 TCGA-95-7944 TCGA-95-A4VK TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
         568          377          121         1332          775          181 
TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-99-8025 
          87          147           15          148          115          427 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD TCGA-L4-A4E5 TCGA-L9-A443 
         459           44          170          287          578          116 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4T4 
           6          285          622          353         1946         1954 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TK 
        1957         1980         1970         1971 

$`AMP PEAK 26(17Q23.1) WILD-TYPE`
TCGA-05-4384 TCGA-05-4390 TCGA-05-4396 TCGA-05-4403 TCGA-05-4405 TCGA-05-4422 
         426         1126         1947          578          610          365 
TCGA-05-4426 TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
         791          730          457          151          882          670 
TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
          30           62           14          182          264         1952 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4630 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F 
        1962         1147         1073          448         1971          133 
TCGA-44-2655 TCGA-44-2659 TCGA-44-2661 TCGA-44-2665 TCGA-44-2666 TCGA-44-3398 
        1324         1367          741         1301           97         1163 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6145 TCGA-44-6146 
         722         1013          863          383          328          302 
TCGA-44-6147 TCGA-44-6774 TCGA-44-6776 TCGA-44-6778 TCGA-44-7659 TCGA-44-7669 
         845          658         1938         1864          444         1970 
TCGA-44-7671 TCGA-44-7672 TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
         535          719          337          351          415           76 
TCGA-49-4486 TCGA-49-4494 TCGA-49-4506 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
        1932         1081          999          896          157         1700 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 
        2174         2146          455          785          944          246 
TCGA-50-5932 TCGA-50-5942 TCGA-50-7109 TCGA-50-8460 TCGA-53-7626 TCGA-53-A4EZ 
        1091          883          255          105         1971          280 
TCGA-55-1596 TCGA-55-6543 TCGA-55-6969 TCGA-55-6972 TCGA-55-6980 TCGA-55-6983 
        1375            2         1239         1475           67         1826 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1233         2151         1170          121            6            4 
TCGA-55-7574 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 TCGA-55-7910 
          95         1958           39           39           24          197 
TCGA-55-7914 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
           3           33           21            6           43           26 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 
          47           15           46          216           44           29 
TCGA-55-8508 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-8615 
          15            9            3          146          536           15 
TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A492 TCGA-55-A493 
          49          106           33           42            1           28 
TCGA-55-A4DF TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 TCGA-62-A46V TCGA-62-A472 
          47         1216         1289         2696         2199          910 
TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
        1189         1686         1968           62         1305          864 
TCGA-64-5781 TCGA-67-3773 TCGA-67-3774 TCGA-67-6216 TCGA-69-7761 TCGA-69-7763 
        1559          427          385          141          186          690 
TCGA-69-7765 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-69-A59K TCGA-73-4659 
         165           89          100           77          214          711 
TCGA-73-4670 TCGA-73-4677 TCGA-73-7498 TCGA-75-7025 TCGA-75-7027 TCGA-78-7148 
         131           38          621         1967         1956         1944 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
        1963         1202          760         1957         1961         1963 
TCGA-78-7160 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7535 TCGA-78-7536 
         678         1940         1950         1934         1972         1949 
TCGA-78-7537 TCGA-78-7540 TCGA-78-8648 TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 
        1944          881         1971         1965         1972          824 
TCGA-86-7701 TCGA-86-7714 TCGA-86-7954 TCGA-86-8054 TCGA-86-8073 TCGA-86-8076 
          11         1968         1963          745           13          489 
TCGA-86-8278 TCGA-86-8280 TCGA-86-8281 TCGA-86-8359 TCGA-86-8671 TCGA-86-8674 
         476           16         1955           26           18          405 
TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6840 TCGA-91-6849 
          39         1940           60          310          372           35 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
         492          197          174           36           44          218 
TCGA-93-7347 TCGA-95-7947 TCGA-95-7948 TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
         297          477          476          964         1965         1932 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-A4M2 TCGA-97-A4M7 
          22          107          182         1965          197          271 
TCGA-99-7458 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 
         392          154          114          282          238          435 
TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T7 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TF 
        1967         1951         1954         1951         1944         1970 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A5C7 
         142         1955         1490 

  AMP PEAK 26(17Q23.1) MUTATED AMP PEAK 26(17Q23.1) WILD-TYPE 
                             2                              1 
  AMP PEAK 26(17Q23.1) MUTATED AMP PEAK 26(17Q23.1) WILD-TYPE 
                          2370                           2696 
  AMP PEAK 26(17Q23.1) MUTATED AMP PEAK 26(17Q23.1) WILD-TYPE 
                           455                            477 
[1] "2.0 - 2370.0 (455.0)" "1.0 - 2696.0 (477.0)"
[1] "hr=" "1"  
D26V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 26(17Q23.1) MUTATED         3       47       66        20        33
  AMP PEAK 26(17Q23.1) WILD-TYPE       1       66       65        23        36
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 26(17Q23.1) MUTATED           37          8       13
  AMP PEAK 26(17Q23.1) WILD-TYPE         30          3       10
D26V3, multiclass
            clus
vv           AMP PEAK 26(17Q23.1) MUTATED AMP PEAK 26(17Q23.1) WILD-TYPE
  STAGE I                               3                              1
  STAGE IA                             47                             66
  STAGE IB                             66                             65
  STAGE IIA                            20                             23
  STAGE IIB                            33                             36
  STAGE IIIA                           37                             30
  STAGE IIIB                            8                              3
  STAGE IV                             13                             10
[1] 8 2
[1] TRUE
[1] "dimension of 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(17Q23.1) MUTATED    60 137  19   9
  AMP PEAK 26(17Q23.1) WILD-TYPE  83 122  21   9
D26V4, multiclass
    clus
vv   AMP PEAK 26(17Q23.1) MUTATED AMP PEAK 26(17Q23.1) WILD-TYPE
  T1                           60                             83
  T2                          137                            122
  T3                           19                             21
  T4                            9                              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 26(17Q23.1) MUTATED   138  43    41
  AMP PEAK 26(17Q23.1) WILD-TYPE 157  42    31
D26V5, multiclass
       clus
vv      AMP PEAK 26(17Q23.1) MUTATED AMP PEAK 26(17Q23.1) WILD-TYPE
  N0                             138                            157
  N1                              43                             42
  N2+N3                           41                             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"
                                vv
clus                              M0  M1 M1A M1B  MX
  AMP PEAK 26(17Q23.1) MUTATED   159  11   0   2  55
  AMP PEAK 26(17Q23.1) WILD-TYPE 158   7   1   1  64
D26V6, multiclass
     clus
vv    AMP PEAK 26(17Q23.1) MUTATED AMP PEAK 26(17Q23.1) WILD-TYPE
  M0                           159                            158
  M1                            11                              7
  M1A                            0                              1
  M1B                            2                              1
  MX                            55                             64
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V7, binary
                                cls
clus                               0   1
  AMP PEAK 26(17Q23.1) MUTATED   124 103
  AMP PEAK 26(17Q23.1) WILD-TYPE 124 111
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 26(17Q23.1) MUTATED    124  103
  AMP PEAK 26(17Q23.1) WILD-TYPE  124  111
        clus
vv       AMP PEAK 26(17Q23.1) MUTATED AMP PEAK 26(17Q23.1) WILD-TYPE
  FEMALE                          124                            124
  MALE                            103                            111
[1] 2 2
[1] FALSE
D26V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 26(17Q23.1) MUTATED                            5
  AMP PEAK 26(17Q23.1) WILD-TYPE                          8
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 26(17Q23.1) MUTATED                                  49
  AMP PEAK 26(17Q23.1) WILD-TYPE                                44
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 26(17Q23.1) MUTATED                                                  150
  AMP PEAK 26(17Q23.1) WILD-TYPE                                                144
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 26(17Q23.1) MUTATED                                            1
  AMP PEAK 26(17Q23.1) WILD-TYPE                                          3
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 26(17Q23.1) MUTATED                                               6
  AMP PEAK 26(17Q23.1) WILD-TYPE                                            13
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 26(17Q23.1) MUTATED                                2
  AMP PEAK 26(17Q23.1) WILD-TYPE                              0
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 26(17Q23.1) MUTATED                                    3
  AMP PEAK 26(17Q23.1) WILD-TYPE                                  1
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 26(17Q23.1) MUTATED                              1
  AMP PEAK 26(17Q23.1) WILD-TYPE                            1
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 26(17Q23.1) MUTATED                               5
  AMP PEAK 26(17Q23.1) WILD-TYPE                            14
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 26(17Q23.1) MUTATED                                 0
  AMP PEAK 26(17Q23.1) WILD-TYPE                               1
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 26(17Q23.1) MUTATED                                               4
  AMP PEAK 26(17Q23.1) WILD-TYPE                                             0
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 26(17Q23.1) MUTATED                              1
  AMP PEAK 26(17Q23.1) WILD-TYPE                            6
D26V9, multiclass
                                                    clus
vv                                                   AMP PEAK 26(17Q23.1) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            49
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          150
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 6
  LUNG CLEAR CELL ADENOCARCINOMA                                                2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            3
  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                                                   AMP PEAK 26(17Q23.1) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              44
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            144
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  13
  LUNG CLEAR CELL ADENOCARCINOMA                                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              1
  LUNG MUCINOUS ADENOCARCINOMA                                                    1
  LUNG PAPILLARY ADENOCARCINOMA                                                  14
  LUNG SIGNET RING ADENOCARCINOMA                                                 1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                   0
  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"
D26V10, binary
                                cls
clus                               0   1
  AMP PEAK 26(17Q23.1) MUTATED    10 217
  AMP PEAK 26(17Q23.1) WILD-TYPE  11 224
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 26(17Q23.1) MUTATED     10  217
  AMP PEAK 26(17Q23.1) WILD-TYPE   11  224
     clus
vv    AMP PEAK 26(17Q23.1) MUTATED AMP PEAK 26(17Q23.1) WILD-TYPE
  NO                            10                             11
  YES                          217                            224
[1] 2 2
[1] FALSE
D26V11, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 26(17Q23.1) MUTATED   154   4   2  15
  AMP PEAK 26(17Q23.1) WILD-TYPE 164   7   2   4
D26V12, multiclass
    clus
vv   AMP PEAK 26(17Q23.1) MUTATED AMP PEAK 26(17Q23.1) WILD-TYPE
  R0                          154                            164
  R1                            4                              7
  R2                            2                              2
  RX                           15                              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 26(17Q23.1) MUTATED                                  1     4
  AMP PEAK 26(17Q23.1) WILD-TYPE                                0     2
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 26(17Q23.1) MUTATED                          10   177
  AMP PEAK 26(17Q23.1) WILD-TYPE                        16   185
D26V13, multiclass
                                  clus
vv                                 AMP PEAK 26(17Q23.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  10
  WHITE                                                     177
                                  clus
vv                                 AMP PEAK 26(17Q23.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         2
  BLACK OR AFRICAN AMERICAN                                    16
  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"
D26V14, binary
                                cls
clus                               0   1
  AMP PEAK 26(17Q23.1) MUTATED     5 157
  AMP PEAK 26(17Q23.1) WILD-TYPE   2 175
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 26(17Q23.1) MUTATED      5  157
  AMP PEAK 26(17Q23.1) WILD-TYPE    2  175
                        clus
vv                       AMP PEAK 26(17Q23.1) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          157
                        clus
vv                       AMP PEAK 26(17Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            175
[1] 2 2
[1] FALSE

Clustering(27) Variable = AMP PEAK 27(18Q11.2) MUTATION ANALYSIS
D27V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 27(18Q11.2) MUTATED    71  19
  AMP PEAK 27(18Q11.2) WILD-TYPE 250  63
  AMP PEAK 27(18Q11.2) MUTATED AMP PEAK 27(18Q11.2) WILD-TYPE 
                            90                            313 
  AMP PEAK 27(18Q11.2) MUTATED AMP PEAK 27(18Q11.2) WILD-TYPE 
                            19                             63 
$`AMP PEAK 27(18Q11.2) MUTATED`
TCGA-05-4390 TCGA-05-4396 TCGA-05-4410 TCGA-05-4415 TCGA-05-4420 TCGA-05-4424 
        1126         1947         1958         1997          912          913 
TCGA-05-4433 TCGA-05-5425 TCGA-05-5428 TCGA-38-4631 TCGA-38-4632 TCGA-44-2659 
         730          882          670          354         1357         1367 
TCGA-44-5644 TCGA-44-6144 TCGA-44-6146 TCGA-44-6778 TCGA-44-7660 TCGA-44-7662 
         863          723          302         1864          592          218 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7672 TCGA-44-8119 TCGA-44-A47A 
         557         1970          882          719           99          466 
TCGA-49-4514 TCGA-49-6743 TCGA-49-6745 TCGA-49-6761 TCGA-50-5068 TCGA-50-5931 
        1700          369          522          354         1499          267 
TCGA-53-7813 TCGA-55-1592 TCGA-55-1595 TCGA-55-6642 TCGA-55-6980 TCGA-55-7728 
         424          701         1479          993           67           24 
TCGA-55-7907 TCGA-55-8089 TCGA-55-8096 TCGA-55-8508 TCGA-55-8511 TCGA-55-8615 
          16          100           47           15            9           15 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
           5           47          162         1970         2696         1445 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-5779 TCGA-69-7764 TCGA-69-7973 
        1728          628         1189          864          414          230 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-73-4662 TCGA-73-4668 TCGA-73-4675 
          89          382          100          912          467           40 
TCGA-73-4676 TCGA-75-6214 TCGA-75-7031 TCGA-78-7148 TCGA-78-7150 TCGA-78-7155 
         164         1970         1965         1944         1963         1957 
TCGA-78-7167 TCGA-78-7542 TCGA-78-8655 TCGA-78-8662 TCGA-86-7713 TCGA-86-7955 
        1937         1952         1981         1964          422          508 
TCGA-86-8055 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8358 TCGA-86-8359 
          10           13           24          479           19           26 
TCGA-86-8585 TCGA-86-A4D0 TCGA-91-6829 TCGA-91-6831 TCGA-91-6840 TCGA-91-8499 
          35           30         1940          310          372           36 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7554 TCGA-97-8175 TCGA-97-8179 TCGA-97-8552 
         964         1965          775           87           15          115 

$`AMP PEAK 27(18Q11.2) WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4398 TCGA-05-4403 
        1523          607          426         1369         1431          578 
TCGA-05-4405 TCGA-05-4417 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 
         610          455          365          669          791          791 
TCGA-05-4430 TCGA-05-4432 TCGA-05-5420 TCGA-05-5423 TCGA-05-5429 TCGA-05-5715 
         761          761          457          151           30           62 
TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
          14          225          182          264         1952         1962 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-6178 TCGA-38-7271 
        1147         1492          864         1073          448         1971 
TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2662 
         133         1324         1429          400          741         1280 
TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 
        1301           97          246         1130         1163         1036 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6145 TCGA-44-6147 
         190          722         1013          383          328          845 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6779 
         704          658          705         1938         1942         1978 
TCGA-44-7659 TCGA-44-7661 TCGA-44-7671 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 
         444          366          535          385          260          486 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
         287          337          351          415           76         1932 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
        1081         1421          428          999          268          896 
TCGA-49-4512 TCGA-49-6742 TCGA-49-6744 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
         157          445          890         2174         2146          455 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 
         785          944          246          282         1091         2370 
TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6597 
         653          567          883          764          686         1015 
TCGA-50-7109 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1594 
         255          105         1986         1971          280         1178 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6712 TCGA-55-6969 TCGA-55-6971 
        1375           87            2           24         1239           25 
TCGA-55-6972 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 
        1475         1826         1233         2151         1170           18 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
          35          121            6            4           95           40 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7815 TCGA-55-7903 
        1958           39           39           34           54           19 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
         197           21            3           31            5           33 
TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8097 
          21            6           43           26            4           15 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
          33           46           66          216           44           23 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 
          29           11            8          228            3          146 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
         202          536           48           49           66          106 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
          33           42           29           48         1952            1 
TCGA-55-A493 TCGA-62-8395 TCGA-62-8397 TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 
          28         1216         1289         2067         2199         1246 
TCGA-62-A472 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
         910         1686         1126         1968         1959           62 
TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 
        1305         1559          866           31          610          573 
TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
         427          385          174          141          422          202 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 TCGA-69-8254 
         186          690          165          184           70           77 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4666 
         129          214           61         1600          711          800 
TCGA-73-4670 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-75-7025 TCGA-75-7027 
         131           38          621          519         1967         1956 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 
        1973         1988         1950         1093         1202          760 
TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
        1948         1961         1963         1221          678          215 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
        1940         1950         1934         1965         1972         1949 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
        1944          327          881          994         1949         1971 
TCGA-78-8660 TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 
        1954         1965         1972          824         1959           11 
TCGA-86-7711 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8056 
         630         1968          591         1963          745         1963 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8281 TCGA-86-8668 
         489          476          482           16         1955           45 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
          34           18           15          455          405           10 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 TCGA-91-6835 TCGA-91-6836 
          14           39          323           60           79          417 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
         842          224           35          492          197          174 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 
          44          218          297          127          186           34 
TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK 
           2          568          377          477          476          121 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
        1932         1332          181           22          107          182 
TCGA-97-8174 TCGA-97-8177 TCGA-97-8547 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 
        1965          147          148          197          271          392 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
         427          459           44          170          154          114 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
         287          282          238          578          435          116 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
           6          285          622          353         1946         1967 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
        1951         1954         1954         1957         1980         1951 
TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
        1944         1970         1970          142         1955         1971 
TCGA-MP-A5C7 
        1490 

  AMP PEAK 27(18Q11.2) MUTATED AMP PEAK 27(18Q11.2) WILD-TYPE 
                             5                              1 
  AMP PEAK 27(18Q11.2) MUTATED AMP PEAK 27(18Q11.2) WILD-TYPE 
                          2696                           2370 
  AMP PEAK 27(18Q11.2) MUTATED AMP PEAK 27(18Q11.2) WILD-TYPE 
                         539.5                          455.0 
[1] "5.0 - 2696.0 (539.5)" "1.0 - 2370.0 (455.0)"
[1] "hr=" "1"  
D27V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 27(18Q11.2) MUTATED         2       19       32        11        11
  AMP PEAK 27(18Q11.2) WILD-TYPE       2       94       99        32        58
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 27(18Q11.2) MUTATED           15          3        2
  AMP PEAK 27(18Q11.2) WILD-TYPE         52          8       21
D27V3, multiclass
            clus
vv           AMP PEAK 27(18Q11.2) MUTATED AMP PEAK 27(18Q11.2) WILD-TYPE
  STAGE I                               2                              2
  STAGE IA                             19                             94
  STAGE IB                             32                             99
  STAGE IIA                            11                             32
  STAGE IIB                            11                             58
  STAGE IIIA                           15                             52
  STAGE IIIB                            3                              8
  STAGE IV                              2                             21
[1] 8 2
[1] TRUE
[1] "dimension of 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(18Q11.2) MUTATED    28  57   7   3
  AMP PEAK 27(18Q11.2) WILD-TYPE 115 202  33  15
D27V4, multiclass
    clus
vv   AMP PEAK 27(18Q11.2) MUTATED AMP PEAK 27(18Q11.2) WILD-TYPE
  T1                           28                            115
  T2                           57                            202
  T3                            7                             33
  T4                            3                             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(18Q11.2) MUTATED    62  18    15
  AMP PEAK 27(18Q11.2) WILD-TYPE 233  67    57
D27V5, multiclass
       clus
vv      AMP PEAK 27(18Q11.2) MUTATED AMP PEAK 27(18Q11.2) WILD-TYPE
  N0                              62                            233
  N1                              18                             67
  N2+N3                           15                             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"
                                vv
clus                              M0  M1 M1A M1B  MX
  AMP PEAK 27(18Q11.2) MUTATED    64   2   0   0  28
  AMP PEAK 27(18Q11.2) WILD-TYPE 253  16   1   3  91
D27V6, multiclass
     clus
vv    AMP PEAK 27(18Q11.2) MUTATED AMP PEAK 27(18Q11.2) WILD-TYPE
  M0                            64                            253
  M1                             2                             16
  M1A                            0                              1
  M1B                            0                              3
  MX                            28                             91
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V7, binary
                                cls
clus                               0   1
  AMP PEAK 27(18Q11.2) MUTATED    46  49
  AMP PEAK 27(18Q11.2) WILD-TYPE 202 165
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(18Q11.2) MUTATED     46   49
  AMP PEAK 27(18Q11.2) WILD-TYPE  202  165
        clus
vv       AMP PEAK 27(18Q11.2) MUTATED AMP PEAK 27(18Q11.2) WILD-TYPE
  FEMALE                           46                            202
  MALE                             49                            165
[1] 2 2
[1] FALSE
D27V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 27(18Q11.2) MUTATED                            4
  AMP PEAK 27(18Q11.2) WILD-TYPE                          9
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 27(18Q11.2) MUTATED                                  16
  AMP PEAK 27(18Q11.2) WILD-TYPE                                77
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 27(18Q11.2) MUTATED                                                   56
  AMP PEAK 27(18Q11.2) WILD-TYPE                                                238
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 27(18Q11.2) MUTATED                                            0
  AMP PEAK 27(18Q11.2) WILD-TYPE                                          4
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 27(18Q11.2) MUTATED                                               5
  AMP PEAK 27(18Q11.2) WILD-TYPE                                            14
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 27(18Q11.2) MUTATED                                2
  AMP PEAK 27(18Q11.2) WILD-TYPE                              0
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 27(18Q11.2) MUTATED                                    1
  AMP PEAK 27(18Q11.2) WILD-TYPE                                  3
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 27(18Q11.2) MUTATED                              1
  AMP PEAK 27(18Q11.2) WILD-TYPE                            1
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 27(18Q11.2) MUTATED                               6
  AMP PEAK 27(18Q11.2) WILD-TYPE                            13
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 27(18Q11.2) MUTATED                                 0
  AMP PEAK 27(18Q11.2) WILD-TYPE                               1
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 27(18Q11.2) MUTATED                                               2
  AMP PEAK 27(18Q11.2) WILD-TYPE                                             2
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 27(18Q11.2) MUTATED                              2
  AMP PEAK 27(18Q11.2) WILD-TYPE                            5
D27V9, multiclass
                                                    clus
vv                                                   AMP PEAK 27(18Q11.2) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            16
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           56
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    0
  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                                                  2
                                                    clus
vv                                                   AMP PEAK 27(18Q11.2) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              77
  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                                              3
  LUNG MUCINOUS ADENOCARCINOMA                                                    1
  LUNG PAPILLARY ADENOCARCINOMA                                                  13
  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"
D27V10, binary
                                cls
clus                               0   1
  AMP PEAK 27(18Q11.2) MUTATED     2  93
  AMP PEAK 27(18Q11.2) WILD-TYPE  19 348
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(18Q11.2) MUTATED      2   93
  AMP PEAK 27(18Q11.2) WILD-TYPE   19  348
     clus
vv    AMP PEAK 27(18Q11.2) MUTATED AMP PEAK 27(18Q11.2) WILD-TYPE
  NO                             2                             19
  YES                           93                            348
[1] 2 2
[1] FALSE
D27V11, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 27(18Q11.2) MUTATED    61   2   0   5
  AMP PEAK 27(18Q11.2) WILD-TYPE 257   9   4  14
D27V12, multiclass
    clus
vv   AMP PEAK 27(18Q11.2) MUTATED AMP PEAK 27(18Q11.2) WILD-TYPE
  R0                           61                            257
  R1                            2                              9
  R2                            0                              4
  RX                            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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 27(18Q11.2) MUTATED                                  1     1
  AMP PEAK 27(18Q11.2) WILD-TYPE                                0     5
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 27(18Q11.2) MUTATED                           5    72
  AMP PEAK 27(18Q11.2) WILD-TYPE                        21   290
D27V13, multiclass
                                  clus
vv                                 AMP PEAK 27(18Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   5
  WHITE                                                      72
                                  clus
vv                                 AMP PEAK 27(18Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         5
  BLACK OR AFRICAN AMERICAN                                    21
  WHITE                                                       290
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V14, binary
                                cls
clus                               0   1
  AMP PEAK 27(18Q11.2) MUTATED     1  64
  AMP PEAK 27(18Q11.2) WILD-TYPE   6 268
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(18Q11.2) MUTATED      1   64
  AMP PEAK 27(18Q11.2) WILD-TYPE    6  268
                        clus
vv                       AMP PEAK 27(18Q11.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           64
                        clus
vv                       AMP PEAK 27(18Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            268
[1] 2 2
[1] FALSE

Clustering(28) Variable = AMP PEAK 28(19Q12) MUTATION ANALYSIS
D28V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 28(19Q12) MUTATED    94  17
  AMP PEAK 28(19Q12) WILD-TYPE 227  65
  AMP PEAK 28(19Q12) MUTATED AMP PEAK 28(19Q12) WILD-TYPE 
                         111                          292 
  AMP PEAK 28(19Q12) MUTATED AMP PEAK 28(19Q12) WILD-TYPE 
                          17                           65 
$`AMP PEAK 28(19Q12) MUTATED`
TCGA-05-4389 TCGA-05-4390 TCGA-05-4398 TCGA-05-4410 TCGA-05-4415 TCGA-05-4424 
        1369         1126         1431         1958         1997          913 
TCGA-05-4432 TCGA-05-5425 TCGA-05-5428 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 
         761          882          670          225          182          264 
TCGA-38-4628 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-44-2662 TCGA-44-3918 
        1492         1073          354         1357         1280         1036 
TCGA-44-5644 TCGA-44-6144 TCGA-44-6147 TCGA-44-6776 TCGA-44-7660 TCGA-44-7667 
         863          723          845         1938          592          557 
TCGA-44-7669 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        1970          535           99          466          287          337 
TCGA-44-A4SS TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-50-5049 TCGA-50-5066 
         415          445          369          890         2146          944 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5946 TCGA-50-6597 TCGA-53-7624 TCGA-53-7813 
         246          282          686         1015         1986          424 
TCGA-53-A4EZ TCGA-55-1594 TCGA-55-6971 TCGA-55-6972 TCGA-55-7907 TCGA-55-7995 
         280         1178           25         1475           16            5 
TCGA-55-8085 TCGA-55-8092 TCGA-55-8301 TCGA-55-8302 TCGA-55-8507 TCGA-55-8614 
          33           26           44           23            8          536 
TCGA-55-8615 TCGA-55-8620 TCGA-55-A48Z TCGA-55-A491 TCGA-55-A493 TCGA-55-A4DF 
          15           66           29         1952           28           47 
TCGA-62-8399 TCGA-64-1678 TCGA-64-1679 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
        2696         1189         1686         1305          864         1559 
TCGA-69-7760 TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 
         202          690          414          230           70           89 
TCGA-69-7980 TCGA-69-8253 TCGA-69-A59K TCGA-73-4675 TCGA-78-7148 TCGA-78-7150 
         382          100          214           40         1944         1963 
TCGA-78-7154 TCGA-80-5608 TCGA-86-7713 TCGA-86-7953 TCGA-86-8055 TCGA-86-8073 
        1948         1972          422          591           10           13 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8673 
          24          479           19           26           35          455 
TCGA-86-A456 TCGA-91-6829 TCGA-91-6830 TCGA-91-6840 TCGA-95-7043 TCGA-95-7567 
          10         1940           60          372            2          568 
TCGA-95-7944 TCGA-95-A4VK TCGA-97-7554 TCGA-97-7937 TCGA-97-8172 TCGA-97-8174 
         377          121          775          181          182         1965 
TCGA-97-8175 TCGA-97-8179 TCGA-99-8025 TCGA-99-8033 TCGA-L9-A443 TCGA-MN-A4N4 
          87           15          427          170          116          622 
TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4TH 
        1954         1954          142 

$`AMP PEAK 28(19Q12) WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4403 TCGA-05-4405 
        1523          607          426         1947          578          610 
TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 
         455          912          365          669          791          791 
TCGA-05-4430 TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5429 TCGA-05-5715 
         761          730          457          151           30           62 
TCGA-35-3615 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4629 TCGA-38-6178 
          14         1952         1962         1147          864          448 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 
        1971          133         1324         1429          400         1367 
TCGA-44-2661 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 
         741         1301           97          246         1130         1163 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6145 TCGA-44-6146 
         190          722         1013          383          328          302 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
         704          658          705         1942         1864         1978 
TCGA-44-7659 TCGA-44-7661 TCGA-44-7662 TCGA-44-7670 TCGA-44-7672 TCGA-44-8117 
         444          366          218          882          719          385 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47G TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 
         260          486          351           76         1932         1081 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
        1421          428          999          268          896          157 
TCGA-49-4514 TCGA-49-6745 TCGA-49-6761 TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 
        1700          522          354         2174          455          785 
TCGA-50-5068 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 
        1499          267         1091         2370          653          567 
TCGA-50-5942 TCGA-50-5944 TCGA-50-7109 TCGA-50-8460 TCGA-53-7626 TCGA-55-1592 
         883          764          255          105         1971          701 
TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
        1479         1375           87            2          993           24 
TCGA-55-6969 TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
        1239           67         1826         1233         2151         1170 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
          18           35          121            6            4           95 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
          40         1958           39           39           34           24 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
          54           19          197           21            3           31 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8094 TCGA-55-8096 
          21          100            6           43            4           47 
TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8505 
          15           33           46           66          216           29 
TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
          11           15          228            9            3          146 
TCGA-55-8514 TCGA-55-8616 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
         202           48           49          106           33           42 
TCGA-55-A490 TCGA-55-A492 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 
          48            1            5          162         1216         1289 
TCGA-62-8398 TCGA-62-8402 TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 
        1970         1445         2067         2199         1246          910 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
        1728          628         1126         1968         1959           62 
TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 
         866           31          610          573          427          385 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7761 TCGA-69-7765 TCGA-69-7974 
         174          141          422          186          165          184 
TCGA-69-8254 TCGA-69-8255 TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
          77          129           61         1600          711          912 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
         800          467          131          164           38          621 
TCGA-73-7499 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 TCGA-78-7145 
         519         1970         1967         1956         1965         1973 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7155 
        1988         1950         1093         1202          760         1957 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
        1961         1963         1221          678          215         1940 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
        1950         1934         1937         1965         1972         1949 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
        1944          327          881         1952          994         1949 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 TCGA-83-5908 
        1971         1981         1954         1964         1965          824 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 TCGA-86-7954 TCGA-86-7955 
        1959           11          630         1968         1963          508 
TCGA-86-8054 TCGA-86-8056 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
         745         1963          489          476          482           16 
TCGA-86-8281 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 
        1955           45           34           18           15          405 
TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6831 TCGA-91-6835 
          30           14           39          323          310           79 
TCGA-91-6836 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
         417          842          224           35          492          197 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
         174           36           44          218          297          127 
TCGA-93-8067 TCGA-95-7039 TCGA-95-7947 TCGA-95-7948 TCGA-97-7546 TCGA-97-7547 
         186           34          477          476          964         1965 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7941 TCGA-97-8171 TCGA-97-8177 TCGA-97-8547 
        1932         1332           22          107          147          148 
TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 
         115          197          271          392          459           44 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
         154          114          287          282          238          578 
TCGA-L4-A4E6 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
         435            6          285          353         1946         1967 
TCGA-MP-A4T2 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TE 
        1951         1957         1980         1951         1944         1970 
TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
        1970         1955         1971         1490 

  AMP PEAK 28(19Q12) MUTATED AMP PEAK 28(19Q12) WILD-TYPE 
                           2                            1 
  AMP PEAK 28(19Q12) MUTATED AMP PEAK 28(19Q12) WILD-TYPE 
                        2696                         2370 
  AMP PEAK 28(19Q12) MUTATED AMP PEAK 28(19Q12) WILD-TYPE 
                       427.0                        476.5 
[1] "2.0 - 2696.0 (427.0)" "1.0 - 2370.0 (476.5)"
[1] "hr=" "1.2"
D28V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 28(19Q12) MUTATED         1       29       36        12        18
  AMP PEAK 28(19Q12) WILD-TYPE       3       84       95        31        51
                              vv
clus                           STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 28(19Q12) MUTATED           21          5        6
  AMP PEAK 28(19Q12) WILD-TYPE         46          6       17
D28V3, multiclass
            clus
vv           AMP PEAK 28(19Q12) MUTATED AMP PEAK 28(19Q12) WILD-TYPE
  STAGE I                             1                            3
  STAGE IA                           29                           84
  STAGE IB                           36                           95
  STAGE IIA                          12                           31
  STAGE IIB                          18                           51
  STAGE IIIA                         21                           46
  STAGE IIIB                          5                            6
  STAGE IV                            6                           17
[1] 8 2
[1] TRUE
[1] "dimension of 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(19Q12) MUTATED    37  71  14   4
  AMP PEAK 28(19Q12) WILD-TYPE 106 188  26  14
D28V4, multiclass
    clus
vv   AMP PEAK 28(19Q12) MUTATED AMP PEAK 28(19Q12) WILD-TYPE
  T1                         37                          106
  T2                         71                          188
  T3                         14                           26
  T4                          4                           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 28(19Q12) MUTATED    79  24    23
  AMP PEAK 28(19Q12) WILD-TYPE 216  61    49
D28V5, multiclass
       clus
vv      AMP PEAK 28(19Q12) MUTATED AMP PEAK 28(19Q12) WILD-TYPE
  N0                            79                          216
  N1                            24                           61
  N2+N3                         23                           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"
                              vv
clus                            M0  M1 M1A M1B  MX
  AMP PEAK 28(19Q12) MUTATED    91   5   0   1  30
  AMP PEAK 28(19Q12) WILD-TYPE 226  13   1   2  89
D28V6, multiclass
     clus
vv    AMP PEAK 28(19Q12) MUTATED AMP PEAK 28(19Q12) WILD-TYPE
  M0                          91                          226
  M1                           5                           13
  M1A                          0                            1
  M1B                          1                            2
  MX                          30                           89
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V7, binary
                              cls
clus                             0   1
  AMP PEAK 28(19Q12) MUTATED    58  70
  AMP PEAK 28(19Q12) WILD-TYPE 190 144
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 28(19Q12) MUTATED     58   70
  AMP PEAK 28(19Q12) WILD-TYPE  190  144
        clus
vv       AMP PEAK 28(19Q12) MUTATED AMP PEAK 28(19Q12) WILD-TYPE
  FEMALE                         58                          190
  MALE                           70                          144
[1] 2 2
[1] FALSE
D28V8, continuous
                              vv
clus                           LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 28(19Q12) MUTATED                            6
  AMP PEAK 28(19Q12) WILD-TYPE                          7
                              vv
clus                           LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 28(19Q12) MUTATED                                  28
  AMP PEAK 28(19Q12) WILD-TYPE                                65
                              vv
clus                           LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 28(19Q12) MUTATED                                                   73
  AMP PEAK 28(19Q12) WILD-TYPE                                                221
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 28(19Q12) MUTATED                                            0
  AMP PEAK 28(19Q12) WILD-TYPE                                          4
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 28(19Q12) MUTATED                                               5
  AMP PEAK 28(19Q12) WILD-TYPE                                            14
                              vv
clus                           LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 28(19Q12) MUTATED                                1
  AMP PEAK 28(19Q12) WILD-TYPE                              1
                              vv
clus                           LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 28(19Q12) MUTATED                                    1
  AMP PEAK 28(19Q12) WILD-TYPE                                  3
                              vv
clus                           LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 28(19Q12) MUTATED                              0
  AMP PEAK 28(19Q12) WILD-TYPE                            2
                              vv
clus                           LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 28(19Q12) MUTATED                               9
  AMP PEAK 28(19Q12) WILD-TYPE                            10
                              vv
clus                           LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 28(19Q12) MUTATED                                 1
  AMP PEAK 28(19Q12) WILD-TYPE                               0
                              vv
clus                           LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 28(19Q12) MUTATED                                               2
  AMP PEAK 28(19Q12) WILD-TYPE                                             2
                              vv
clus                           MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 28(19Q12) MUTATED                              2
  AMP PEAK 28(19Q12) WILD-TYPE                            5
D28V9, multiclass
                                                    clus
vv                                                   AMP PEAK 28(19Q12) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                  6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                          28
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         73
  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                                               9
  LUNG SIGNET RING ADENOCARCINOMA                                             1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                               2
  MUCINOUS (COLLOID) CARCINOMA                                                2
                                                    clus
vv                                                   AMP PEAK 28(19Q12) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                    7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            65
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          221
  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                                                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"
D28V10, binary
                              cls
clus                             0   1
  AMP PEAK 28(19Q12) MUTATED     4 124
  AMP PEAK 28(19Q12) WILD-TYPE  17 317
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 28(19Q12) MUTATED      4  124
  AMP PEAK 28(19Q12) WILD-TYPE   17  317
     clus
vv    AMP PEAK 28(19Q12) MUTATED AMP PEAK 28(19Q12) WILD-TYPE
  NO                           4                           17
  YES                        124                          317
[1] 2 2
[1] FALSE
D28V11, continuous
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 28(19Q12) MUTATED    80   3   1   6
  AMP PEAK 28(19Q12) WILD-TYPE 238   8   3  13
D28V12, multiclass
    clus
vv   AMP PEAK 28(19Q12) MUTATED AMP PEAK 28(19Q12) WILD-TYPE
  R0                         80                          238
  R1                          3                            8
  R2                          1                            3
  RX                          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                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 28(19Q12) MUTATED                                  0     1
  AMP PEAK 28(19Q12) WILD-TYPE                                1     5
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 28(19Q12) MUTATED                           8   101
  AMP PEAK 28(19Q12) WILD-TYPE                        18   261
D28V13, multiclass
                                  clus
vv                                 AMP PEAK 28(19Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     1
  BLACK OR AFRICAN AMERICAN                                 8
  WHITE                                                   101
                                  clus
vv                                 AMP PEAK 28(19Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  18
  WHITE                                                     261
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V14, binary
                              cls
clus                             0   1
  AMP PEAK 28(19Q12) MUTATED     2  96
  AMP PEAK 28(19Q12) WILD-TYPE   5 236
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 28(19Q12) MUTATED      2   96
  AMP PEAK 28(19Q12) WILD-TYPE    5  236
                        clus
vv                       AMP PEAK 28(19Q12) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                         96
                        clus
vv                       AMP PEAK 28(19Q12) WILD-TYPE
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          236
[1] 2 2
[1] FALSE

Clustering(29) Variable = AMP PEAK 29(20P11.21) MUTATION ANALYSIS
D29V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 29(20P11.21) MUTATED   120  37
  AMP PEAK 29(20P11.21) WILD-TYPE 201  45
  AMP PEAK 29(20P11.21) MUTATED AMP PEAK 29(20P11.21) WILD-TYPE 
                            157                             246 
  AMP PEAK 29(20P11.21) MUTATED AMP PEAK 29(20P11.21) WILD-TYPE 
                             37                              45 
$`AMP PEAK 29(20P11.21) MUTATED`
TCGA-05-4249 TCGA-05-4389 TCGA-05-4390 TCGA-05-4417 TCGA-05-4424 TCGA-05-4430 
        1523         1369         1126          455          913          761 
TCGA-05-4432 TCGA-05-5420 TCGA-05-5425 TCGA-35-5375 TCGA-38-4625 TCGA-38-4627 
         761          457          882          264         1952         1147 
TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-44-2657 TCGA-44-3919 
        1073          354         1357          448          400          190 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6147 TCGA-44-6774 TCGA-44-6775 
         863          383          723          845          658          705 
TCGA-44-6778 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7671 
        1864          592          218          557         1970          535 
TCGA-44-7672 TCGA-44-8119 TCGA-44-A479 TCGA-44-A47B TCGA-44-A47F TCGA-44-A4SS 
         719           99          486          287          337          415 
TCGA-44-A4SU TCGA-49-4494 TCGA-49-4501 TCGA-49-4506 TCGA-49-4510 TCGA-49-6744 
          76         1081         1421          999          896          890 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5066 TCGA-50-5068 TCGA-50-5931 TCGA-50-5935 
        2174         2146          944         1499          267          653 
TCGA-50-5941 TCGA-50-5946 TCGA-50-7109 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
         567          686          255          424          280          701 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6969 TCGA-55-6972 
        1375           87            2          993         1239         1475 
TCGA-55-7284 TCGA-55-7574 TCGA-55-7724 TCGA-55-7726 TCGA-55-7995 TCGA-55-8085 
         121           95         1958           39            5           33 
TCGA-55-8087 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 
          21           26           47           15           33           46 
TCGA-55-8207 TCGA-55-8302 TCGA-55-8507 TCGA-55-8508 TCGA-55-8512 TCGA-55-8514 
          66           23            8           15            3          202 
TCGA-55-8614 TCGA-55-8615 TCGA-55-A48Z TCGA-55-A491 TCGA-55-A493 TCGA-55-A494 
         536           15           29         1952           28            5 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8399 TCGA-62-8402 TCGA-64-1677 TCGA-64-1678 
          47          162         2696         1445          628         1189 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 
        1968         1959           62           31          610          573 
TCGA-69-7764 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-73-4658 
         414           70           89          382          100         1600 
TCGA-73-4662 TCGA-73-4668 TCGA-73-4675 TCGA-73-4677 TCGA-73-7499 TCGA-75-7027 
         912          467           40           38          519         1956 
TCGA-75-7031 TCGA-78-7152 TCGA-78-7154 TCGA-78-7155 TCGA-78-7159 TCGA-78-7163 
        1965         1202         1948         1957         1221         1950 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
        1937         1965         1972         1949         1944          327 
TCGA-78-7542 TCGA-78-8640 TCGA-78-8660 TCGA-83-5908 TCGA-86-6851 TCGA-86-7713 
        1952         1949         1954          824         1959          422 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8073 TCGA-86-8075 TCGA-86-8358 TCGA-86-8585 
         745           10           13          479           19           35 
TCGA-86-8669 TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
          34         1940          310           79          417          372 
TCGA-91-6847 TCGA-91-8499 TCGA-91-A4BC TCGA-93-8067 TCGA-95-7039 TCGA-97-7546 
         842           36           44          186           34          964 
TCGA-97-7553 TCGA-97-7937 TCGA-97-8174 TCGA-97-8175 TCGA-97-8179 TCGA-97-8552 
        1332          181         1965           87           15          115 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4T2 TCGA-MP-A4T7 TCGA-MP-A4TE 
         285          622          353         1951         1954         1970 
TCGA-MP-A4TF 
        1970 

$`AMP PEAK 29(20P11.21) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 
         607          426         1947         1431          578          610 
TCGA-05-4410 TCGA-05-4415 TCGA-05-4420 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 
        1958         1997          912          365          669          791 
TCGA-05-4427 TCGA-05-4433 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
         791          730          151          670           30           62 
TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-38-4626 TCGA-38-4628 TCGA-38-4629 
          14          225          182         1962         1492          864 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2659 TCGA-44-2661 
        1971          133         1324         1429         1367          741 
TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 
        1280         1301           97          246         1130         1163 
TCGA-44-3918 TCGA-44-4112 TCGA-44-5643 TCGA-44-6145 TCGA-44-6146 TCGA-44-6148 
        1036          722         1013          328          302          704 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 TCGA-44-7661 TCGA-44-7670 
        1938         1942         1978          444          366          882 
TCGA-44-8117 TCGA-44-8120 TCGA-44-A47A TCGA-44-A47G TCGA-49-4486 TCGA-49-4505 
         385          260          466          351         1932          428 
TCGA-49-4507 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6745 
         268          157         1700          445          369          522 
TCGA-49-6761 TCGA-50-5051 TCGA-50-5055 TCGA-50-5072 TCGA-50-5930 TCGA-50-5932 
         354          455          785          246          282         1091 
TCGA-50-5933 TCGA-50-5942 TCGA-50-5944 TCGA-50-6597 TCGA-50-8460 TCGA-53-7624 
        2370          883          764         1015          105         1986 
TCGA-53-7626 TCGA-55-1594 TCGA-55-1595 TCGA-55-6712 TCGA-55-6971 TCGA-55-6980 
        1971         1178         1479           24           25           67 
TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 
        1826         1233         2151         1170           18           35 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7576 TCGA-55-7725 TCGA-55-7727 TCGA-55-7728 
           6            4           40           39           34           24 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
          54           19           16          197           21            3 
TCGA-55-7994 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8094 TCGA-55-8299 
          31          100            6           43            4          216 
TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 TCGA-55-8510 TCGA-55-8511 TCGA-55-8513 
          44           29           11          228            9          146 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
          48           49           66          106           33           42 
TCGA-55-A490 TCGA-55-A492 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-A46U 
          48            1         1216         1289         1970         2067 
TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1679 TCGA-64-1680 
        2199         1246          910         1728         1686         1126 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3773 TCGA-67-3774 
        1305          864         1559          866          427          385 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
         174          141          422          202          186          690 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
         165          230          184           77          129          214 
TCGA-71-6725 TCGA-73-4659 TCGA-73-4666 TCGA-73-4670 TCGA-73-4676 TCGA-73-7498 
          61          711          800          131          164          621 
TCGA-75-6214 TCGA-75-7025 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
        1970         1967         1973         1988         1950         1944 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7153 TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 
        1093         1963          760         1961         1963          678 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7166 TCGA-78-7540 TCGA-78-7633 TCGA-78-8648 
         215         1940         1934          881          994         1971 
TCGA-78-8655 TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 TCGA-86-7701 TCGA-86-7711 
        1981         1964         1965         1972           11          630 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8056 TCGA-86-8074 
        1968          591         1963          508         1963           24 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8281 TCGA-86-8359 
         489          476          482           16         1955           26 
TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
          45           18           15          455          405           10 
TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 TCGA-91-6848 
          30           14           39          323           60          224 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 
          35          492          197          174          218          297 
TCGA-93-7348 TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
         127            2          568          377          477          476 
TCGA-95-A4VK TCGA-97-7547 TCGA-97-7552 TCGA-97-7554 TCGA-97-7941 TCGA-97-8171 
         121         1965         1932          775           22          107 
TCGA-97-8172 TCGA-97-8177 TCGA-97-8547 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 
         182          147          148          197          271          392 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
         427          459           44          170          154          114 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
         287          282          238          578          435          116 
TCGA-L9-A444 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4T9 
           6         1946         1967         1954         1957         1980 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
        1951         1944          142         1955         1971         1490 

  AMP PEAK 29(20P11.21) MUTATED AMP PEAK 29(20P11.21) WILD-TYPE 
                              2                               1 
  AMP PEAK 29(20P11.21) MUTATED AMP PEAK 29(20P11.21) WILD-TYPE 
                           2696                            2370 
  AMP PEAK 29(20P11.21) MUTATED AMP PEAK 29(20P11.21) WILD-TYPE 
                          536.0                           439.5 
[1] "2.0 - 2696.0 (536.0)" "1.0 - 2370.0 (439.5)"
[1] "hr=" "1.5"
D29V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 29(20P11.21) MUTATED         3       46       63        17        22
  AMP PEAK 29(20P11.21) WILD-TYPE       1       67       68        26        47
                                 vv
clus                              STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 29(20P11.21) MUTATED           19          3        6
  AMP PEAK 29(20P11.21) WILD-TYPE         48          8       17
D29V3, multiclass
            clus
vv           AMP PEAK 29(20P11.21) MUTATED AMP PEAK 29(20P11.21) WILD-TYPE
  STAGE I                                3                               1
  STAGE IA                              46                              67
  STAGE IB                              63                              68
  STAGE IIA                             17                              26
  STAGE IIB                             22                              47
  STAGE IIIA                            19                              48
  STAGE IIIB                             3                               8
  STAGE IV                               6                              17
[1] 8 2
[1] TRUE
[1] "dimension of 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(20P11.21) MUTATED    54 110  12   3
  AMP PEAK 29(20P11.21) WILD-TYPE  89 149  28  15
D29V4, multiclass
    clus
vv   AMP PEAK 29(20P11.21) MUTATED AMP PEAK 29(20P11.21) WILD-TYPE
  T1                            54                              89
  T2                           110                             149
  T3                            12                              28
  T4                             3                              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(20P11.21) MUTATED   126  30    18
  AMP PEAK 29(20P11.21) WILD-TYPE 169  55    54
D29V5, multiclass
       clus
vv      AMP PEAK 29(20P11.21) MUTATED AMP PEAK 29(20P11.21) WILD-TYPE
  N0                              126                             169
  N1                               30                              55
  N2+N3                            18                              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"
                                 vv
clus                               M0  M1 M1A M1B  MX
  AMP PEAK 29(20P11.21) MUTATED   117   5   0   1  53
  AMP PEAK 29(20P11.21) WILD-TYPE 200  13   1   2  66
D29V6, multiclass
     clus
vv    AMP PEAK 29(20P11.21) MUTATED AMP PEAK 29(20P11.21) WILD-TYPE
  M0                            117                             200
  M1                              5                              13
  M1A                             0                               1
  M1B                             1                               2
  MX                             53                              66
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V7, binary
                                 cls
clus                                0   1
  AMP PEAK 29(20P11.21) MUTATED    92  87
  AMP PEAK 29(20P11.21) WILD-TYPE 156 127
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 29(20P11.21) MUTATED     92   87
  AMP PEAK 29(20P11.21) WILD-TYPE  156  127
        clus
vv       AMP PEAK 29(20P11.21) MUTATED AMP PEAK 29(20P11.21) WILD-TYPE
  FEMALE                            92                             156
  MALE                              87                             127
[1] 2 2
[1] FALSE
D29V8, continuous
                                 vv
clus                              LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 29(20P11.21) MUTATED                            6
  AMP PEAK 29(20P11.21) WILD-TYPE                          7
                                 vv
clus                              LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 29(20P11.21) MUTATED                                  27
  AMP PEAK 29(20P11.21) WILD-TYPE                                66
                                 vv
clus                              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 29(20P11.21) MUTATED                                                  124
  AMP PEAK 29(20P11.21) WILD-TYPE                                                170
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 29(20P11.21) MUTATED                                            1
  AMP PEAK 29(20P11.21) WILD-TYPE                                          3
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 29(20P11.21) MUTATED                                               7
  AMP PEAK 29(20P11.21) WILD-TYPE                                            12
                                 vv
clus                              LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 29(20P11.21) MUTATED                                0
  AMP PEAK 29(20P11.21) WILD-TYPE                              2
                                 vv
clus                              LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 29(20P11.21) MUTATED                                    2
  AMP PEAK 29(20P11.21) WILD-TYPE                                  2
                                 vv
clus                              LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 29(20P11.21) MUTATED                              0
  AMP PEAK 29(20P11.21) WILD-TYPE                            2
                                 vv
clus                              LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 29(20P11.21) MUTATED                               7
  AMP PEAK 29(20P11.21) WILD-TYPE                            12
                                 vv
clus                              LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 29(20P11.21) MUTATED                                 1
  AMP PEAK 29(20P11.21) WILD-TYPE                               0
                                 vv
clus                              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 29(20P11.21) MUTATED                                               3
  AMP PEAK 29(20P11.21) WILD-TYPE                                             1
                                 vv
clus                              MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 29(20P11.21) MUTATED                              1
  AMP PEAK 29(20P11.21) WILD-TYPE                            6
D29V9, multiclass
                                                    clus
vv                                                   AMP PEAK 29(20P11.21) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                     6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             27
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           124
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  7
  LUNG CLEAR CELL ADENOCARCINOMA                                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             2
  LUNG MUCINOUS ADENOCARCINOMA                                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                                  7
  LUNG SIGNET RING ADENOCARCINOMA                                                1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                  3
  MUCINOUS (COLLOID) CARCINOMA                                                   1
                                                    clus
vv                                                   AMP PEAK 29(20P11.21) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                       7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                               66
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             170
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                       3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                   12
  LUNG CLEAR CELL ADENOCARCINOMA                                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                               2
  LUNG MUCINOUS ADENOCARCINOMA                                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                                   12
  LUNG SIGNET RING ADENOCARCINOMA                                                  0
  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"
D29V10, binary
                                 cls
clus                                0   1
  AMP PEAK 29(20P11.21) MUTATED     7 172
  AMP PEAK 29(20P11.21) WILD-TYPE  14 269
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 29(20P11.21) MUTATED      7  172
  AMP PEAK 29(20P11.21) WILD-TYPE   14  269
     clus
vv    AMP PEAK 29(20P11.21) MUTATED AMP PEAK 29(20P11.21) WILD-TYPE
  NO                              7                              14
  YES                           172                             269
[1] 2 2
[1] FALSE
D29V11, continuous
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 29(20P11.21) MUTATED   116   6   2   6
  AMP PEAK 29(20P11.21) WILD-TYPE 202   5   2  13
D29V12, multiclass
    clus
vv   AMP PEAK 29(20P11.21) MUTATED AMP PEAK 29(20P11.21) WILD-TYPE
  R0                           116                             202
  R1                             6                               5
  R2                             2                               2
  RX                             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                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 29(20P11.21) MUTATED                                  1     2
  AMP PEAK 29(20P11.21) WILD-TYPE                                0     4
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 29(20P11.21) MUTATED                          14   139
  AMP PEAK 29(20P11.21) WILD-TYPE                        12   223
D29V13, multiclass
                                  clus
vv                                 AMP PEAK 29(20P11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   14
  WHITE                                                      139
                                  clus
vv                                 AMP PEAK 29(20P11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          4
  BLACK OR AFRICAN AMERICAN                                     12
  WHITE                                                        223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V14, binary
                                 cls
clus                                0   1
  AMP PEAK 29(20P11.21) MUTATED     2 131
  AMP PEAK 29(20P11.21) WILD-TYPE   5 201
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 29(20P11.21) MUTATED      2  131
  AMP PEAK 29(20P11.21) WILD-TYPE    5  201
                        clus
vv                       AMP PEAK 29(20P11.21) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           131
                        clus
vv                       AMP PEAK 29(20P11.21) WILD-TYPE
  HISPANIC OR LATINO                                   5
  NOT HISPANIC OR LATINO                             201
[1] 2 2
[1] FALSE

Clustering(30) Variable = AMP PEAK 30(20Q13.33) MUTATION ANALYSIS
D30V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 30(20Q13.33) MUTATED   157  38
  AMP PEAK 30(20Q13.33) WILD-TYPE 164  44
  AMP PEAK 30(20Q13.33) MUTATED AMP PEAK 30(20Q13.33) WILD-TYPE 
                            195                             208 
  AMP PEAK 30(20Q13.33) MUTATED AMP PEAK 30(20Q13.33) WILD-TYPE 
                             38                              44 
$`AMP PEAK 30(20Q13.33) MUTATED`
TCGA-05-4389 TCGA-05-4390 TCGA-05-4405 TCGA-05-4415 TCGA-05-4420 TCGA-05-4422 
        1369         1126          610         1997          912          365 
TCGA-05-4424 TCGA-05-4432 TCGA-05-5423 TCGA-05-5428 TCGA-35-5375 TCGA-38-4625 
         913          761          151          670          264         1952 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4631 TCGA-38-6178 TCGA-44-2656 
        1147         1492          864          354          448         1429 
TCGA-44-2657 TCGA-44-2662 TCGA-44-3918 TCGA-44-3919 TCGA-44-5644 TCGA-44-5645 
         400         1280         1036          190          863          383 
TCGA-44-6144 TCGA-44-6147 TCGA-44-6774 TCGA-44-6775 TCGA-44-6778 TCGA-44-7660 
         723          845          658          705         1864          592 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
         218          557         1970          882          535          719 
TCGA-44-8117 TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
         385           99          486          466          287          337 
TCGA-44-A4SU TCGA-49-4494 TCGA-49-4501 TCGA-49-4506 TCGA-49-4510 TCGA-49-4512 
          76         1081         1421          999          896          157 
TCGA-49-4514 TCGA-50-5045 TCGA-50-5049 TCGA-50-5066 TCGA-50-5068 TCGA-50-5931 
        1700         2174         2146          944         1499          267 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 TCGA-50-6597 
        2370          653          567          764          686         1015 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 
         424          280          701         1178         1375           87 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6972 TCGA-55-7284 
           2          993           24         1239         1475          121 
TCGA-55-7724 TCGA-55-7726 TCGA-55-7907 TCGA-55-7910 TCGA-55-7995 TCGA-55-8085 
        1958           39           16          197            5           33 
TCGA-55-8087 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 
          21           26           47           15           33           46 
TCGA-55-8207 TCGA-55-8302 TCGA-55-8507 TCGA-55-8508 TCGA-55-8512 TCGA-55-8514 
          66           23            8           15            3          202 
TCGA-55-8615 TCGA-55-8620 TCGA-55-A48Z TCGA-55-A491 TCGA-55-A493 TCGA-55-A494 
          15           66           29         1952           28            5 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8397 TCGA-62-8399 TCGA-62-8402 TCGA-64-1676 
          47          162         1289         2696         1445         1728 
TCGA-64-1677 TCGA-64-1678 TCGA-64-1681 TCGA-64-5774 TCGA-64-5779 TCGA-64-5781 
         628         1189         1968         1959          864         1559 
TCGA-67-3771 TCGA-67-3772 TCGA-67-6215 TCGA-67-6216 TCGA-69-7761 TCGA-69-7763 
         610          573          174          141          186          690 
TCGA-69-7764 TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
         414          230           70           89          382          100 
TCGA-69-8255 TCGA-71-6725 TCGA-73-4658 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
         129           61         1600          912          800          467 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4677 TCGA-73-7499 TCGA-75-6214 TCGA-75-7031 
         131           40           38          519         1970         1965 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7159 TCGA-78-7161 
        1202          760         1948         1957         1221          215 
TCGA-78-7163 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7542 
        1950         1965         1972         1949         1944         1952 
TCGA-78-8640 TCGA-78-8660 TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 TCGA-86-7954 
        1949         1954         1972          824         1959         1963 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8073 TCGA-86-8075 TCGA-86-8278 
         508          745           10           13          479          476 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 TCGA-86-8669 TCGA-91-6828 
         482           16           26           35           34          323 
TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6847 TCGA-91-7771 
        1940          310           79          417          842          492 
TCGA-91-8499 TCGA-91-A4BC TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 
          36           44          186           34            2          568 
TCGA-95-7947 TCGA-97-7546 TCGA-97-7553 TCGA-97-7937 TCGA-97-8175 TCGA-97-8177 
         477          964         1332          181           87          147 
TCGA-97-8179 TCGA-97-8552 TCGA-99-8025 TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L9-A444 
          15          115          427          282          578            6 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4T2 TCGA-MP-A4T7 
         285          622          353         1946         1951         1954 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
        1970         1970          142 

$`AMP PEAK 30(20Q13.33) WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4398 TCGA-05-4403 
        1523          607          426         1947         1431          578 
TCGA-05-4410 TCGA-05-4417 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 
        1958          455          669          791          791          761 
TCGA-05-4433 TCGA-05-5420 TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
         730          457          882           30           62           14 
TCGA-35-4122 TCGA-35-4123 TCGA-38-4626 TCGA-38-4630 TCGA-38-4632 TCGA-38-7271 
         225          182         1962         1073         1357         1971 
TCGA-38-A44F TCGA-44-2655 TCGA-44-2659 TCGA-44-2661 TCGA-44-2665 TCGA-44-2666 
         133         1324         1367          741         1301           97 
TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-4112 TCGA-44-5643 TCGA-44-6145 
         246         1130         1163          722         1013          328 
TCGA-44-6146 TCGA-44-6148 TCGA-44-6776 TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 
         302          704         1938         1942         1978          444 
TCGA-44-7661 TCGA-44-8120 TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4505 
         366          260          351          415         1932          428 
TCGA-49-4507 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
         268          445          369          890          522          354 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5072 TCGA-50-5930 TCGA-50-5932 TCGA-50-5942 
         455          785          246          282         1091          883 
TCGA-50-7109 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-55-1595 TCGA-55-6971 
         255          105         1986         1971         1479           25 
TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 
          67         1826         1233         2151         1170           18 
TCGA-55-7283 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7725 
          35            6            4           95           40           39 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 TCGA-55-7914 
          34           24           54           19           21            3 
TCGA-55-7994 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8094 TCGA-55-8299 
          31          100            6           43            4          216 
TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 TCGA-55-8510 TCGA-55-8511 TCGA-55-8513 
          44           29           11          228            9          146 
TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
         536           48           49          106           33           42 
TCGA-55-A490 TCGA-55-A492 TCGA-62-8395 TCGA-62-8398 TCGA-62-A46U TCGA-62-A46V 
          48            1         1216         1970         2067         2199 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1679 TCGA-64-1680 TCGA-64-5775 TCGA-64-5778 
        1246          910         1686         1126           62         1305 
TCGA-64-5815 TCGA-67-3770 TCGA-67-3773 TCGA-67-3774 TCGA-67-6217 TCGA-69-7760 
         866           31          427          385          422          202 
TCGA-69-7765 TCGA-69-7974 TCGA-69-8254 TCGA-69-A59K TCGA-73-4659 TCGA-73-4676 
         165          184           77          214          711          164 
TCGA-73-7498 TCGA-75-7025 TCGA-75-7027 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
         621         1967         1956         1973         1988         1950 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 
        1944         1093         1963         1961         1963          678 
TCGA-78-7162 TCGA-78-7166 TCGA-78-7167 TCGA-78-7539 TCGA-78-7540 TCGA-78-7633 
        1940         1934         1937          327          881          994 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5607 TCGA-86-7701 TCGA-86-7711 
        1971         1981         1964         1965           11          630 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-8056 TCGA-86-8074 TCGA-86-8076 
         422         1968          591         1963           24          489 
TCGA-86-8281 TCGA-86-8358 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1955           19           45           18           15          455 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6830 
         405           10           30           14           39           60 
TCGA-91-6840 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD 
         372          224           35          197          174          218 
TCGA-93-7347 TCGA-93-7348 TCGA-95-7944 TCGA-95-7948 TCGA-95-A4VK TCGA-97-7547 
         297          127          377          476          121         1965 
TCGA-97-7552 TCGA-97-7554 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        1932          775           22          107          182         1965 
TCGA-97-8547 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 
         148          197          271          392          459           44 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L4-A4E6 
         170          154          114          287          238          435 
TCGA-L9-A443 TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
         116         1967         1954         1957         1980         1951 
TCGA-MP-A4TC TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
        1944         1955         1971         1490 

  AMP PEAK 30(20Q13.33) MUTATED AMP PEAK 30(20Q13.33) WILD-TYPE 
                              2                               1 
  AMP PEAK 30(20Q13.33) MUTATED AMP PEAK 30(20Q13.33) WILD-TYPE 
                           2696                            2199 
  AMP PEAK 30(20Q13.33) MUTATED AMP PEAK 30(20Q13.33) WILD-TYPE 
                          535.0                           426.5 
[1] "2.0 - 2696.0 (535.0)" "1.0 - 2199.0 (426.5)"
[1] "hr=" "1"  
D30V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 30(20Q13.33) MUTATED         3       57       74        21        31
  AMP PEAK 30(20Q13.33) WILD-TYPE       1       56       57        22        38
                                 vv
clus                              STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 30(20Q13.33) MUTATED           25          5        7
  AMP PEAK 30(20Q13.33) WILD-TYPE         42          6       16
D30V3, multiclass
            clus
vv           AMP PEAK 30(20Q13.33) MUTATED AMP PEAK 30(20Q13.33) WILD-TYPE
  STAGE I                                3                               1
  STAGE IA                              57                              56
  STAGE IB                              74                              57
  STAGE IIA                             21                              22
  STAGE IIB                             31                              38
  STAGE IIIA                            25                              42
  STAGE IIIB                             5                               6
  STAGE IV                               7                              16
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  AMP PEAK 30(20Q13.33) MUTATED    68 131  19   4
  AMP PEAK 30(20Q13.33) WILD-TYPE  75 128  21  14
D30V4, multiclass
    clus
vv   AMP PEAK 30(20Q13.33) MUTATED AMP PEAK 30(20Q13.33) WILD-TYPE
  T1                            68                              75
  T2                           131                             128
  T3                            19                              21
  T4                             4                              14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1 N2+N3
  AMP PEAK 30(20Q13.33) MUTATED   152  39    28
  AMP PEAK 30(20Q13.33) WILD-TYPE 143  46    44
D30V5, multiclass
       clus
vv      AMP PEAK 30(20Q13.33) MUTATED AMP PEAK 30(20Q13.33) WILD-TYPE
  N0                              152                             143
  N1                               39                              46
  N2+N3                            28                              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"
                                 vv
clus                               M0  M1 M1A M1B  MX
  AMP PEAK 30(20Q13.33) MUTATED   153   5   0   2  60
  AMP PEAK 30(20Q13.33) WILD-TYPE 164  13   1   1  59
D30V6, multiclass
     clus
vv    AMP PEAK 30(20Q13.33) MUTATED AMP PEAK 30(20Q13.33) WILD-TYPE
  M0                            153                             164
  M1                              5                              13
  M1A                             0                               1
  M1B                             2                               1
  MX                             60                              59
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V7, binary
                                 cls
clus                                0   1
  AMP PEAK 30(20Q13.33) MUTATED   119 104
  AMP PEAK 30(20Q13.33) WILD-TYPE 129 110
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 30(20Q13.33) MUTATED    119  104
  AMP PEAK 30(20Q13.33) WILD-TYPE  129  110
        clus
vv       AMP PEAK 30(20Q13.33) MUTATED AMP PEAK 30(20Q13.33) WILD-TYPE
  FEMALE                           119                             129
  MALE                             104                             110
[1] 2 2
[1] FALSE
D30V8, continuous
                                 vv
clus                              LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 30(20Q13.33) MUTATED                            9
  AMP PEAK 30(20Q13.33) WILD-TYPE                          4
                                 vv
clus                              LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 30(20Q13.33) MUTATED                                  38
  AMP PEAK 30(20Q13.33) WILD-TYPE                                55
                                 vv
clus                              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 30(20Q13.33) MUTATED                                                  149
  AMP PEAK 30(20Q13.33) WILD-TYPE                                                145
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 30(20Q13.33) MUTATED                                            1
  AMP PEAK 30(20Q13.33) WILD-TYPE                                          3
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 30(20Q13.33) MUTATED                                              10
  AMP PEAK 30(20Q13.33) WILD-TYPE                                             9
                                 vv
clus                              LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 30(20Q13.33) MUTATED                                0
  AMP PEAK 30(20Q13.33) WILD-TYPE                              2
                                 vv
clus                              LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 30(20Q13.33) MUTATED                                    2
  AMP PEAK 30(20Q13.33) WILD-TYPE                                  2
                                 vv
clus                              LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 30(20Q13.33) MUTATED                              0
  AMP PEAK 30(20Q13.33) WILD-TYPE                            2
                                 vv
clus                              LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 30(20Q13.33) MUTATED                               8
  AMP PEAK 30(20Q13.33) WILD-TYPE                            11
                                 vv
clus                              LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 30(20Q13.33) MUTATED                                 1
  AMP PEAK 30(20Q13.33) WILD-TYPE                               0
                                 vv
clus                              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 30(20Q13.33) MUTATED                                               4
  AMP PEAK 30(20Q13.33) WILD-TYPE                                             0
                                 vv
clus                              MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 30(20Q13.33) MUTATED                              1
  AMP PEAK 30(20Q13.33) WILD-TYPE                            6
D30V9, multiclass
                                                    clus
vv                                                   AMP PEAK 30(20Q13.33) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                     9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             38
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           149
  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                                                  8
  LUNG SIGNET RING ADENOCARCINOMA                                                1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                  4
  MUCINOUS (COLLOID) CARCINOMA                                                   1
                                                    clus
vv                                                   AMP PEAK 30(20Q13.33) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                       4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                               55
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             145
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                       3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                    9
  LUNG CLEAR CELL ADENOCARCINOMA                                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                               2
  LUNG MUCINOUS ADENOCARCINOMA                                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                                   11
  LUNG SIGNET RING ADENOCARCINOMA                                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                    0
  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"
D30V10, binary
                                 cls
clus                                0   1
  AMP PEAK 30(20Q13.33) MUTATED     9 214
  AMP PEAK 30(20Q13.33) WILD-TYPE  12 227
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 30(20Q13.33) MUTATED      9  214
  AMP PEAK 30(20Q13.33) WILD-TYPE   12  227
     clus
vv    AMP PEAK 30(20Q13.33) MUTATED AMP PEAK 30(20Q13.33) WILD-TYPE
  NO                              9                              12
  YES                           214                             227
[1] 2 2
[1] FALSE
D30V11, continuous
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 30(20Q13.33) MUTATED   146   6   2   9
  AMP PEAK 30(20Q13.33) WILD-TYPE 172   5   2  10
D30V12, multiclass
    clus
vv   AMP PEAK 30(20Q13.33) MUTATED AMP PEAK 30(20Q13.33) WILD-TYPE
  R0                           146                             172
  R1                             6                               5
  R2                             2                               2
  RX                             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                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 30(20Q13.33) MUTATED                                  1     3
  AMP PEAK 30(20Q13.33) WILD-TYPE                                0     3
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 30(20Q13.33) MUTATED                          15   175
  AMP PEAK 30(20Q13.33) WILD-TYPE                        11   187
D30V13, multiclass
                                  clus
vv                                 AMP PEAK 30(20Q13.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        3
  BLACK OR AFRICAN AMERICAN                                   15
  WHITE                                                      175
                                  clus
vv                                 AMP PEAK 30(20Q13.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          3
  BLACK OR AFRICAN AMERICAN                                     11
  WHITE                                                        187
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V14, binary
                                 cls
clus                                0   1
  AMP PEAK 30(20Q13.33) MUTATED     4 164
  AMP PEAK 30(20Q13.33) WILD-TYPE   3 168
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 30(20Q13.33) MUTATED      4  164
  AMP PEAK 30(20Q13.33) WILD-TYPE    3  168
                        clus
vv                       AMP PEAK 30(20Q13.33) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           164
                        clus
vv                       AMP PEAK 30(20Q13.33) WILD-TYPE
  HISPANIC OR LATINO                                   3
  NOT HISPANIC OR LATINO                             168
[1] 2 2
[1] FALSE

Clustering(31) Variable = AMP PEAK 31(22Q11.22) MUTATION ANALYSIS
D31V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 31(22Q11.22) MUTATED    54  17
  AMP PEAK 31(22Q11.22) WILD-TYPE 267  65
  AMP PEAK 31(22Q11.22) MUTATED AMP PEAK 31(22Q11.22) WILD-TYPE 
                             71                             332 
  AMP PEAK 31(22Q11.22) MUTATED AMP PEAK 31(22Q11.22) WILD-TYPE 
                             17                              65 
$`AMP PEAK 31(22Q11.22) MUTATED`
TCGA-05-4398 TCGA-05-4410 TCGA-05-4420 TCGA-05-5428 TCGA-38-4625 TCGA-38-A44F 
        1431         1958          912          670         1952          133 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-5644 TCGA-44-6147 TCGA-44-6777 
        1163         1036          190          863          845         1942 
TCGA-44-6779 TCGA-44-7662 TCGA-44-7669 TCGA-44-7670 TCGA-44-8117 TCGA-44-A47A 
        1978          218         1970          882          385          466 
TCGA-44-A47F TCGA-49-6742 TCGA-49-6743 TCGA-50-5931 TCGA-50-5944 TCGA-50-5946 
         337          445          369          267          764          686 
TCGA-55-1592 TCGA-55-1596 TCGA-55-6712 TCGA-55-7574 TCGA-55-7724 TCGA-55-7726 
         701         1375           24           95         1958           39 
TCGA-55-7907 TCGA-55-8091 TCGA-55-8096 TCGA-55-8506 TCGA-55-8511 TCGA-55-8514 
          16           43           47           11            9          202 
TCGA-55-8614 TCGA-55-A490 TCGA-55-A491 TCGA-62-8397 TCGA-62-8398 TCGA-62-8402 
         536           48         1952         1289         1970         1445 
TCGA-64-1679 TCGA-67-3770 TCGA-67-3771 TCGA-69-7979 TCGA-69-8253 TCGA-73-4675 
        1686           31          610           89          100           40 
TCGA-75-7031 TCGA-78-7150 TCGA-78-7154 TCGA-78-7155 TCGA-78-7536 TCGA-78-8662 
        1965         1963         1948         1957         1949         1964 
TCGA-86-7713 TCGA-86-7955 TCGA-86-8055 TCGA-86-8280 TCGA-86-8358 TCGA-86-A4D0 
         422          508           10           16           19           30 
TCGA-91-6847 TCGA-95-7567 TCGA-95-7944 TCGA-97-7553 TCGA-97-8174 TCGA-97-8552 
         842          568          377         1332         1965          115 
TCGA-J2-A4AE TCGA-MP-A4SW TCGA-MP-A4T7 TCGA-MP-A4TC TCGA-MP-A5C7 
         282         1967         1954         1944         1490 

$`AMP PEAK 31(22Q11.22) WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 
        1523          607          426         1369         1126         1947 
TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4422 TCGA-05-4424 
         578          610         1997          455          365          913 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
         669          791          791          761          761          730 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
         457          151          882           30           62           14 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
         225          182          264         1962         1147         1492 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
         864         1073          354         1357          448         1971 
TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 
        1324         1429          400         1367          741         1280 
TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-4112 TCGA-44-5643 
        1301           97          246         1130          722         1013 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6148 TCGA-44-6774 
         383          723          328          302          704          658 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6778 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
         705         1938         1864          444          592          366 
TCGA-44-7667 TCGA-44-7671 TCGA-44-7672 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 
         557          535          719           99          260          486 
TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 
         287          351          415           76         1932         1081 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
        1421          428          999          268          896          157 
TCGA-49-4514 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-50-5045 TCGA-50-5049 
        1700          890          522          354         2174         2146 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
         455          785          944         1499          246          282 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 TCGA-50-6597 
        1091         2370          653          567          883         1015 
TCGA-50-7109 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
         255          105         1986         1971          424          280 
TCGA-55-1594 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6969 
        1178         1479           87            2          993         1239 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 
          25         1475           67         1826         1233         2151 
TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1170           18           35          121            6            4 
TCGA-55-7576 TCGA-55-7725 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 
          40           39           34           24           54           19 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
         197           21            3           31            5           33 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8092 TCGA-55-8094 TCGA-55-8097 
          21          100            6           26            4           15 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
          33           46           66          216           44           23 
TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 
          29            8           15          228            3          146 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
          15           48           49           66          106           33 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
          42           29            1           28            5           47 
TCGA-55-A4DG TCGA-62-8395 TCGA-62-8399 TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 
         162         1216         2696         2067         2199         1246 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-1680 TCGA-64-1681 
         910         1728          628         1189         1126         1968 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
        1959           62         1305          864         1559          866 
TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
         573          427          385          174          141          422 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
         202          186          690          414          165          230 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
         184           70          382           77          129          214 
TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
          61         1600          711          912          800          467 
TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-75-6214 
         131          164           38          621          519         1970 
TCGA-75-7025 TCGA-75-7027 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
        1967         1956         1973         1988         1950         1944 
TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
        1093         1202          760         1961         1963         1221 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
         678          215         1940         1950         1934         1937 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
        1965         1972         1944          327          881         1952 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-80-5607 
         994         1949         1971         1981         1954         1965 
TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 
        1972          824         1959           11          630         1968 
TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
         591         1963          745         1963           13           24 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8281 TCGA-86-8359 
         479          489          476          482         1955           26 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
          35           45           34           18           15          455 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
         405           10           14           39          323         1940 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6848 
          60          310           79          417          372          224 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
          35          492          197          174           36           44 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 
         218          297          127          186           34            2 
TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
         477          476          121          964         1965         1932 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 
         775          181           22          107          182           87 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 
         147           15          148          197          271          392 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
         427          459           44          170          154          114 
TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
         287          238          578          435          116            6 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4T2 TCGA-MP-A4T4 
         285          622          353         1946         1951         1954 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
        1957         1980         1951         1970         1970          142 
TCGA-MP-A4TI TCGA-MP-A4TK 
        1955         1971 

  AMP PEAK 31(22Q11.22) MUTATED AMP PEAK 31(22Q11.22) WILD-TYPE 
                              9                               1 
  AMP PEAK 31(22Q11.22) MUTATED AMP PEAK 31(22Q11.22) WILD-TYPE 
                           1978                            2696 
  AMP PEAK 31(22Q11.22) MUTATED AMP PEAK 31(22Q11.22) WILD-TYPE 
                          670.0                           451.5 
[1] "9.0 - 1978.0 (670.0)" "1.0 - 2696.0 (451.5)"
[1] "hr=" "1.2"
D31V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 31(22Q11.22) MUTATED         1       16       28        13        12
  AMP PEAK 31(22Q11.22) WILD-TYPE       3       97      103        30        57
                                 vv
clus                              STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 31(22Q11.22) MUTATED           12          1        1
  AMP PEAK 31(22Q11.22) WILD-TYPE         55         10       22
D31V3, multiclass
            clus
vv           AMP PEAK 31(22Q11.22) MUTATED AMP PEAK 31(22Q11.22) WILD-TYPE
  STAGE I                                1                               3
  STAGE IA                              16                              97
  STAGE IB                              28                             103
  STAGE IIA                             13                              30
  STAGE IIB                             12                              57
  STAGE IIIA                            12                              55
  STAGE IIIB                             1                              10
  STAGE IV                               1                              22
[1] 8 2
[1] TRUE
[1] "dimension of 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 31(22Q11.22) MUTATED    24  53   6   1
  AMP PEAK 31(22Q11.22) WILD-TYPE 119 206  34  17
D31V4, multiclass
    clus
vv   AMP PEAK 31(22Q11.22) MUTATED AMP PEAK 31(22Q11.22) WILD-TYPE
  T1                            24                             119
  T2                            53                             206
  T3                             6                              34
  T4                             1                              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 31(22Q11.22) MUTATED    52  18    12
  AMP PEAK 31(22Q11.22) WILD-TYPE 243  67    60
D31V5, multiclass
       clus
vv      AMP PEAK 31(22Q11.22) MUTATED AMP PEAK 31(22Q11.22) WILD-TYPE
  N0                               52                             243
  N1                               18                              67
  N2+N3                            12                              60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               M0  M1 M1A M1B  MX
  AMP PEAK 31(22Q11.22) MUTATED    54   1   0   0  28
  AMP PEAK 31(22Q11.22) WILD-TYPE 263  17   1   3  91
D31V6, multiclass
     clus
vv    AMP PEAK 31(22Q11.22) MUTATED AMP PEAK 31(22Q11.22) WILD-TYPE
  M0                             54                             263
  M1                              1                              17
  M1A                             0                               1
  M1B                             0                               3
  MX                             28                              91
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V7, binary
                                 cls
clus                                0   1
  AMP PEAK 31(22Q11.22) MUTATED    50  34
  AMP PEAK 31(22Q11.22) WILD-TYPE 198 180
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 31(22Q11.22) MUTATED     50   34
  AMP PEAK 31(22Q11.22) WILD-TYPE  198  180
        clus
vv       AMP PEAK 31(22Q11.22) MUTATED AMP PEAK 31(22Q11.22) WILD-TYPE
  FEMALE                            50                             198
  MALE                              34                             180
[1] 2 2
[1] FALSE
D31V8, continuous
                                 vv
clus                              LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 31(22Q11.22) MUTATED                            2
  AMP PEAK 31(22Q11.22) WILD-TYPE                         11
                                 vv
clus                              LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 31(22Q11.22) MUTATED                                  11
  AMP PEAK 31(22Q11.22) WILD-TYPE                                82
                                 vv
clus                              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 31(22Q11.22) MUTATED                                                   64
  AMP PEAK 31(22Q11.22) WILD-TYPE                                                230
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 31(22Q11.22) MUTATED                                            0
  AMP PEAK 31(22Q11.22) WILD-TYPE                                          4
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 31(22Q11.22) MUTATED                                               3
  AMP PEAK 31(22Q11.22) WILD-TYPE                                            16
                                 vv
clus                              LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 31(22Q11.22) MUTATED                                1
  AMP PEAK 31(22Q11.22) WILD-TYPE                              1
                                 vv
clus                              LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 31(22Q11.22) MUTATED                                    1
  AMP PEAK 31(22Q11.22) WILD-TYPE                                  3
                                 vv
clus                              LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 31(22Q11.22) MUTATED                              0
  AMP PEAK 31(22Q11.22) WILD-TYPE                            2
                                 vv
clus                              LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 31(22Q11.22) MUTATED                               1
  AMP PEAK 31(22Q11.22) WILD-TYPE                            18
                                 vv
clus                              LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 31(22Q11.22) MUTATED                                 0
  AMP PEAK 31(22Q11.22) WILD-TYPE                               1
                                 vv
clus                              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 31(22Q11.22) MUTATED                                               0
  AMP PEAK 31(22Q11.22) WILD-TYPE                                             4
                                 vv
clus                              MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 31(22Q11.22) MUTATED                              1
  AMP PEAK 31(22Q11.22) WILD-TYPE                            6
D31V9, multiclass
                                                    clus
vv                                                   AMP PEAK 31(22Q11.22) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                     2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             11
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            64
  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 31(22Q11.22) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                               82
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             230
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                       4
  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                                                     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"
D31V10, binary
                                 cls
clus                                0   1
  AMP PEAK 31(22Q11.22) MUTATED     3  81
  AMP PEAK 31(22Q11.22) WILD-TYPE  18 360
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 31(22Q11.22) MUTATED      3   81
  AMP PEAK 31(22Q11.22) WILD-TYPE   18  360
     clus
vv    AMP PEAK 31(22Q11.22) MUTATED AMP PEAK 31(22Q11.22) WILD-TYPE
  NO                              3                              18
  YES                            81                             360
[1] 2 2
[1] FALSE
D31V11, continuous
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 31(22Q11.22) MUTATED    58   1   0   3
  AMP PEAK 31(22Q11.22) WILD-TYPE 260  10   4  16
D31V12, multiclass
    clus
vv   AMP PEAK 31(22Q11.22) MUTATED AMP PEAK 31(22Q11.22) WILD-TYPE
  R0                            58                             260
  R1                             1                              10
  R2                             0                               4
  RX                             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                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 31(22Q11.22) MUTATED                                  0     1
  AMP PEAK 31(22Q11.22) WILD-TYPE                                1     5
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 31(22Q11.22) MUTATED                           5    67
  AMP PEAK 31(22Q11.22) WILD-TYPE                        21   295
D31V13, multiclass
                                  clus
vv                                 AMP PEAK 31(22Q11.22) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                    5
  WHITE                                                       67
                                  clus
vv                                 AMP PEAK 31(22Q11.22) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          5
  BLACK OR AFRICAN AMERICAN                                     21
  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"
D31V14, binary
                                 cls
clus                                0   1
  AMP PEAK 31(22Q11.22) MUTATED     1  58
  AMP PEAK 31(22Q11.22) WILD-TYPE   6 274
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 31(22Q11.22) MUTATED      1   58
  AMP PEAK 31(22Q11.22) WILD-TYPE    6  274
                        clus
vv                       AMP PEAK 31(22Q11.22) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            58
                        clus
vv                       AMP PEAK 31(22Q11.22) WILD-TYPE
  HISPANIC OR LATINO                                   6
  NOT HISPANIC OR LATINO                             274
[1] 2 2
[1] FALSE

Clustering(32) Variable = AMP PEAK 32(XQ28) MUTATION ANALYSIS
D32V1, survival
                             sevent
clus2                           0   1
  AMP PEAK 32(XQ28) MUTATED    94  30
  AMP PEAK 32(XQ28) WILD-TYPE 227  52
  AMP PEAK 32(XQ28) MUTATED AMP PEAK 32(XQ28) WILD-TYPE 
                        124                         279 
  AMP PEAK 32(XQ28) MUTATED AMP PEAK 32(XQ28) WILD-TYPE 
                         30                          52 
$`AMP PEAK 32(XQ28) MUTATED`
TCGA-05-4382 TCGA-05-4390 TCGA-05-4405 TCGA-05-4425 TCGA-05-4426 TCGA-05-4432 
         607         1126          610          669          791          761 
TCGA-05-5423 TCGA-05-5428 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4629 
         151          670          225          182          264          864 
TCGA-38-4631 TCGA-38-7271 TCGA-44-2659 TCGA-44-3918 TCGA-44-5644 TCGA-44-5645 
         354         1971         1367         1036          863          383 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7661 TCGA-44-7662 TCGA-44-7669 TCGA-44-8117 
        1864         1978          366          218         1970          385 
TCGA-44-A47A TCGA-44-A4SU TCGA-49-4494 TCGA-49-4505 TCGA-49-4507 TCGA-49-4512 
         466           76         1081          428          268          157 
TCGA-49-6744 TCGA-49-6761 TCGA-50-5045 TCGA-50-5933 TCGA-50-5941 TCGA-50-5946 
         890          354         2174         2370          567          686 
TCGA-50-7109 TCGA-53-7624 TCGA-55-1592 TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 
         255         1986          701         1479         1375           87 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6985 TCGA-55-6987 TCGA-55-7281 
           2          993           24         1233         1170           18 
TCGA-55-7576 TCGA-55-7726 TCGA-55-7907 TCGA-55-7994 TCGA-55-8090 TCGA-55-8092 
          40           39           16           31            6           26 
TCGA-55-8096 TCGA-55-A48Z TCGA-55-A491 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
          47           29         1952            5           47          162 
TCGA-62-8399 TCGA-62-A46U TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-1680 
        2696         2067         1728          628         1189         1126 
TCGA-64-5815 TCGA-67-3772 TCGA-67-6215 TCGA-69-7764 TCGA-69-7979 TCGA-71-6725 
         866          573          174          414           89           61 
TCGA-73-4666 TCGA-73-4670 TCGA-73-4676 TCGA-73-7499 TCGA-75-6214 TCGA-75-7025 
         800          131          164          519         1970         1967 
TCGA-75-7031 TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 TCGA-78-7154 TCGA-78-7155 
        1965         1988         1950         1093         1948         1957 
TCGA-78-7161 TCGA-78-7163 TCGA-78-7166 TCGA-78-7220 TCGA-78-7535 TCGA-78-7542 
         215         1950         1934         1965         1972         1952 
TCGA-78-8640 TCGA-78-8655 TCGA-83-5908 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
        1949         1981          824          508          745           10 
TCGA-86-8075 TCGA-86-8280 TCGA-86-8281 TCGA-86-8358 TCGA-86-8359 TCGA-86-8673 
         479           16         1955           19           26          455 
TCGA-86-A4P7 TCGA-91-6829 TCGA-91-7771 TCGA-91-8496 TCGA-91-8499 TCGA-95-7043 
          14         1940          492          197           36            2 
TCGA-95-7567 TCGA-97-7554 TCGA-97-7937 TCGA-97-8172 TCGA-97-8179 TCGA-97-8547 
         568          775          181          182           15          148 
TCGA-97-A4M7 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SW 
         271            6          285          622          353         1967 
TCGA-MP-A4T4 TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TK 
        1954         1970         1955         1971 

$`AMP PEAK 32(XQ28) WILD-TYPE`
TCGA-05-4249 TCGA-05-4384 TCGA-05-4389 TCGA-05-4396 TCGA-05-4398 TCGA-05-4403 
        1523          426         1369         1947         1431          578 
TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        1958         1997          455          912          365          913 
TCGA-05-4427 TCGA-05-4430 TCGA-05-4433 TCGA-05-5420 TCGA-05-5425 TCGA-05-5429 
         791          761          730          457          882           30 
TCGA-05-5715 TCGA-35-3615 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
          62           14         1952         1962         1147         1492 
TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 
        1073         1357          448          133         1324         1429 
TCGA-44-2657 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
         400          741         1280         1301           97          246 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-6144 
        1130         1163          190          722         1013          723 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
         328          302          845          704          658          705 
TCGA-44-6776 TCGA-44-6777 TCGA-44-7659 TCGA-44-7660 TCGA-44-7667 TCGA-44-7670 
        1938         1942          444          592          557          882 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B 
         535          719           99          260          486          287 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4501 TCGA-49-4506 
         337          351          415         1932         1421          999 
TCGA-49-4510 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6745 TCGA-50-5049 
         896         1700          445          369          522         2146 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
         455          785          944         1499          246          282 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5935 TCGA-50-5942 TCGA-50-5944 TCGA-50-6597 
         267         1091          653          883          764         1015 
TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-6969 
         105         1971          424          280         1178         1239 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 TCGA-55-6983 TCGA-55-6986 TCGA-55-7283 
          25         1475           67         1826         2151           35 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7724 TCGA-55-7725 
         121            6            4           95         1958           39 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 
          34           24           54           19          197           21 
TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8091 
           3            5           33           21          100           43 
TCGA-55-8094 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 
           4           15           33           46           66          216 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
          44           23           29           11            8           15 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
         228            9            3          146          202          536 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
          15           48           49           66          106           33 
TCGA-55-A48Y TCGA-55-A490 TCGA-55-A492 TCGA-55-A493 TCGA-62-8395 TCGA-62-8397 
          42           48            1           28         1216         1289 
TCGA-62-8398 TCGA-62-8402 TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 TCGA-64-1679 
        1970         1445         2199         1246          910         1686 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
        1968         1959           62         1305          864         1559 
TCGA-67-3770 TCGA-67-3771 TCGA-67-3773 TCGA-67-3774 TCGA-67-6216 TCGA-67-6217 
          31          610          427          385          141          422 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
         202          186          690          165          230          184 
TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
          70          382          100           77          129          214 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4668 TCGA-73-4675 TCGA-73-4677 
        1600          711          912          467           40           38 
TCGA-73-7498 TCGA-75-7027 TCGA-78-7145 TCGA-78-7148 TCGA-78-7150 TCGA-78-7152 
         621         1956         1973         1944         1963         1202 
TCGA-78-7153 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7162 
         760         1961         1963         1221          678         1940 
TCGA-78-7167 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7633 
        1937         1949         1944          327          881          994 
TCGA-78-8648 TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 TCGA-86-6851 
        1971         1954         1964         1965         1972         1959 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
          11          630          422         1968          591         1963 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
        1963           13           24          489          476          482 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 
          35           45           34           18           15          405 
TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 TCGA-91-6831 
          10           30           39          323           60          310 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
          79          417          372          842          224           35 
TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
         174           44          218          297          127          186 
TCGA-95-7039 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-97-7546 
          34          377          477          476          121          964 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 
        1965         1932         1332           22          107         1965 
TCGA-97-8175 TCGA-97-8177 TCGA-97-8552 TCGA-97-A4M2 TCGA-99-7458 TCGA-99-8025 
          87          147          115          197          392          427 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
         459           44          170          154          114          287 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-MP-A4SV 
         282          238          578          435          116         1946 
TCGA-MP-A4T2 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
        1951         1954         1957         1980         1951         1944 
TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A5C7 
        1970          142         1490 

  AMP PEAK 32(XQ28) MUTATED AMP PEAK 32(XQ28) WILD-TYPE 
                          2                           1 
  AMP PEAK 32(XQ28) MUTATED AMP PEAK 32(XQ28) WILD-TYPE 
                       2696                        2199 
  AMP PEAK 32(XQ28) MUTATED AMP PEAK 32(XQ28) WILD-TYPE 
                        590                         435 
[1] "2.0 - 2696.0 (590.0)" "1.0 - 2199.0 (435.0)"
[1] "hr=" "1.3"
D32V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 32(XQ28) MUTATED         1       33       40        14        23
  AMP PEAK 32(XQ28) WILD-TYPE       3       80       91        29        46
                             vv
clus                          STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 32(XQ28) MUTATED           19          3        8
  AMP PEAK 32(XQ28) WILD-TYPE         48          8       15
D32V3, multiclass
            clus
vv           AMP PEAK 32(XQ28) MUTATED AMP PEAK 32(XQ28) WILD-TYPE
  STAGE I                            1                           3
  STAGE IA                          33                          80
  STAGE IB                          40                          91
  STAGE IIA                         14                          29
  STAGE IIB                         23                          46
  STAGE IIIA                        19                          48
  STAGE IIIB                         3                           8
  STAGE IV                           8                          15
[1] 8 2
[1] TRUE
[1] "dimension of 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 32(XQ28) MUTATED    39  86  12   3
  AMP PEAK 32(XQ28) WILD-TYPE 104 173  28  15
D32V4, multiclass
    clus
vv   AMP PEAK 32(XQ28) MUTATED AMP PEAK 32(XQ28) WILD-TYPE
  T1                        39                         104
  T2                        86                         173
  T3                        12                          28
  T4                         3                          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 32(XQ28) MUTATED    84  32    22
  AMP PEAK 32(XQ28) WILD-TYPE 211  53    50
D32V5, multiclass
       clus
vv      AMP PEAK 32(XQ28) MUTATED AMP PEAK 32(XQ28) WILD-TYPE
  N0                           84                         211
  N1                           32                          53
  N2+N3                        22                          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"
                             vv
clus                           M0  M1 M1A M1B  MX
  AMP PEAK 32(XQ28) MUTATED    93   8   0   0  38
  AMP PEAK 32(XQ28) WILD-TYPE 224  10   1   3  81
D32V6, multiclass
     clus
vv    AMP PEAK 32(XQ28) MUTATED AMP PEAK 32(XQ28) WILD-TYPE
  M0                         93                         224
  M1                          8                          10
  M1A                         0                           1
  M1B                         0                           3
  MX                         38                          81
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V7, binary
                             cls
clus                            0   1
  AMP PEAK 32(XQ28) MUTATED    71  70
  AMP PEAK 32(XQ28) WILD-TYPE 177 144
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 32(XQ28) MUTATED     71   70
  AMP PEAK 32(XQ28) WILD-TYPE  177  144
        clus
vv       AMP PEAK 32(XQ28) MUTATED AMP PEAK 32(XQ28) WILD-TYPE
  FEMALE                        71                         177
  MALE                          70                         144
[1] 2 2
[1] FALSE
D32V8, continuous
                             vv
clus                          LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 32(XQ28) MUTATED                            4
  AMP PEAK 32(XQ28) WILD-TYPE                          9
                             vv
clus                          LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 32(XQ28) MUTATED                                  27
  AMP PEAK 32(XQ28) WILD-TYPE                                66
                             vv
clus                          LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 32(XQ28) MUTATED                                                   98
  AMP PEAK 32(XQ28) WILD-TYPE                                                196
                             vv
clus                          LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 32(XQ28) MUTATED                                            1
  AMP PEAK 32(XQ28) WILD-TYPE                                          3
                             vv
clus                          LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 32(XQ28) MUTATED                                               4
  AMP PEAK 32(XQ28) WILD-TYPE                                            15
                             vv
clus                          LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 32(XQ28) MUTATED                                1
  AMP PEAK 32(XQ28) WILD-TYPE                              1
                             vv
clus                          LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 32(XQ28) MUTATED                                    2
  AMP PEAK 32(XQ28) WILD-TYPE                                  2
                             vv
clus                          LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 32(XQ28) MUTATED                              0
  AMP PEAK 32(XQ28) WILD-TYPE                            2
                             vv
clus                          LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 32(XQ28) MUTATED                               4
  AMP PEAK 32(XQ28) WILD-TYPE                            15
                             vv
clus                          LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 32(XQ28) MUTATED                                 0
  AMP PEAK 32(XQ28) WILD-TYPE                               1
                             vv
clus                          LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 32(XQ28) MUTATED                                               0
  AMP PEAK 32(XQ28) WILD-TYPE                                             4
                             vv
clus                          MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 32(XQ28) MUTATED                              0
  AMP PEAK 32(XQ28) WILD-TYPE                            7
D32V9, multiclass
                                                    clus
vv                                                   AMP PEAK 32(XQ28) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                 4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                         27
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                        98
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                 1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                              4
  LUNG CLEAR CELL ADENOCARCINOMA                                             1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                         2
  LUNG MUCINOUS ADENOCARCINOMA                                               0
  LUNG PAPILLARY ADENOCARCINOMA                                              4
  LUNG SIGNET RING ADENOCARCINOMA                                            0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                              0
  MUCINOUS (COLLOID) CARCINOMA                                               0
                                                    clus
vv                                                   AMP PEAK 32(XQ28) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                   9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           66
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         196
  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                                               15
  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"
D32V10, binary
                             cls
clus                            0   1
  AMP PEAK 32(XQ28) MUTATED     9 132
  AMP PEAK 32(XQ28) WILD-TYPE  12 309
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 32(XQ28) MUTATED      9  132
  AMP PEAK 32(XQ28) WILD-TYPE   12  309
     clus
vv    AMP PEAK 32(XQ28) MUTATED AMP PEAK 32(XQ28) WILD-TYPE
  NO                          9                          12
  YES                       132                         309
[1] 2 2
[1] FALSE
D32V11, continuous
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK 32(XQ28) MUTATED    99   4   1   3
  AMP PEAK 32(XQ28) WILD-TYPE 219   7   3  16
D32V12, multiclass
    clus
vv   AMP PEAK 32(XQ28) MUTATED AMP PEAK 32(XQ28) WILD-TYPE
  R0                        99                         219
  R1                         4                           7
  R2                         1                           3
  RX                         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                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 32(XQ28) MUTATED                                  0     3
  AMP PEAK 32(XQ28) WILD-TYPE                                1     3
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 32(XQ28) MUTATED                           7   108
  AMP PEAK 32(XQ28) WILD-TYPE                        19   254
D32V13, multiclass
                                  clus
vv                                 AMP PEAK 32(XQ28) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    3
  BLACK OR AFRICAN AMERICAN                                7
  WHITE                                                  108
                                  clus
vv                                 AMP PEAK 32(XQ28) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 19
  WHITE                                                    254
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V14, binary
                             cls
clus                            0   1
  AMP PEAK 32(XQ28) MUTATED     1  92
  AMP PEAK 32(XQ28) WILD-TYPE   6 240
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 32(XQ28) MUTATED      1   92
  AMP PEAK 32(XQ28) WILD-TYPE    6  240
                        clus
vv                       AMP PEAK 32(XQ28) MUTATED AMP PEAK 32(XQ28) WILD-TYPE
  HISPANIC OR LATINO                             1                           6
  NOT HISPANIC OR LATINO                        92                         240
[1] 2 2
[1] FALSE

Clustering(33) Variable = DEL PEAK  1(1P36.13) MUTATION ANALYSIS
D33V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  1(1P36.13) MUTATED    71  22
  DEL PEAK  1(1P36.13) WILD-TYPE 250  60
  DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE 
                            93                            310 
  DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE 
                            22                             60 
$`DEL PEAK  1(1P36.13) MUTATED`
TCGA-05-4249 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 TCGA-05-4398 TCGA-05-4415 
        1523         1369         1126         1947         1431         1997 
TCGA-05-4417 TCGA-05-4424 TCGA-05-4425 TCGA-05-5420 TCGA-05-5425 TCGA-05-5429 
         455          913          669          457          882           30 
TCGA-35-3615 TCGA-38-4625 TCGA-44-2666 TCGA-44-3918 TCGA-44-5643 TCGA-44-6144 
          14         1952           97         1036         1013          723 
TCGA-44-6779 TCGA-44-7660 TCGA-44-A479 TCGA-44-A47F TCGA-49-4494 TCGA-49-4506 
        1978          592          486          337         1081          999 
TCGA-49-4507 TCGA-49-6745 TCGA-49-6761 TCGA-50-5051 TCGA-50-5932 TCGA-50-5935 
         268          522          354          455         1091          653 
TCGA-50-7109 TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6986 TCGA-55-7283 
         255         1479         1375           87         2151           35 
TCGA-55-7911 TCGA-55-7914 TCGA-55-8090 TCGA-55-8205 TCGA-55-8507 TCGA-55-8508 
          21            3            6           33            8           15 
TCGA-55-8615 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 TCGA-55-A494 
          15           42           29         1952            1            5 
TCGA-62-8398 TCGA-62-A46U TCGA-62-A46V TCGA-62-A472 TCGA-64-1677 TCGA-64-5774 
        1970         2067         2199          910          628         1959 
TCGA-64-5778 TCGA-64-5815 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7973 
        1305          866          202          186          690          230 
TCGA-69-7978 TCGA-73-4659 TCGA-73-4666 TCGA-73-4670 TCGA-73-4675 TCGA-73-4677 
          70          711          800          131           40           38 
TCGA-75-7027 TCGA-75-7031 TCGA-78-7146 TCGA-78-7148 TCGA-78-7153 TCGA-78-7154 
        1956         1965         1988         1944          760         1948 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7536 TCGA-78-8655 TCGA-80-5608 TCGA-86-6851 
        1221          678         1949         1981         1972         1959 
TCGA-86-7701 TCGA-86-7713 TCGA-86-8054 TCGA-86-8358 TCGA-86-8669 TCGA-91-6828 
          11          422          745           19           34          323 
TCGA-91-6830 TCGA-91-7771 TCGA-91-8499 TCGA-95-7043 TCGA-95-7944 TCGA-97-8172 
          60          492           36            2          377          182 
TCGA-MP-A4T7 TCGA-MP-A4TC TCGA-MP-A4TE 
        1954         1944         1970 

$`DEL PEAK  1(1P36.13) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 TCGA-05-4420 
         607          426          578          610         1958          912 
TCGA-05-4422 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
         365          791          791          761          761          730 
TCGA-05-5423 TCGA-05-5428 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 
         151          670           62          225          182          264 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
        1962         1147         1492          864         1073          354 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 
        1357          448         1971          133         1324         1429 
TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2668 
         400         1367          741         1280         1301          246 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5644 TCGA-44-5645 
        1130         1163          190          722          863          383 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
         328          302          845          704          658          705 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-7659 TCGA-44-7661 TCGA-44-7662 
        1938         1942         1864          444          366          218 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
         557         1970          882          535          719          385 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS 
          99          260          466          287          351          415 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4501 TCGA-49-4505 TCGA-49-4510 TCGA-49-4512 
          76         1932         1421          428          896          157 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-50-5045 TCGA-50-5049 
        1700          445          369          890         2174         2146 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
         785          944         1499          246          282          267 
TCGA-50-5933 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6597 
        2370          567          883          764          686         1015 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
         105         1986         1971          424          280          701 
TCGA-55-1594 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6971 
        1178            2          993           24         1239           25 
TCGA-55-6972 TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 TCGA-55-6987 TCGA-55-7281 
        1475           67         1826         1233         1170           18 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
         121            6            4           95           40         1958 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 
          39           39           34           24           54           19 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
          16          197           31            5           33           21 
TCGA-55-8089 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
         100           43           26            4           47           15 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
          46           66          216           44           23           29 
TCGA-55-8506 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
          11          228            9            3          146          202 
TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
         536           48           49           66          106           33 
TCGA-55-A490 TCGA-55-A493 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 
          48           28           47          162         1216         1289 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A471 TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 
        2696         1445         1246         1728         1189         1686 
TCGA-64-1680 TCGA-64-1681 TCGA-64-5775 TCGA-64-5779 TCGA-64-5781 TCGA-67-3770 
        1126         1968           62          864         1559           31 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 
         610          573          427          385          174          141 
TCGA-67-6217 TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 TCGA-69-7979 TCGA-69-7980 
         422          414          165          184           89          382 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 
         100           77          129          214           61         1600 
TCGA-73-4662 TCGA-73-4668 TCGA-73-4676 TCGA-73-7498 TCGA-73-7499 TCGA-75-6214 
         912          467          164          621          519         1970 
TCGA-75-7025 TCGA-78-7145 TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        1967         1973         1950         1093         1963         1202 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        1957         1961         1963          215         1940         1950 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 
        1934         1937         1965         1972         1944          327 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8660 
         881         1952          994         1949         1971         1954 
TCGA-78-8662 TCGA-80-5607 TCGA-83-5908 TCGA-86-7711 TCGA-86-7714 TCGA-86-7953 
        1964         1965          824          630         1968          591 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
        1963          508           10         1963           13           24 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8281 
         479          489          476          482           16         1955 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
          26           35           45           18           15          455 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 
         405           10           30           14           39         1940 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
         310           79          417          372          842          224 
TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
          35          197          174           44          218          297 
TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7567 TCGA-95-7947 TCGA-95-7948 
         127          186           34          568          477          476 
TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
         121          964         1965         1932         1332          775 
TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 
         181           22          107         1965           87          147 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 
          15          148          115          197          271          392 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
         427          459           44          170          154          114 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
         287          282          238          578          435          116 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
           6          285          622          353         1946         1967 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TF 
        1951         1954         1957         1980         1951         1970 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
         142         1955         1971         1490 

  DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE 
                             1                              2 
  DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE 
                          2199                           2696 
  DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE 
                         669.0                          431.5 
[1] "1.0 - 2199.0 (669.0)" "2.0 - 2696.0 (431.5)"
[1] "hr=" "1.2"
D33V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK  1(1P36.13) MUTATED         1       23       22         8        18
  DEL PEAK  1(1P36.13) WILD-TYPE       3       90      109        35        51
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK  1(1P36.13) MUTATED           24          4        7
  DEL PEAK  1(1P36.13) WILD-TYPE         43          7       16
D33V3, multiclass
            clus
vv           DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE
  STAGE I                               1                              3
  STAGE IA                             23                             90
  STAGE IB                             22                            109
  STAGE IIA                             8                             35
  STAGE IIB                            18                             51
  STAGE IIIA                           24                             43
  STAGE IIIB                            4                              7
  STAGE IV                              7                             16
[1] 8 2
[1] TRUE
[1] "dimension of 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    29  57  15   5
  DEL PEAK  1(1P36.13) WILD-TYPE 114 202  25  13
D33V4, multiclass
    clus
vv   DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE
  T1                           29                            114
  T2                           57                            202
  T3                           15                             25
  T4                            5                             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    59  22    25
  DEL PEAK  1(1P36.13) WILD-TYPE 236  63    47
D33V5, multiclass
       clus
vv      DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE
  N0                              59                            236
  N1                              22                             63
  N2+N3                           25                             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"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK  1(1P36.13) MUTATED    76   7   0   0  24
  DEL PEAK  1(1P36.13) WILD-TYPE 241  11   1   3  95
D33V6, multiclass
     clus
vv    DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE
  M0                            76                            241
  M1                             7                             11
  M1A                            0                              1
  M1B                            0                              3
  MX                            24                             95
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V7, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.13) MUTATED    49  58
  DEL PEAK  1(1P36.13) WILD-TYPE 199 156
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.13) MUTATED     49   58
  DEL PEAK  1(1P36.13) WILD-TYPE  199  156
        clus
vv       DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE
  FEMALE                           49                            199
  MALE                             58                            156
[1] 2 2
[1] FALSE
D33V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK  1(1P36.13) MUTATED                            4
  DEL PEAK  1(1P36.13) WILD-TYPE                          9
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK  1(1P36.13) MUTATED                                  26
  DEL PEAK  1(1P36.13) WILD-TYPE                                67
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  1(1P36.13) MUTATED                                                   68
  DEL PEAK  1(1P36.13) WILD-TYPE                                                226
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK  1(1P36.13) MUTATED                                            0
  DEL PEAK  1(1P36.13) WILD-TYPE                                          4
                                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                                  4
                                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                            18
                                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                                               1
  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                            5
D33V9, multiclass
                                                    clus
vv                                                   DEL PEAK  1(1P36.13) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            26
  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                                            0
  LUNG MUCINOUS ADENOCARCINOMA                                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                                 1
  LUNG SIGNET RING ADENOCARCINOMA                                               1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 1
  MUCINOUS (COLLOID) CARCINOMA                                                  2
                                                    clus
vv                                                   DEL PEAK  1(1P36.13) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              67
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            226
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  16
  LUNG CLEAR CELL ADENOCARCINOMA                                                  1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              4
  LUNG MUCINOUS ADENOCARCINOMA                                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                                  18
  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"
D33V10, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.13) MUTATED     5 102
  DEL PEAK  1(1P36.13) WILD-TYPE  16 339
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.13) MUTATED      5  102
  DEL PEAK  1(1P36.13) WILD-TYPE   16  339
     clus
vv    DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE
  NO                             5                             16
  YES                          102                            339
[1] 2 2
[1] FALSE
D33V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK  1(1P36.13) MUTATED    73   3   2   4
  DEL PEAK  1(1P36.13) WILD-TYPE 245   8   2  15
D33V12, multiclass
    clus
vv   DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE
  R0                           73                            245
  R1                            3                              8
  R2                            2                              2
  RX                            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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  1(1P36.13) MUTATED                                  0     2
  DEL PEAK  1(1P36.13) WILD-TYPE                                1     4
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1P36.13) MUTATED                           4    79
  DEL PEAK  1(1P36.13) WILD-TYPE                        22   283
D33V13, multiclass
                                  clus
vv                                 DEL PEAK  1(1P36.13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   4
  WHITE                                                      79
                                  clus
vv                                 DEL PEAK  1(1P36.13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    22
  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"
D33V14, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.13) MUTATED     1  72
  DEL PEAK  1(1P36.13) WILD-TYPE   6 260
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.13) MUTATED      1   72
  DEL PEAK  1(1P36.13) WILD-TYPE    6  260
                        clus
vv                       DEL PEAK  1(1P36.13) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           72
                        clus
vv                       DEL PEAK  1(1P36.13) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            260
[1] 2 2
[1] FALSE

Clustering(34) Variable = DEL PEAK  2(1P13.1) MUTATION ANALYSIS
D34V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  2(1P13.1) MUTATED    98  24
  DEL PEAK  2(1P13.1) WILD-TYPE 223  58
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                          122                           281 
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                           24                            58 
$`DEL PEAK  2(1P13.1) MUTATED`
TCGA-05-4249 TCGA-05-4389 TCGA-05-4390 TCGA-05-4398 TCGA-05-4415 TCGA-05-4417 
        1523         1369         1126         1431         1997          455 
TCGA-05-4422 TCGA-05-4433 TCGA-05-5715 TCGA-38-4625 TCGA-38-4628 TCGA-44-2665 
         365          730           62         1952         1492         1301 
TCGA-44-2668 TCGA-44-3918 TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 TCGA-44-A47F 
         246         1036         1013          863          723          337 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
        1081         1421          999          268          896          157 
TCGA-49-4514 TCGA-49-6743 TCGA-49-6745 TCGA-49-6761 TCGA-50-5051 TCGA-50-5932 
        1700          369          522          354          455         1091 
TCGA-50-5935 TCGA-50-5946 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1596 TCGA-55-5899 
         653          686          424          280         1375           87 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6986 TCGA-55-7283 TCGA-55-7907 TCGA-55-7911 
          25         1475         2151           35           16           21 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
          31            5            6           43           26            4 
TCGA-55-8205 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8512 TCGA-55-8615 
          33           29            8           15            3           15 
TCGA-55-A48Y TCGA-55-A492 TCGA-55-A4DF TCGA-62-8402 TCGA-62-A46U TCGA-62-A46V 
          42            1           47         1445         2067         2199 
TCGA-64-1678 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-67-3770 
        1189         1959           62         1305          864           31 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3774 TCGA-69-7761 TCGA-69-7763 TCGA-69-7973 
         610          573          385          186          690          230 
TCGA-71-6725 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4670 TCGA-73-4675 
          61          711          912          800          131           40 
TCGA-73-4677 TCGA-73-7498 TCGA-75-7027 TCGA-75-7031 TCGA-78-7146 TCGA-78-7148 
          38          621         1956         1965         1988         1944 
TCGA-78-7149 TCGA-78-7153 TCGA-78-7154 TCGA-78-7160 TCGA-78-7163 TCGA-78-7167 
        1093          760         1948          678         1950         1937 
TCGA-78-7220 TCGA-78-7539 TCGA-80-5608 TCGA-86-6851 TCGA-86-7701 TCGA-86-8054 
        1965          327         1972         1959           11          745 
TCGA-86-8278 TCGA-86-8358 TCGA-86-8668 TCGA-86-8669 TCGA-86-A4D0 TCGA-91-6828 
         476           19           45           34           30          323 
TCGA-91-6836 TCGA-91-6848 TCGA-91-7771 TCGA-91-8497 TCGA-93-7348 TCGA-93-8067 
         417          224          492          174          127          186 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-95-7947 TCGA-97-7554 TCGA-97-8172 
          34            2          568          477          775          182 
TCGA-97-8547 TCGA-97-8552 TCGA-J2-8192 TCGA-MP-A4SW TCGA-MP-A4T7 TCGA-MP-A4TH 
         148          115          154         1967         1954          142 
TCGA-MP-A4TK TCGA-MP-A5C7 
        1971         1490 

$`DEL PEAK  2(1P13.1) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 
         607          426         1947          578          610         1958 
TCGA-05-4420 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 
         912          913          669          791          791          761 
TCGA-05-4432 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
         761          457          151          882          670           30 
TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4626 TCGA-38-4627 
          14          225          182          264         1962         1147 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
         864         1073          354         1357          448         1971 
TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 
         133         1324         1429          400         1367          741 
TCGA-44-2662 TCGA-44-2666 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 
        1280           97         1130         1163          190          722 
TCGA-44-5645 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
         383          328          302          845          704          658 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
         705         1938         1942         1864         1978          444 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
         592          366          218          557         1970          882 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 
         535          719          385           99          260          486 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
         466          287          351          415           76         1932 
TCGA-49-4505 TCGA-49-6742 TCGA-49-6744 TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 
         428          445          890         2174         2146          785 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 
         944         1499          246          282          267         2370 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 
         567          883          764         1015          255          105 
TCGA-53-7624 TCGA-53-7626 TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-6543 
        1986         1971          701         1178         1479            2 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 
         993           24         1239           67         1826         1233 
TCGA-55-6987 TCGA-55-7281 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        1170           18          121            6            4           95 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
          40         1958           39           39           34           24 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7910 TCGA-55-7914 TCGA-55-8085 TCGA-55-8087 
          54           19          197            3           33           21 
TCGA-55-8089 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 
         100           47           15           46           66          216 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8510 TCGA-55-8511 TCGA-55-8513 
          44           23           11          228            9          146 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
         202          536           48           49           66          106 
TCGA-55-A48X TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A493 TCGA-55-A494 
          33           29           48         1952           28            5 
TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-A471 
         162         1216         1289         1970         2696         1246 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 
         910         1728          628         1686         1126         1968 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
        1559          866          427          174          141          422 
TCGA-69-7760 TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
         202          414          165          184           70           89 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-73-4658 
         382          100           77          129          214         1600 
TCGA-73-4668 TCGA-73-4676 TCGA-73-7499 TCGA-75-6214 TCGA-75-7025 TCGA-78-7145 
         467          164          519         1970         1967         1973 
TCGA-78-7147 TCGA-78-7150 TCGA-78-7152 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
        1950         1963         1202         1957         1961         1963 
TCGA-78-7159 TCGA-78-7161 TCGA-78-7162 TCGA-78-7166 TCGA-78-7535 TCGA-78-7536 
        1221          215         1940         1934         1972         1949 
TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
        1944          881         1952          994         1949         1971 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 TCGA-83-5908 TCGA-86-7711 
        1981         1954         1964         1965          824          630 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 
         422         1968          591         1963          508           10 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8279 
        1963           13           24          479          489          482 
TCGA-86-8280 TCGA-86-8281 TCGA-86-8359 TCGA-86-8585 TCGA-86-8671 TCGA-86-8672 
          16         1955           26           35           18           15 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 
         455          405           10           14           39         1940 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6849 
          60          310           79          372          842           35 
TCGA-91-8496 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-95-7944 
         197           36           44          218          297          377 
TCGA-95-7948 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
         476          121          964         1965         1932         1332 
TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 
         181           22          107         1965           87          147 
TCGA-97-8179 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
          15          197          271          392          427          459 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
          44          170          114          287          282          238 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
         578          435          116            6          285          622 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4T9 
         353         1946         1951         1954         1957         1980 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TI 
        1951         1944         1970         1970         1955 

  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                            1                             2 
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                         2199                          2696 
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                        476.5                         459.0 
[1] "1.0 - 2199.0 (476.5)" "2.0 - 2696.0 (459.0)"
[1] "hr=" "1"  
D34V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK  2(1P13.1) MUTATED         1       29       34         9        21
  DEL PEAK  2(1P13.1) WILD-TYPE       3       84       97        34        48
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK  2(1P13.1) MUTATED           28          5       10
  DEL PEAK  2(1P13.1) WILD-TYPE         39          6       13
D34V3, multiclass
            clus
vv           DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  STAGE I                              1                             3
  STAGE IA                            29                            84
  STAGE IB                            34                            97
  STAGE IIA                            9                            34
  STAGE IIB                           21                            48
  STAGE IIIA                          28                            39
  STAGE IIIB                           5                             6
  STAGE IV                            10                            13
[1] 8 2
[1] TRUE
[1] "dimension of 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    35  80  13   8
  DEL PEAK  2(1P13.1) WILD-TYPE 108 179  27  10
D34V4, multiclass
    clus
vv   DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  T1                          35                           108
  T2                          80                           179
  T3                          13                            27
  T4                           8                            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    83  27    27
  DEL PEAK  2(1P13.1) WILD-TYPE 212  58    45
D34V5, multiclass
       clus
vv      DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  N0                             83                           212
  N1                             27                            58
  N2+N3                          27                            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"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK  2(1P13.1) MUTATED    94   8   0   2  32
  DEL PEAK  2(1P13.1) WILD-TYPE 223  10   1   1  87
D34V6, multiclass
     clus
vv    DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  M0                           94                           223
  M1                            8                            10
  M1A                           0                             1
  M1B                           2                             1
  MX                           32                            87
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V7, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.1) MUTATED    73  64
  DEL PEAK  2(1P13.1) WILD-TYPE 175 150
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.1) MUTATED     73   64
  DEL PEAK  2(1P13.1) WILD-TYPE  175  150
        clus
vv       DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  FEMALE                          73                           175
  MALE                            64                           150
[1] 2 2
[1] FALSE
D34V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  DEL PEAK  2(1P13.1) MUTATED                            6
  DEL PEAK  2(1P13.1) WILD-TYPE                          7
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK  2(1P13.1) MUTATED                                  28
  DEL PEAK  2(1P13.1) WILD-TYPE                                65
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  2(1P13.1) MUTATED                                                   84
  DEL PEAK  2(1P13.1) WILD-TYPE                                                210
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK  2(1P13.1) MUTATED                                            1
  DEL PEAK  2(1P13.1) WILD-TYPE                                          3
                               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                                    1
  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                               6
  DEL PEAK  2(1P13.1) WILD-TYPE                            13
                               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                                               0
  DEL PEAK  2(1P13.1) WILD-TYPE                                             4
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK  2(1P13.1) MUTATED                              2
  DEL PEAK  2(1P13.1) WILD-TYPE                            5
D34V9, multiclass
                                                    clus
vv                                                   DEL PEAK  2(1P13.1) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           28
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          84
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                   1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                7
  LUNG CLEAR CELL ADENOCARCINOMA                                               1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                           1
  LUNG MUCINOUS ADENOCARCINOMA                                                 0
  LUNG PAPILLARY ADENOCARCINOMA                                                6
  LUNG SIGNET RING ADENOCARCINOMA                                              1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                0
  MUCINOUS (COLLOID) CARCINOMA                                                 2
                                                    clus
vv                                                   DEL PEAK  2(1P13.1) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             65
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           210
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 12
  LUNG CLEAR CELL ADENOCARCINOMA                                                 1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             3
  LUNG MUCINOUS ADENOCARCINOMA                                                   2
  LUNG PAPILLARY ADENOCARCINOMA                                                 13
  LUNG SIGNET RING ADENOCARCINOMA                                                0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                  4
  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"
D34V10, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.1) MUTATED     6 131
  DEL PEAK  2(1P13.1) WILD-TYPE  15 310
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.1) MUTATED      6  131
  DEL PEAK  2(1P13.1) WILD-TYPE   15  310
     clus
vv    DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  NO                            6                            15
  YES                         131                           310
[1] 2 2
[1] FALSE
D34V11, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  2(1P13.1) MUTATED    94   2   2   7
  DEL PEAK  2(1P13.1) WILD-TYPE 224   9   2  12
D34V12, multiclass
    clus
vv   DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  R0                          94                           224
  R1                           2                             9
  R2                           2                             2
  RX                           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                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  2(1P13.1) MUTATED                                  0     3
  DEL PEAK  2(1P13.1) WILD-TYPE                                1     3
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(1P13.1) MUTATED                           5   109
  DEL PEAK  2(1P13.1) WILD-TYPE                        21   253
D34V13, multiclass
                                  clus
vv                                 DEL PEAK  2(1P13.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                  5
  WHITE                                                    109
                                  clus
vv                                 DEL PEAK  2(1P13.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        3
  BLACK OR AFRICAN AMERICAN                                   21
  WHITE                                                      253
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V14, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.1) MUTATED     1  98
  DEL PEAK  2(1P13.1) WILD-TYPE   6 234
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.1) MUTATED      1   98
  DEL PEAK  2(1P13.1) WILD-TYPE    6  234
                        clus
vv                       DEL PEAK  2(1P13.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          98
                        clus
vv                       DEL PEAK  2(1P13.1) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           234
[1] 2 2
[1] FALSE

Clustering(35) Variable = DEL PEAK  3(2Q22.1) MUTATION ANALYSIS
D35V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  3(2Q22.1) MUTATED    30   8
  DEL PEAK  3(2Q22.1) WILD-TYPE 291  74
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           38                           365 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                            8                            74 
$`DEL PEAK  3(2Q22.1) MUTATED`
TCGA-05-4415 TCGA-38-4625 TCGA-44-2659 TCGA-44-6778 TCGA-44-6779 TCGA-44-8119 
        1997         1952         1367         1864         1978           99 
TCGA-44-A4SS TCGA-50-5051 TCGA-50-5946 TCGA-53-7624 TCGA-55-6986 TCGA-55-8097 
         415          455          686         1986         2151           15 
TCGA-55-8508 TCGA-55-A492 TCGA-55-A4DF TCGA-62-8397 TCGA-64-1676 TCGA-67-3772 
          15            1           47         1289         1728          573 
TCGA-69-7760 TCGA-71-6725 TCGA-73-4670 TCGA-73-7499 TCGA-75-7031 TCGA-78-7150 
         202           61          131          519         1965         1963 
TCGA-78-7153 TCGA-78-7220 TCGA-78-7536 TCGA-86-7701 TCGA-86-8054 TCGA-86-8074 
         760         1965         1949           11          745           24 
TCGA-86-8358 TCGA-91-6829 TCGA-91-6848 TCGA-93-8067 TCGA-95-7039 TCGA-97-7554 
          19         1940          224          186           34          775 
TCGA-97-8172 TCGA-L9-A444 
         182            6 

$`DEL PEAK  3(2Q22.1) WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 
        1523          607          426         1369         1126         1947 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 TCGA-05-4417 TCGA-05-4420 
        1431          578          610         1958          455          912 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 
         365          913          669          791          791          761 
TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
         761          730          457          151          882          670 
TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 
          30           62           14          225          182          264 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
        1962         1147         1492          864         1073          354 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 
        1357          448         1971          133         1324         1429 
TCGA-44-2657 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
         400          741         1280         1301           97          246 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
        1130         1163         1036          190          722         1013 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
         863          383          723          328          302          845 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-7659 
         704          658          705         1938         1942          444 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
         592          366          218          557         1970          882 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
         535          719          385          260          486          466 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 
         287          337          351           76         1932         1081 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
        1421          428          999          268          896          157 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
        1700          445          369          890          522          354 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
        2174         2146          785          944         1499          246 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 
         282          267         1091         2370          653          567 
TCGA-50-5942 TCGA-50-5944 TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 TCGA-53-7626 
         883          764         1015          255          105         1971 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 
         424          280          701         1178         1479         1375 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6971 
          87            2          993           24         1239           25 
TCGA-55-6972 TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 TCGA-55-6987 TCGA-55-7281 
        1475           67         1826         1233         1170           18 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
          35          121            6            4           95           40 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
        1958           39           39           34           24           54 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
          19           16          197           21            3           31 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
           5           33           21          100            6           43 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
          26            4           47           33           46           66 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
         216           44           23           29           11            8 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
         228            9            3          146          202          536 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
          15           48           49           66          106           33 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A493 TCGA-55-A494 
          42           29           48         1952           28            5 
TCGA-55-A4DG TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46U 
         162         1216         1970         2696         1445         2067 
TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 
        2199         1246          910          628         1189         1686 
TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
        1126         1968         1959           62         1305          864 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3773 TCGA-67-3774 
        1559          866           31          610          427          385 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
         174          141          422          186          690          414 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
         165          230          184           70           89          382 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-73-4658 TCGA-73-4659 
         100           77          129          214         1600          711 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
         912          800          467           40          164           38 
TCGA-73-7498 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7145 TCGA-78-7146 
         621         1970         1967         1956         1973         1988 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 TCGA-78-7154 TCGA-78-7155 
        1950         1944         1093         1202         1948         1957 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
        1961         1963         1221          678          215         1940 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 
        1950         1934         1937         1972         1944          327 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
         881         1952          994         1949         1971         1981 
TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 
        1954         1964         1965         1972          824         1959 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
         630          422         1968          591         1963          508 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
          10         1963           13          479          489          476 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8281 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
         482           16         1955           26           35           45 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
          34           18           15          455          405           10 
TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 TCGA-91-6831 
          30           14           39          323           60          310 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6849 TCGA-91-7771 
          79          417          372          842           35          492 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
         197          174           36           44          218          297 
TCGA-93-7348 TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
         127            2          568          377          477          476 
TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 
         121          964         1965         1932         1332          181 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 
          22          107         1965           87          147           15 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
         148          115          197          271          392          427 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
         459           44          170          154          114          287 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-MN-A4N1 
         282          238          578          435          116          285 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 
         622          353         1946         1967         1951         1954 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TE 
        1954         1957         1980         1951         1944         1970 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
        1970          142         1955         1971         1490 

  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                            1                             2 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                         2151                          2696 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                          546                           459 
[1] "1.0 - 2151.0 (546.0)" "2.0 - 2696.0 (459.0)"
[1] "hr=" "1.5"
D35V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK  3(2Q22.1) MUTATED         0        8       13         2         9
  DEL PEAK  3(2Q22.1) WILD-TYPE       4      105      118        41        60
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK  3(2Q22.1) MUTATED            7          1        4
  DEL PEAK  3(2Q22.1) WILD-TYPE         60         10       19
D35V3, multiclass
            clus
vv           DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  STAGE I                              0                             4
  STAGE IA                             8                           105
  STAGE IB                            13                           118
  STAGE IIA                            2                            41
  STAGE IIB                            9                            60
  STAGE IIIA                           7                            60
  STAGE IIIB                           1                            10
  STAGE IV                             4                            19
[1] 8 2
[1] TRUE
[1] "dimension of 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    10  28   5   1
  DEL PEAK  3(2Q22.1) WILD-TYPE 133 231  35  17
D35V4, multiclass
    clus
vv   DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  T1                          10                           133
  T2                          28                           231
  T3                           5                            35
  T4                           1                            17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1 N2+N3
  DEL PEAK  3(2Q22.1) MUTATED    29   7     8
  DEL PEAK  3(2Q22.1) WILD-TYPE 266  78    64
D35V5, multiclass
       clus
vv      DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  N0                             29                           266
  N1                              7                            78
  N2+N3                           8                            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"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK  3(2Q22.1) MUTATED    28   4   0   0  12
  DEL PEAK  3(2Q22.1) WILD-TYPE 289  14   1   3 107
D35V6, multiclass
     clus
vv    DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  M0                           28                           289
  M1                            4                            14
  M1A                           0                             1
  M1B                           0                             3
  MX                           12                           107
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V7, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q22.1) MUTATED    24  20
  DEL PEAK  3(2Q22.1) WILD-TYPE 224 194
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED     24   20
  DEL PEAK  3(2Q22.1) WILD-TYPE  224  194
        clus
vv       DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  FEMALE                          24                           224
  MALE                            20                           194
[1] 2 2
[1] FALSE
D35V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  DEL PEAK  3(2Q22.1) MUTATED                            4
  DEL PEAK  3(2Q22.1) WILD-TYPE                          9
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK  3(2Q22.1) MUTATED                                   8
  DEL PEAK  3(2Q22.1) WILD-TYPE                                85
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  3(2Q22.1) MUTATED                                                   26
  DEL PEAK  3(2Q22.1) WILD-TYPE                                                268
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK  3(2Q22.1) MUTATED                                            0
  DEL PEAK  3(2Q22.1) WILD-TYPE                                          4
                               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                                  4
                               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                               2
  DEL PEAK  3(2Q22.1) WILD-TYPE                            17
                               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                                             4
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK  3(2Q22.1) MUTATED                              2
  DEL PEAK  3(2Q22.1) WILD-TYPE                            5
D35V9, multiclass
                                                    clus
vv                                                   DEL PEAK  3(2Q22.1) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            8
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          26
  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                                                2
  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                                                     9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             85
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           268
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 17
  LUNG CLEAR CELL ADENOCARCINOMA                                                 2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             4
  LUNG MUCINOUS ADENOCARCINOMA                                                   2
  LUNG PAPILLARY ADENOCARCINOMA                                                 17
  LUNG SIGNET RING ADENOCARCINOMA                                                1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                  4
  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"
D35V10, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q22.1) MUTATED     2  42
  DEL PEAK  3(2Q22.1) WILD-TYPE  19 399
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED      2   42
  DEL PEAK  3(2Q22.1) WILD-TYPE   19  399
     clus
vv    DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  NO                            2                            19
  YES                          42                           399
[1] 2 2
[1] FALSE
D35V11, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  3(2Q22.1) MUTATED    29   0   0   2
  DEL PEAK  3(2Q22.1) WILD-TYPE 289  11   4  17
D35V12, multiclass
    clus
vv   DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  R0                          29                           289
  R1                           0                            11
  R2                           0                             4
  RX                           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                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  3(2Q22.1) MUTATED                                  0     2
  DEL PEAK  3(2Q22.1) WILD-TYPE                                1     4
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  3(2Q22.1) MUTATED                           2    35
  DEL PEAK  3(2Q22.1) WILD-TYPE                        24   327
D35V13, multiclass
                                  clus
vv                                 DEL PEAK  3(2Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                  2
  WHITE                                                     35
                                  clus
vv                                 DEL PEAK  3(2Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   24
  WHITE                                                      327
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V14, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q22.1) MUTATED     1  30
  DEL PEAK  3(2Q22.1) WILD-TYPE   6 302
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED      1   30
  DEL PEAK  3(2Q22.1) WILD-TYPE    6  302
                        clus
vv                       DEL PEAK  3(2Q22.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          30
                        clus
vv                       DEL PEAK  3(2Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           302
[1] 2 2
[1] FALSE

Clustering(36) Variable = DEL PEAK  4(2Q37.3) MUTATION ANALYSIS
D36V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  4(2Q37.3) MUTATED    46   6
  DEL PEAK  4(2Q37.3) WILD-TYPE 275  76
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           52                           351 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                            6                            76 
$`DEL PEAK  4(2Q37.3) MUTATED`
TCGA-05-4390 TCGA-38-4625 TCGA-38-4628 TCGA-44-2656 TCGA-44-2659 TCGA-44-2661 
        1126         1952         1492         1429         1367          741 
TCGA-44-3918 TCGA-44-6145 TCGA-44-8117 TCGA-44-8119 TCGA-50-5931 TCGA-50-5946 
        1036          328          385           99          267          686 
TCGA-53-7624 TCGA-53-7813 TCGA-55-1595 TCGA-55-1596 TCGA-55-6642 TCGA-55-6985 
        1986          424         1479         1375          993         1233 
TCGA-55-6986 TCGA-55-A4DG TCGA-62-8397 TCGA-62-8399 TCGA-64-1676 TCGA-64-1677 
        2151          162         1289         2696         1728          628 
TCGA-67-3771 TCGA-67-3773 TCGA-69-7760 TCGA-69-7764 TCGA-69-7979 TCGA-69-7980 
         610          427          202          414           89          382 
TCGA-71-6725 TCGA-73-7499 TCGA-75-7031 TCGA-78-7153 TCGA-78-7542 TCGA-86-7954 
          61          519         1965          760         1952         1963 
TCGA-86-8054 TCGA-86-8074 TCGA-86-8279 TCGA-91-6829 TCGA-91-6831 TCGA-91-6847 
         745           24          482         1940          310          842 
TCGA-91-8499 TCGA-95-7039 TCGA-95-7944 TCGA-95-7948 TCGA-97-7554 TCGA-97-8172 
          36           34          377          476          775          182 
TCGA-97-8547 TCGA-97-A4M7 TCGA-L4-A4E5 TCGA-L9-A444 
         148          271          578            6 

$`DEL PEAK  4(2Q37.3) WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4396 TCGA-05-4398 
        1523          607          426         1369         1947         1431 
TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 
         578          610         1958         1997          455          912 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 
         365          913          669          791          791          761 
TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
         761          730          457          151          882          670 
TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 
          30           62           14          225          182          264 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
        1962         1147          864         1073          354         1357 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2657 TCGA-44-2662 
         448         1971          133         1324          400         1280 
TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 
        1301           97          246         1130         1163          190 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6146 
         722         1013          863          383          723          302 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
         845          704          658          705         1938         1942 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
        1864         1978          444          592          366          218 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8120 
         557         1970          882          535          719          260 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
         486          466          287          337          351          415 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
          76         1932         1081         1421          428          999 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
         268          896          157         1700          445          369 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
         890          522          354         2174         2146          455 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5932 
         785          944         1499          246          282         1091 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-6597 
        2370          653          567          883          764         1015 
TCGA-50-7109 TCGA-50-8460 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 
         255          105         1971          280          701         1178 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6712 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 
          87            2           24         1239           25         1475 
TCGA-55-6980 TCGA-55-6983 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
          67         1826         1170           18           35          121 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
           6            4           95           40         1958           39 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 
          39           34           24           54           19           16 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
         197           21            3           31            5           33 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
          21          100            6           43           26            4 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 
          47           15           33           46           66          216 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
          44           23           29           11            8           15 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
         228            9            3          146          202          536 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
          15           48           49           66          106           33 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
          42           29           48         1952            1           28 
TCGA-55-A494 TCGA-55-A4DF TCGA-62-8395 TCGA-62-8398 TCGA-62-8402 TCGA-62-A46U 
           5           47         1216         1970         1445         2067 
TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 
        2199         1246          910         1189         1686         1126 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
        1968         1959           62         1305          864         1559 
TCGA-64-5815 TCGA-67-3770 TCGA-67-3772 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 
         866           31          573          385          174          141 
TCGA-67-6217 TCGA-69-7761 TCGA-69-7763 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
         422          186          690          165          230          184 
TCGA-69-7978 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-73-4658 
          70          100           77          129          214         1600 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
         711          912          800          467          131           40 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 
         164           38          621         1970         1967         1956 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
        1973         1988         1950         1944         1093         1963 
TCGA-78-7152 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
        1202         1948         1957         1961         1963         1221 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
         678          215         1940         1950         1934         1937 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
        1965         1972         1949         1944          327          881 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
         994         1949         1971         1981         1954         1964 
TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
        1965         1972          824         1959           11          630 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 
         422         1968          591          508           10         1963 
TCGA-86-8073 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8281 
          13          479          489          476           16         1955 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
          19           26           35           45           34           18 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 
          15          455          405           10           30           14 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
          39          323           60           79          417          372 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC 
         224           35          492          197          174           44 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7043 TCGA-95-7567 
         218          297          127          186            2          568 
TCGA-95-7947 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
         477          121          964         1965         1932         1332 
TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 
         181           22          107         1965           87          147 
TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M2 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
          15          115          197          392          427          459 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
          44          170          154          114          287          282 
TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
         238          435          116          285          622          353 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 
        1946         1967         1951         1954         1954         1957 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
        1980         1951         1944         1970         1970          142 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
        1955         1971         1490 

  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                            6                             1 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                         2696                          2370 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                          619                           455 
[1] "6.0 - 2696.0 (619.0)" "1.0 - 2370.0 (455.0)"
[1] "hr=" "2.2"
D36V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK  4(2Q37.3) MUTATED         2       14       23         2        10
  DEL PEAK  4(2Q37.3) WILD-TYPE       2       99      108        41        59
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK  4(2Q37.3) MUTATED            7          1        2
  DEL PEAK  4(2Q37.3) WILD-TYPE         60         10       21
D36V3, multiclass
            clus
vv           DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  STAGE I                              2                             2
  STAGE IA                            14                            99
  STAGE IB                            23                           108
  STAGE IIA                            2                            41
  STAGE IIB                           10                            59
  STAGE IIIA                           7                            60
  STAGE IIIB                           1                            10
  STAGE IV                             2                            21
[1] 8 2
[1] TRUE
[1] "dimension of 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(2Q37.3) MUTATED    18  37   5   1
  DEL PEAK  4(2Q37.3) WILD-TYPE 125 222  35  17
D36V4, multiclass
    clus
vv   DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  T1                          18                           125
  T2                          37                           222
  T3                           5                            35
  T4                           1                            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  4(2Q37.3) MUTATED    46   8     7
  DEL PEAK  4(2Q37.3) WILD-TYPE 249  77    65
D36V5, multiclass
       clus
vv      DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  N0                             46                           249
  N1                              8                            77
  N2+N3                           7                            65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK  4(2Q37.3) MUTATED    47   2   0   0  12
  DEL PEAK  4(2Q37.3) WILD-TYPE 270  16   1   3 107
D36V6, multiclass
     clus
vv    DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  M0                           47                           270
  M1                            2                            16
  M1A                           0                             1
  M1B                           0                             3
  MX                           12                           107
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V7, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q37.3) MUTATED    40  21
  DEL PEAK  4(2Q37.3) WILD-TYPE 208 193
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED     40   21
  DEL PEAK  4(2Q37.3) WILD-TYPE  208  193
        clus
vv       DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  FEMALE                          40                           208
  MALE                            21                           193
[1] 2 2
[1] FALSE
D36V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  DEL PEAK  4(2Q37.3) MUTATED                            4
  DEL PEAK  4(2Q37.3) WILD-TYPE                          9
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK  4(2Q37.3) MUTATED                                  10
  DEL PEAK  4(2Q37.3) WILD-TYPE                                83
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  4(2Q37.3) MUTATED                                                   37
  DEL PEAK  4(2Q37.3) WILD-TYPE                                                257
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK  4(2Q37.3) MUTATED                                            0
  DEL PEAK  4(2Q37.3) WILD-TYPE                                          4
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK  4(2Q37.3) MUTATED                                               4
  DEL PEAK  4(2Q37.3) WILD-TYPE                                            15
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK  4(2Q37.3) MUTATED                                1
  DEL PEAK  4(2Q37.3) WILD-TYPE                              1
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK  4(2Q37.3) MUTATED                                    1
  DEL PEAK  4(2Q37.3) WILD-TYPE                                  3
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK  4(2Q37.3) MUTATED                              0
  DEL PEAK  4(2Q37.3) WILD-TYPE                            2
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK  4(2Q37.3) MUTATED                               3
  DEL PEAK  4(2Q37.3) WILD-TYPE                            16
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK  4(2Q37.3) MUTATED                                 0
  DEL PEAK  4(2Q37.3) WILD-TYPE                               1
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK  4(2Q37.3) MUTATED                                               0
  DEL PEAK  4(2Q37.3) WILD-TYPE                                             4
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK  4(2Q37.3) MUTATED                              1
  DEL PEAK  4(2Q37.3) WILD-TYPE                            6
D36V9, multiclass
                                                    clus
vv                                                   DEL PEAK  4(2Q37.3) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           10
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          37
  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                                                3
  LUNG SIGNET RING ADENOCARCINOMA                                              0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                0
  MUCINOUS (COLLOID) CARCINOMA                                                 1
                                                    clus
vv                                                   DEL PEAK  4(2Q37.3) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             83
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           257
  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                                                 16
  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"
D36V10, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q37.3) MUTATED     0  61
  DEL PEAK  4(2Q37.3) WILD-TYPE  21 380
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED      0   61
  DEL PEAK  4(2Q37.3) WILD-TYPE   21  380
     clus
vv    DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  NO                            0                            21
  YES                          61                           380
[1] 2 2
[1] FALSE
D36V11, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  4(2Q37.3) MUTATED    38   0   0   1
  DEL PEAK  4(2Q37.3) WILD-TYPE 280  11   4  18
D36V12, multiclass
    clus
vv   DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  R0                          38                           280
  R1                           0                            11
  R2                           0                             4
  RX                           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                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  4(2Q37.3) MUTATED                                  0     3
  DEL PEAK  4(2Q37.3) WILD-TYPE                                1     3
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(2Q37.3) MUTATED                           2    49
  DEL PEAK  4(2Q37.3) WILD-TYPE                        24   313
D36V13, multiclass
                                  clus
vv                                 DEL PEAK  4(2Q37.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                  2
  WHITE                                                     49
                                  clus
vv                                 DEL PEAK  4(2Q37.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        3
  BLACK OR AFRICAN AMERICAN                                   24
  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"
D36V14, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q37.3) MUTATED     1  46
  DEL PEAK  4(2Q37.3) WILD-TYPE   6 286
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED      1   46
  DEL PEAK  4(2Q37.3) WILD-TYPE    6  286
                        clus
vv                       DEL PEAK  4(2Q37.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          46
                        clus
vv                       DEL PEAK  4(2Q37.3) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           286
[1] 2 2
[1] FALSE

Clustering(37) Variable = DEL PEAK  5(3P26.3) MUTATION ANALYSIS
D37V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  5(3P26.3) MUTATED   145  34
  DEL PEAK  5(3P26.3) WILD-TYPE 176  48
  DEL PEAK  5(3P26.3) MUTATED DEL PEAK  5(3P26.3) WILD-TYPE 
                          179                           224 
  DEL PEAK  5(3P26.3) MUTATED DEL PEAK  5(3P26.3) WILD-TYPE 
                           34                            48 
$`DEL PEAK  5(3P26.3) MUTATED`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4389 TCGA-05-4390 TCGA-05-4415 TCGA-05-4420 
        1523          607         1369         1126         1997          912 
TCGA-05-4432 TCGA-05-5425 TCGA-05-5715 TCGA-35-5375 TCGA-38-4627 TCGA-38-4628 
         761          882           62          264         1147         1492 
TCGA-38-6178 TCGA-44-2656 TCGA-44-2657 TCGA-44-2668 TCGA-44-5643 TCGA-44-5644 
         448         1429          400          246         1013          863 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6147 TCGA-44-6774 TCGA-44-6776 TCGA-44-6778 
         723          328          845          658         1938         1864 
TCGA-44-6779 TCGA-44-7660 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
        1978          592          882          535          719          385 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47F TCGA-49-4501 TCGA-49-4505 
          99          260          486          337         1421          428 
TCGA-49-4506 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
         999         1700          445          369          890          522 
TCGA-50-5049 TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 TCGA-50-5932 TCGA-50-5935 
        2146         1499          246          267         1091          653 
TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 TCGA-50-6597 TCGA-50-7109 TCGA-53-7624 
         567          764          686         1015          255         1986 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1596 TCGA-55-6983 
        1971          424          280         1178         1375         1826 
TCGA-55-6985 TCGA-55-7570 TCGA-55-7573 TCGA-55-7576 TCGA-55-7724 TCGA-55-7726 
        1233            6            4           40         1958           39 
TCGA-55-7727 TCGA-55-7907 TCGA-55-7910 TCGA-55-7914 TCGA-55-7995 TCGA-55-8090 
          34           16          197            3            5            6 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8206 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
          26            4           46           11            8           15 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8620 TCGA-55-A491 TCGA-55-A492 
         202          536           15           66         1952            1 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-A471 
          47          162         1289         1970         2696         1246 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 TCGA-64-5774 TCGA-64-5779 
        1728          628         1189         1686         1959          864 
TCGA-64-5781 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-6217 TCGA-69-7763 
        1559           31          610          573          422          690 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 
         414          165          230           70           89          100 
TCGA-71-6725 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-7498 
          61          800          467          131           40          621 
TCGA-73-7499 TCGA-75-6214 TCGA-75-7027 TCGA-75-7031 TCGA-78-7146 TCGA-78-7147 
         519         1970         1956         1965         1988         1950 
TCGA-78-7148 TCGA-78-7150 TCGA-78-7159 TCGA-78-7160 TCGA-78-7167 TCGA-78-7535 
        1944         1963         1221          678         1937         1972 
TCGA-78-7536 TCGA-78-7542 TCGA-78-8640 TCGA-78-8660 TCGA-80-5608 TCGA-83-5908 
        1949         1952         1949         1954         1972          824 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 
        1959           11          630          422          591         1963 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8280 
         745           10           13           24          479           16 
TCGA-86-8358 TCGA-86-8585 TCGA-86-8669 TCGA-86-8672 TCGA-86-A4D0 TCGA-91-6829 
          19           35           34           15           30         1940 
TCGA-91-6830 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-8499 TCGA-91-A4BC 
          60           79          372          842           36           44 
TCGA-93-7348 TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-95-7947 TCGA-95-7948 
         127           34            2          568          477          476 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7554 TCGA-97-7937 TCGA-97-8174 TCGA-97-8177 
         964         1965          775          181         1965          147 
TCGA-97-A4M7 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-A4AG TCGA-MN-A4N1 TCGA-MN-A4N4 
         271          170          154          238          285          622 
TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-MP-A4TF TCGA-MP-A4TI 
        1954         1957         1944         1970         1955 

$`DEL PEAK  5(3P26.3) WILD-TYPE`
TCGA-05-4384 TCGA-05-4396 TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 
         426         1947         1431          578          610         1958 
TCGA-05-4417 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 
         455          365          913          669          791          791 
TCGA-05-4430 TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 
         761          730          457          151          670           30 
TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 TCGA-38-4626 TCGA-38-4629 
          14          225          182         1952         1962          864 
TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 
        1073          354         1357         1971          133         1324 
TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-3396 
        1367          741         1280         1301           97         1130 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5645 TCGA-44-6146 
        1163         1036          190          722          383          302 
TCGA-44-6148 TCGA-44-6775 TCGA-44-6777 TCGA-44-7659 TCGA-44-7661 TCGA-44-7662 
         704          705         1942          444          366          218 
TCGA-44-7667 TCGA-44-7669 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS 
         557         1970          466          287          351          415 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
          76         1932         1081          268          896          157 
TCGA-49-6761 TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5930 
         354         2174          455          785          944          282 
TCGA-50-5933 TCGA-50-5942 TCGA-50-8460 TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 
        2370          883          105          701         1479           87 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 
           2          993           24         1239           25         1475 
TCGA-55-6980 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
          67         2151         1170           18           35          121 
TCGA-55-7574 TCGA-55-7725 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 
          95           39           24           54           19           21 
TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8091 TCGA-55-8096 
          31           33           21          100           43           47 
TCGA-55-8097 TCGA-55-8205 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
          15           33           66          216           44           23 
TCGA-55-8505 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8616 
          29          228            9            3          146           48 
TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
          49          106           33           42           29           48 
TCGA-55-A493 TCGA-55-A494 TCGA-62-8395 TCGA-62-8402 TCGA-62-A46U TCGA-62-A46V 
          28            5         1216         1445         2067         2199 
TCGA-62-A472 TCGA-64-1680 TCGA-64-1681 TCGA-64-5775 TCGA-64-5778 TCGA-64-5815 
         910         1126         1968           62         1305          866 
TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 
         427          385          174          141          202          186 
TCGA-69-7974 TCGA-69-7980 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-73-4658 
         184          382           77          129          214         1600 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4676 TCGA-73-4677 TCGA-75-7025 TCGA-78-7145 
         711          912          164           38         1967         1973 
TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
        1093         1202          760         1948         1957         1961 
TCGA-78-7158 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7220 
        1963          215         1940         1950         1934         1965 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 
        1944          327          881          994         1971         1981 
TCGA-78-8662 TCGA-80-5607 TCGA-86-7714 TCGA-86-7955 TCGA-86-8056 TCGA-86-8076 
        1964         1965         1968          508         1963          489 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8281 TCGA-86-8359 TCGA-86-8668 TCGA-86-8671 
         476          482         1955           26           45           18 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
         455          405           10           14           39          323 
TCGA-91-6831 TCGA-91-6836 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
         310          417          224           35          492          197 
TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 TCGA-93-8067 TCGA-95-7944 TCGA-95-A4VK 
         174          218          297          186          377          121 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 
        1932         1332           22          107          182           87 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 TCGA-99-7458 TCGA-99-8025 
          15          148          115          197          392          427 
TCGA-99-8028 TCGA-99-8032 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E5 
         459           44          114          287          282          578 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
         435          116            6          353         1946         1967 
TCGA-MP-A4T2 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TE TCGA-MP-A4TH 
        1951         1954         1980         1951         1970          142 
TCGA-MP-A4TK TCGA-MP-A5C7 
        1971         1490 

  DEL PEAK  5(3P26.3) MUTATED DEL PEAK  5(3P26.3) WILD-TYPE 
                            1                             2 
  DEL PEAK  5(3P26.3) MUTATED DEL PEAK  5(3P26.3) WILD-TYPE 
                         2696                          2370 
  DEL PEAK  5(3P26.3) MUTATED DEL PEAK  5(3P26.3) WILD-TYPE 
                          591                           410 
[1] "1.0 - 2696.0 (591.0)" "2.0 - 2370.0 (410.0)"
[1] "hr=" "1.2"
D37V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK  5(3P26.3) MUTATED         1       46       53        27        33
  DEL PEAK  5(3P26.3) WILD-TYPE       3       67       78        16        36
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK  5(3P26.3) MUTATED           30          4       15
  DEL PEAK  5(3P26.3) WILD-TYPE         37          7        8
D37V3, multiclass
            clus
vv           DEL PEAK  5(3P26.3) MUTATED DEL PEAK  5(3P26.3) WILD-TYPE
  STAGE I                              1                             3
  STAGE IA                            46                            67
  STAGE IB                            53                            78
  STAGE IIA                           27                            16
  STAGE IIB                           33                            36
  STAGE IIIA                          30                            37
  STAGE IIIB                           4                             7
  STAGE IV                            15                             8
[1] 8 2
[1] TRUE
[1] "dimension of 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(3P26.3) MUTATED    64 126  10   7
  DEL PEAK  5(3P26.3) WILD-TYPE  79 133  30  11
D37V4, multiclass
    clus
vv   DEL PEAK  5(3P26.3) MUTATED DEL PEAK  5(3P26.3) WILD-TYPE
  T1                          64                            79
  T2                         126                           133
  T3                          10                            30
  T4                           7                            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  5(3P26.3) MUTATED   122  48    34
  DEL PEAK  5(3P26.3) WILD-TYPE 173  37    38
D37V5, multiclass
       clus
vv      DEL PEAK  5(3P26.3) MUTATED DEL PEAK  5(3P26.3) WILD-TYPE
  N0                            122                           173
  N1                             48                            37
  N2+N3                          34                            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"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK  5(3P26.3) MUTATED   144  12   0   2  49
  DEL PEAK  5(3P26.3) WILD-TYPE 173   6   1   1  70
D37V6, multiclass
     clus
vv    DEL PEAK  5(3P26.3) MUTATED DEL PEAK  5(3P26.3) WILD-TYPE
  M0                          144                           173
  M1                           12                             6
  M1A                           0                             1
  M1B                           2                             1
  MX                           49                            70
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V7, binary
                               cls
clus                              0   1
  DEL PEAK  5(3P26.3) MUTATED   110  99
  DEL PEAK  5(3P26.3) WILD-TYPE 138 115
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P26.3) MUTATED    110   99
  DEL PEAK  5(3P26.3) WILD-TYPE  138  115
        clus
vv       DEL PEAK  5(3P26.3) MUTATED DEL PEAK  5(3P26.3) WILD-TYPE
  FEMALE                         110                           138
  MALE                            99                           115
[1] 2 2
[1] FALSE
D37V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  DEL PEAK  5(3P26.3) MUTATED                            7
  DEL PEAK  5(3P26.3) WILD-TYPE                          6
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK  5(3P26.3) MUTATED                                  43
  DEL PEAK  5(3P26.3) WILD-TYPE                                50
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  5(3P26.3) MUTATED                                                  138
  DEL PEAK  5(3P26.3) WILD-TYPE                                                156
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK  5(3P26.3) MUTATED                                            0
  DEL PEAK  5(3P26.3) WILD-TYPE                                          4
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK  5(3P26.3) MUTATED                                               6
  DEL PEAK  5(3P26.3) WILD-TYPE                                            13
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK  5(3P26.3) MUTATED                                1
  DEL PEAK  5(3P26.3) WILD-TYPE                              1
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK  5(3P26.3) MUTATED                                    2
  DEL PEAK  5(3P26.3) WILD-TYPE                                  2
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK  5(3P26.3) MUTATED                              0
  DEL PEAK  5(3P26.3) WILD-TYPE                            2
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK  5(3P26.3) MUTATED                               7
  DEL PEAK  5(3P26.3) WILD-TYPE                            12
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK  5(3P26.3) MUTATED                                 1
  DEL PEAK  5(3P26.3) WILD-TYPE                               0
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK  5(3P26.3) MUTATED                                               1
  DEL PEAK  5(3P26.3) WILD-TYPE                                             3
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK  5(3P26.3) MUTATED                              3
  DEL PEAK  5(3P26.3) WILD-TYPE                            4
D37V9, multiclass
                                                    clus
vv                                                   DEL PEAK  5(3P26.3) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           43
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         138
  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                                                 3
                                                    clus
vv                                                   DEL PEAK  5(3P26.3) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             50
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           156
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 13
  LUNG CLEAR CELL ADENOCARCINOMA                                                 1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             2
  LUNG MUCINOUS ADENOCARCINOMA                                                   2
  LUNG PAPILLARY ADENOCARCINOMA                                                 12
  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"
D37V10, binary
                               cls
clus                              0   1
  DEL PEAK  5(3P26.3) MUTATED     8 201
  DEL PEAK  5(3P26.3) WILD-TYPE  13 240
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P26.3) MUTATED      8  201
  DEL PEAK  5(3P26.3) WILD-TYPE   13  240
     clus
vv    DEL PEAK  5(3P26.3) MUTATED DEL PEAK  5(3P26.3) WILD-TYPE
  NO                            8                            13
  YES                         201                           240
[1] 2 2
[1] FALSE
D37V11, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  5(3P26.3) MUTATED   140   2   2   7
  DEL PEAK  5(3P26.3) WILD-TYPE 178   9   2  12
D37V12, multiclass
    clus
vv   DEL PEAK  5(3P26.3) MUTATED DEL PEAK  5(3P26.3) WILD-TYPE
  R0                         140                           178
  R1                           2                             9
  R2                           2                             2
  RX                           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                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  5(3P26.3) MUTATED                                  1     2
  DEL PEAK  5(3P26.3) WILD-TYPE                                0     4
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(3P26.3) MUTATED                          15   165
  DEL PEAK  5(3P26.3) WILD-TYPE                        11   197
D37V13, multiclass
                                  clus
vv                                 DEL PEAK  5(3P26.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 15
  WHITE                                                    165
                                  clus
vv                                 DEL PEAK  5(3P26.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   11
  WHITE                                                      197
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V14, binary
                               cls
clus                              0   1
  DEL PEAK  5(3P26.3) MUTATED     4 154
  DEL PEAK  5(3P26.3) WILD-TYPE   3 178
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P26.3) MUTATED      4  154
  DEL PEAK  5(3P26.3) WILD-TYPE    3  178
                        clus
vv                       DEL PEAK  5(3P26.3) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         154
                        clus
vv                       DEL PEAK  5(3P26.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           178
[1] 2 2
[1] FALSE

Clustering(38) Variable = DEL PEAK  6(3P21.31) MUTATION ANALYSIS
D38V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  6(3P21.31) MUTATED   156  37
  DEL PEAK  6(3P21.31) WILD-TYPE 165  45
  DEL PEAK  6(3P21.31) MUTATED DEL PEAK  6(3P21.31) WILD-TYPE 
                           193                            210 
  DEL PEAK  6(3P21.31) MUTATED DEL PEAK  6(3P21.31) WILD-TYPE 
                            37                             45 
$`DEL PEAK  6(3P21.31) MUTATED`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4389 TCGA-05-4390 TCGA-05-4415 TCGA-05-4420 
        1523          607         1369         1126         1997          912 
TCGA-05-4432 TCGA-05-5420 TCGA-05-5425 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 
         761          457          882           62          225          182 
TCGA-35-5375 TCGA-38-4627 TCGA-38-4628 TCGA-38-4630 TCGA-38-6178 TCGA-44-2656 
         264         1147         1492         1073          448         1429 
TCGA-44-2657 TCGA-44-2668 TCGA-44-3918 TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 
         400          246         1036         1013          863          723 
TCGA-44-6145 TCGA-44-6147 TCGA-44-6774 TCGA-44-6776 TCGA-44-6778 TCGA-44-6779 
         328          845          658         1938         1864         1978 
TCGA-44-7660 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
         592          882          535          719          385           99 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47F TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
         260          486          337         1421          428          999 
TCGA-49-4507 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
         268         1700          445          369          890          522 
TCGA-50-5049 TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 TCGA-50-5932 TCGA-50-5935 
        2146         1499          246          267         1091          653 
TCGA-50-5941 TCGA-50-5944 TCGA-50-6597 TCGA-50-7109 TCGA-53-7624 TCGA-53-7626 
         567          764         1015          255         1986         1971 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6983 
         424          280         1178         1375           87         1826 
TCGA-55-6985 TCGA-55-7570 TCGA-55-7573 TCGA-55-7576 TCGA-55-7724 TCGA-55-7726 
        1233            6            4           40         1958           39 
TCGA-55-7727 TCGA-55-7907 TCGA-55-7910 TCGA-55-7914 TCGA-55-7995 TCGA-55-8090 
          34           16          197            3            5            6 
TCGA-55-8094 TCGA-55-8206 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8514 
           4           46           11            8           15          202 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Z TCGA-55-A490 
         536           15           48           66           29           48 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8397 TCGA-62-8398 
        1952            1           47          162         1289         1970 
TCGA-62-8399 TCGA-62-A471 TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-5774 
        2696         1246         1728         1189         1686         1959 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 
         864         1559          866           31          610          573 
TCGA-67-6217 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7978 
         422          690          414          165          230           70 
TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-71-6725 TCGA-73-4666 TCGA-73-4668 
          89          100           77           61          800          467 
TCGA-73-4670 TCGA-73-4675 TCGA-73-7498 TCGA-73-7499 TCGA-75-6214 TCGA-75-7027 
         131           40          621          519         1970         1956 
TCGA-75-7031 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7150 TCGA-78-7159 
        1965         1988         1950         1944         1963         1221 
TCGA-78-7160 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7542 
         678         1937         1965         1972         1949         1952 
TCGA-78-8640 TCGA-78-8660 TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 
        1949         1954         1972          824         1959           11 
TCGA-86-7711 TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 TCGA-86-8073 
         630          591         1963          745           10           13 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8278 TCGA-86-8280 TCGA-86-8358 TCGA-86-8585 
          24          479          476           16           19           35 
TCGA-86-8669 TCGA-86-A4D0 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
          34           30         1940           60          310           79 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-8499 TCGA-91-A4BC TCGA-93-7348 
         372          842          224           36           44          127 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-95-7947 TCGA-95-7948 TCGA-97-7546 
          34            2          568          477          476          964 
TCGA-97-7547 TCGA-97-7554 TCGA-97-7937 TCGA-97-8174 TCGA-97-8177 TCGA-97-A4M7 
        1965          775          181         1965          147          271 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-MN-A4N1 
          44          170          154          238          578          285 
TCGA-MN-A4N4 TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-MP-A4TF 
         622         1967         1951         1957         1944         1970 
TCGA-MP-A4TI 
        1955 

$`DEL PEAK  6(3P21.31) WILD-TYPE`
TCGA-05-4384 TCGA-05-4396 TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 
         426         1947         1431          578          610         1958 
TCGA-05-4417 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 
         455          365          913          669          791          791 
TCGA-05-4430 TCGA-05-4433 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 TCGA-35-3615 
         761          730          151          670           30           14 
TCGA-38-4625 TCGA-38-4626 TCGA-38-4629 TCGA-38-4631 TCGA-38-4632 TCGA-38-7271 
        1952         1962          864          354         1357         1971 
TCGA-38-A44F TCGA-44-2655 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 
         133         1324         1367          741         1280         1301 
TCGA-44-2666 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5645 
          97         1130         1163          190          722          383 
TCGA-44-6146 TCGA-44-6148 TCGA-44-6775 TCGA-44-6777 TCGA-44-7659 TCGA-44-7661 
         302          704          705         1942          444          366 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G 
         218          557         1970          466          287          351 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 TCGA-49-4510 TCGA-49-4512 
         415           76         1932         1081          896          157 
TCGA-49-6761 TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5930 
         354         2174          455          785          944          282 
TCGA-50-5933 TCGA-50-5942 TCGA-50-5946 TCGA-50-8460 TCGA-55-1592 TCGA-55-1595 
        2370          883          686          105          701         1479 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 
           2          993           24         1239           25         1475 
TCGA-55-6980 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
          67         2151         1170           18           35          121 
TCGA-55-7574 TCGA-55-7725 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 
          95           39           24           54           19           21 
TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8091 TCGA-55-8092 
          31           33           21          100           43           26 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 
          47           15           33           66          216           44 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
          23           29          228            9            3          146 
TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A493 TCGA-55-A494 
          49          106           33           42           28            5 
TCGA-62-8395 TCGA-62-8402 TCGA-62-A46U TCGA-62-A46V TCGA-62-A472 TCGA-64-1677 
        1216         1445         2067         2199          910          628 
TCGA-64-1680 TCGA-64-1681 TCGA-64-5775 TCGA-64-5778 TCGA-67-3773 TCGA-67-3774 
        1126         1968           62         1305          427          385 
TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7974 TCGA-69-7980 
         174          141          202          186          184          382 
TCGA-69-8255 TCGA-69-A59K TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4676 
         129          214         1600          711          912          164 
TCGA-73-4677 TCGA-75-7025 TCGA-78-7145 TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 
          38         1967         1973         1093         1202          760 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7161 TCGA-78-7162 
        1948         1957         1961         1963          215         1940 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7633 
        1950         1934         1944          327          881          994 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5607 TCGA-86-7713 TCGA-86-7714 
        1971         1981         1964         1965          422         1968 
TCGA-86-7955 TCGA-86-8056 TCGA-86-8076 TCGA-86-8279 TCGA-86-8281 TCGA-86-8359 
         508         1963          489          482         1955           26 
TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
          45           18           15          455          405           10 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6836 TCGA-91-6849 TCGA-91-7771 
          14           39          323          417           35          492 
TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 TCGA-93-8067 TCGA-95-7944 
         197          174          218          297          186          377 
TCGA-95-A4VK TCGA-97-7552 TCGA-97-7553 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
         121         1932         1332           22          107          182 
TCGA-97-8175 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 TCGA-99-7458 
          87           15          148          115          197          392 
TCGA-99-8025 TCGA-99-8028 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E6 
         427          459          114          287          282          435 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4T4 TCGA-MP-A4T7 
         116            6          353         1946         1954         1954 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TK TCGA-MP-A5C7 
        1980         1951         1970          142         1971         1490 

  DEL PEAK  6(3P21.31) MUTATED DEL PEAK  6(3P21.31) WILD-TYPE 
                             1                              2 
  DEL PEAK  6(3P21.31) MUTATED DEL PEAK  6(3P21.31) WILD-TYPE 
                          2696                           2370 
  DEL PEAK  6(3P21.31) MUTATED DEL PEAK  6(3P21.31) WILD-TYPE 
                         567.0                          419.5 
[1] "1.0 - 2696.0 (567.0)" "2.0 - 2370.0 (419.5)"
[1] "hr=" "1.2"
D38V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK  6(3P21.31) MUTATED         2       51       56        27        33
  DEL PEAK  6(3P21.31) WILD-TYPE       2       62       75        16        36
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK  6(3P21.31) MUTATED           34          4       14
  DEL PEAK  6(3P21.31) WILD-TYPE         33          7        9
D38V3, multiclass
            clus
vv           DEL PEAK  6(3P21.31) MUTATED DEL PEAK  6(3P21.31) WILD-TYPE
  STAGE I                               2                              2
  STAGE IA                             51                             62
  STAGE IB                             56                             75
  STAGE IIA                            27                             16
  STAGE IIB                            33                             36
  STAGE IIIA                           34                             33
  STAGE IIIB                            4                              7
  STAGE IV                             14                              9
[1] 8 2
[1] TRUE
[1] "dimension of 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(3P21.31) MUTATED    71 134   9   6
  DEL PEAK  6(3P21.31) WILD-TYPE  72 125  31  12
D38V4, multiclass
    clus
vv   DEL PEAK  6(3P21.31) MUTATED DEL PEAK  6(3P21.31) WILD-TYPE
  T1                           71                             72
  T2                          134                            125
  T3                            9                             31
  T4                            6                             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  6(3P21.31) MUTATED   128  52    36
  DEL PEAK  6(3P21.31) WILD-TYPE 167  33    36
D38V5, multiclass
       clus
vv      DEL PEAK  6(3P21.31) MUTATED DEL PEAK  6(3P21.31) WILD-TYPE
  N0                             128                            167
  N1                              52                             33
  N2+N3                           36                             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"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK  6(3P21.31) MUTATED   155  11   0   2  51
  DEL PEAK  6(3P21.31) WILD-TYPE 162   7   1   1  68
D38V6, multiclass
     clus
vv    DEL PEAK  6(3P21.31) MUTATED DEL PEAK  6(3P21.31) WILD-TYPE
  M0                           155                            162
  M1                            11                              7
  M1A                            0                              1
  M1B                            2                              1
  MX                            51                             68
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V7, binary
                                cls
clus                               0   1
  DEL PEAK  6(3P21.31) MUTATED   115 107
  DEL PEAK  6(3P21.31) WILD-TYPE 133 107
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  6(3P21.31) MUTATED    115  107
  DEL PEAK  6(3P21.31) WILD-TYPE  133  107
        clus
vv       DEL PEAK  6(3P21.31) MUTATED DEL PEAK  6(3P21.31) WILD-TYPE
  FEMALE                          115                            133
  MALE                            107                            107
[1] 2 2
[1] FALSE
D38V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK  6(3P21.31) MUTATED                            7
  DEL PEAK  6(3P21.31) WILD-TYPE                          6
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK  6(3P21.31) MUTATED                                  45
  DEL PEAK  6(3P21.31) WILD-TYPE                                48
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  6(3P21.31) MUTATED                                                  146
  DEL PEAK  6(3P21.31) WILD-TYPE                                                148
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK  6(3P21.31) MUTATED                                            0
  DEL PEAK  6(3P21.31) WILD-TYPE                                          4
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK  6(3P21.31) MUTATED                                               6
  DEL PEAK  6(3P21.31) WILD-TYPE                                            13
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK  6(3P21.31) MUTATED                                1
  DEL PEAK  6(3P21.31) WILD-TYPE                              1
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK  6(3P21.31) MUTATED                                    2
  DEL PEAK  6(3P21.31) WILD-TYPE                                  2
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK  6(3P21.31) MUTATED                              0
  DEL PEAK  6(3P21.31) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK  6(3P21.31) MUTATED                               8
  DEL PEAK  6(3P21.31) WILD-TYPE                            11
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK  6(3P21.31) MUTATED                                 1
  DEL PEAK  6(3P21.31) WILD-TYPE                               0
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK  6(3P21.31) MUTATED                                               2
  DEL PEAK  6(3P21.31) WILD-TYPE                                             2
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK  6(3P21.31) MUTATED                              4
  DEL PEAK  6(3P21.31) WILD-TYPE                            3
D38V9, multiclass
                                                    clus
vv                                                   DEL PEAK  6(3P21.31) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            45
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          146
  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                                                  4
                                                    clus
vv                                                   DEL PEAK  6(3P21.31) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              48
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            148
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  13
  LUNG CLEAR CELL ADENOCARCINOMA                                                  1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              2
  LUNG MUCINOUS ADENOCARCINOMA                                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                                  11
  LUNG SIGNET RING ADENOCARCINOMA                                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                   2
  MUCINOUS (COLLOID) CARCINOMA                                                    3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V10, binary
                                cls
clus                               0   1
  DEL PEAK  6(3P21.31) MUTATED    10 212
  DEL PEAK  6(3P21.31) WILD-TYPE  11 229
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  6(3P21.31) MUTATED     10  212
  DEL PEAK  6(3P21.31) WILD-TYPE   11  229
     clus
vv    DEL PEAK  6(3P21.31) MUTATED DEL PEAK  6(3P21.31) WILD-TYPE
  NO                            10                             11
  YES                          212                            229
[1] 2 2
[1] FALSE
D38V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK  6(3P21.31) MUTATED   151   3   2   6
  DEL PEAK  6(3P21.31) WILD-TYPE 167   8   2  13
D38V12, multiclass
    clus
vv   DEL PEAK  6(3P21.31) MUTATED DEL PEAK  6(3P21.31) WILD-TYPE
  R0                          151                            167
  R1                            3                              8
  R2                            2                              2
  RX                            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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  6(3P21.31) MUTATED                                  1     2
  DEL PEAK  6(3P21.31) WILD-TYPE                                0     4
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(3P21.31) MUTATED                          15   178
  DEL PEAK  6(3P21.31) WILD-TYPE                        11   184
D38V13, multiclass
                                  clus
vv                                 DEL PEAK  6(3P21.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  15
  WHITE                                                     178
                                  clus
vv                                 DEL PEAK  6(3P21.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    11
  WHITE                                                       184
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V14, binary
                                cls
clus                               0   1
  DEL PEAK  6(3P21.31) MUTATED     4 167
  DEL PEAK  6(3P21.31) WILD-TYPE   3 165
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  6(3P21.31) MUTATED      4  167
  DEL PEAK  6(3P21.31) WILD-TYPE    3  165
                        clus
vv                       DEL PEAK  6(3P21.31) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          167
                        clus
vv                       DEL PEAK  6(3P21.31) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            165
[1] 2 2
[1] FALSE

Clustering(39) Variable = DEL PEAK  7(3Q11.1) MUTATION ANALYSIS
D39V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  7(3Q11.1) MUTATED    90  23
  DEL PEAK  7(3Q11.1) WILD-TYPE 231  59
  DEL PEAK  7(3Q11.1) MUTATED DEL PEAK  7(3Q11.1) WILD-TYPE 
                          113                           290 
  DEL PEAK  7(3Q11.1) MUTATED DEL PEAK  7(3Q11.1) WILD-TYPE 
                           23                            59 
$`DEL PEAK  7(3Q11.1) MUTATED`
TCGA-05-4249 TCGA-05-4389 TCGA-05-4390 TCGA-05-4415 TCGA-05-5420 TCGA-05-5425 
        1523         1369         1126         1997          457          882 
TCGA-05-5715 TCGA-44-6144 TCGA-44-6145 TCGA-44-6774 TCGA-44-6776 TCGA-44-6779 
          62          723          328          658         1938         1978 
TCGA-44-7660 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
         592          535          719          385           99          260 
TCGA-44-A479 TCGA-44-A47F TCGA-49-4506 TCGA-49-6742 TCGA-49-6743 TCGA-50-5068 
         486          337          999          445          369         1499 
TCGA-50-5072 TCGA-50-5932 TCGA-50-5935 TCGA-50-5941 TCGA-50-6597 TCGA-53-7624 
         246         1091          653          567         1015         1986 
TCGA-55-1592 TCGA-55-5899 TCGA-55-6983 TCGA-55-6985 TCGA-55-7283 TCGA-55-7573 
         701           87         1826         1233           35            4 
TCGA-55-7576 TCGA-55-7727 TCGA-55-7910 TCGA-55-8090 TCGA-55-8205 TCGA-55-8206 
          40           34          197            6           33           46 
TCGA-55-8514 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Z TCGA-55-A492 
         202           15           48           66           29            1 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-64-1678 
          47          162         1289         1970         2696         1189 
TCGA-64-5774 TCGA-64-5781 TCGA-67-3770 TCGA-67-3772 TCGA-67-6217 TCGA-69-7763 
        1959         1559           31          573          422          690 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-8253 TCGA-71-6725 
         414          165          230          184          100           61 
TCGA-73-4659 TCGA-73-4675 TCGA-73-7498 TCGA-75-6214 TCGA-75-7027 TCGA-75-7031 
         711           40          621         1970         1956         1965 
TCGA-78-7145 TCGA-78-7148 TCGA-78-7160 TCGA-78-7161 TCGA-78-7167 TCGA-78-7220 
        1973         1944          678          215         1937         1965 
TCGA-78-7535 TCGA-78-7536 TCGA-78-8660 TCGA-80-5608 TCGA-83-5908 TCGA-86-7701 
        1972         1949         1954         1972          824           11 
TCGA-86-7954 TCGA-86-8054 TCGA-86-8073 TCGA-86-8075 TCGA-86-8280 TCGA-86-8585 
        1963          745           13          479           16           35 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6847 TCGA-91-7771 TCGA-91-8497 TCGA-91-8499 
         310           79          842          492          174           36 
TCGA-93-7348 TCGA-95-7039 TCGA-95-7567 TCGA-95-7948 TCGA-97-7546 TCGA-97-7554 
         127           34          568          476          964          775 
TCGA-97-7937 TCGA-97-8172 TCGA-97-8174 TCGA-97-8177 TCGA-99-8032 TCGA-J2-8192 
         181          182         1965          147           44          154 
TCGA-J2-A4AG TCGA-MP-A4TC TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TK 
         238         1944         1970         1955         1971 

$`DEL PEAK  7(3Q11.1) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 
         607          426         1947         1431          578          610 
TCGA-05-4410 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
        1958          455          912          365          913          669 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 
         791          791          761          761          730          151 
TCGA-05-5428 TCGA-05-5429 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 
         670           30           14          225          182          264 
TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 
        1952         1962         1147         1492          864         1073 
TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 
         354         1357          448         1971          133         1324 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 
        1429          400         1367          741         1280         1301 
TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
          97          246         1130         1163         1036          190 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6146 TCGA-44-6147 
         722         1013          863          383          302          845 
TCGA-44-6148 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-7659 TCGA-44-7661 
         704          705         1942         1864          444          366 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-A47A TCGA-44-A47B 
         218          557         1970          882          466          287 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 
         351          415           76         1932         1081         1421 
TCGA-49-4505 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6744 
         428          268          896          157         1700          890 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
         522          354         2174         2146          455          785 
TCGA-50-5066 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5942 TCGA-50-5944 
         944          282          267         2370          883          764 
TCGA-50-5946 TCGA-50-7109 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
         686          255          105         1971          424          280 
TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
        1178         1479         1375            2          993           24 
TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 TCGA-55-6986 TCGA-55-6987 
        1239           25         1475           67         2151         1170 
TCGA-55-7281 TCGA-55-7284 TCGA-55-7570 TCGA-55-7574 TCGA-55-7724 TCGA-55-7725 
          18          121            6           95         1958           39 
TCGA-55-7726 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 
          39           24           54           19           16           21 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
           3           31            5           33           21          100 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8207 
          43           26            4           47           15           66 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
         216           44           23           29           11            8 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 
          15          228            9            3          146          536 
TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A490 TCGA-55-A491 
          49          106           33           42           48         1952 
TCGA-55-A493 TCGA-55-A494 TCGA-62-8395 TCGA-62-8402 TCGA-62-A46U TCGA-62-A46V 
          28            5         1216         1445         2067         2199 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1680 
        1246          910         1728          628         1686         1126 
TCGA-64-1681 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 TCGA-67-3771 
        1968           62         1305          864          866          610 
TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 
         427          385          174          141          202          186 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
          70           89          382           77          129          214 
TCGA-73-4658 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 
        1600          912          800          467          131          164 
TCGA-73-4677 TCGA-73-7499 TCGA-75-7025 TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 
          38          519         1967         1988         1950         1093 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
        1963         1202          760         1948         1957         1961 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7537 
        1963         1221         1940         1950         1934         1944 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
         327          881         1952          994         1949         1971 
TCGA-78-8655 TCGA-78-8662 TCGA-80-5607 TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 
        1981         1964         1965         1959          630          422 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 
        1968          591          508           10         1963           24 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8281 TCGA-86-8358 TCGA-86-8359 
         489          476          482         1955           19           26 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
          45           34           18           15          455          405 
TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
          10           30           14           39          323         1940 
TCGA-91-6830 TCGA-91-6836 TCGA-91-6840 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 
          60          417          372          224           35          197 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-8067 TCGA-95-7043 TCGA-95-7944 
          44          218          297          186            2          377 
TCGA-95-7947 TCGA-95-A4VK TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7941 
         477          121         1965         1932         1332           22 
TCGA-97-8171 TCGA-97-8175 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 
         107           87           15          148          115          197 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8033 TCGA-J2-8194 
         271          392          427          459          170          114 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
         287          282          578          435          116            6 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 
         285          622          353         1946         1967         1951 
TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TE 
        1954         1954         1957         1980         1951         1970 
TCGA-MP-A4TH TCGA-MP-A5C7 
         142         1490 

  DEL PEAK  7(3Q11.1) MUTATED DEL PEAK  7(3Q11.1) WILD-TYPE 
                            1                             2 
  DEL PEAK  7(3Q11.1) MUTATED DEL PEAK  7(3Q11.1) WILD-TYPE 
                         2696                          2370 
  DEL PEAK  7(3Q11.1) MUTATED DEL PEAK  7(3Q11.1) WILD-TYPE 
                          492                           455 
[1] "1.0 - 2696.0 (492.0)" "2.0 - 2370.0 (455.0)"
[1] "hr=" "1.3"
D39V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK  7(3Q11.1) MUTATED         0       29       36         9        22
  DEL PEAK  7(3Q11.1) WILD-TYPE       4       84       95        34        47
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK  7(3Q11.1) MUTATED           23          3        8
  DEL PEAK  7(3Q11.1) WILD-TYPE         44          8       15
D39V3, multiclass
            clus
vv           DEL PEAK  7(3Q11.1) MUTATED DEL PEAK  7(3Q11.1) WILD-TYPE
  STAGE I                              0                             4
  STAGE IA                            29                            84
  STAGE IB                            36                            95
  STAGE IIA                            9                            34
  STAGE IIB                           22                            47
  STAGE IIIA                          23                            44
  STAGE IIIB                           3                             8
  STAGE IV                             8                            15
[1] 8 2
[1] TRUE
[1] "dimension of 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(3Q11.1) MUTATED    36  80   9   5
  DEL PEAK  7(3Q11.1) WILD-TYPE 107 179  31  13
D39V4, multiclass
    clus
vv   DEL PEAK  7(3Q11.1) MUTATED DEL PEAK  7(3Q11.1) WILD-TYPE
  T1                          36                           107
  T2                          80                           179
  T3                           9                            31
  T4                           5                            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  7(3Q11.1) MUTATED    80  24    26
  DEL PEAK  7(3Q11.1) WILD-TYPE 215  61    46
D39V5, multiclass
       clus
vv      DEL PEAK  7(3Q11.1) MUTATED DEL PEAK  7(3Q11.1) WILD-TYPE
  N0                             80                           215
  N1                             24                            61
  N2+N3                          26                            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"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK  7(3Q11.1) MUTATED    92   6   0   1  31
  DEL PEAK  7(3Q11.1) WILD-TYPE 225  12   1   2  88
D39V6, multiclass
     clus
vv    DEL PEAK  7(3Q11.1) MUTATED DEL PEAK  7(3Q11.1) WILD-TYPE
  M0                           92                           225
  M1                            6                            12
  M1A                           0                             1
  M1B                           1                             2
  MX                           31                            88
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V7, binary
                               cls
clus                              0   1
  DEL PEAK  7(3Q11.1) MUTATED    72  58
  DEL PEAK  7(3Q11.1) WILD-TYPE 176 156
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3Q11.1) MUTATED     72   58
  DEL PEAK  7(3Q11.1) WILD-TYPE  176  156
        clus
vv       DEL PEAK  7(3Q11.1) MUTATED DEL PEAK  7(3Q11.1) WILD-TYPE
  FEMALE                          72                           176
  MALE                            58                           156
[1] 2 2
[1] FALSE
D39V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  DEL PEAK  7(3Q11.1) MUTATED                            4
  DEL PEAK  7(3Q11.1) WILD-TYPE                          9
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK  7(3Q11.1) MUTATED                                  30
  DEL PEAK  7(3Q11.1) WILD-TYPE                                63
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  7(3Q11.1) MUTATED                                                   80
  DEL PEAK  7(3Q11.1) WILD-TYPE                                                214
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK  7(3Q11.1) MUTATED                                            0
  DEL PEAK  7(3Q11.1) WILD-TYPE                                          4
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK  7(3Q11.1) MUTATED                                               5
  DEL PEAK  7(3Q11.1) WILD-TYPE                                            14
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK  7(3Q11.1) MUTATED                                1
  DEL PEAK  7(3Q11.1) WILD-TYPE                              1
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK  7(3Q11.1) MUTATED                                    1
  DEL PEAK  7(3Q11.1) WILD-TYPE                                  3
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK  7(3Q11.1) MUTATED                              0
  DEL PEAK  7(3Q11.1) WILD-TYPE                            2
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK  7(3Q11.1) MUTATED                               5
  DEL PEAK  7(3Q11.1) WILD-TYPE                            14
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK  7(3Q11.1) MUTATED                                 1
  DEL PEAK  7(3Q11.1) WILD-TYPE                               0
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK  7(3Q11.1) MUTATED                                               1
  DEL PEAK  7(3Q11.1) WILD-TYPE                                             3
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK  7(3Q11.1) MUTATED                              2
  DEL PEAK  7(3Q11.1) WILD-TYPE                            5
D39V9, multiclass
                                                    clus
vv                                                   DEL PEAK  7(3Q11.1) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           30
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          80
  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                                                 2
                                                    clus
vv                                                   DEL PEAK  7(3Q11.1) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             63
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           214
  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                                                 14
  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"
D39V10, binary
                               cls
clus                              0   1
  DEL PEAK  7(3Q11.1) MUTATED     6 124
  DEL PEAK  7(3Q11.1) WILD-TYPE  15 317
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3Q11.1) MUTATED      6  124
  DEL PEAK  7(3Q11.1) WILD-TYPE   15  317
     clus
vv    DEL PEAK  7(3Q11.1) MUTATED DEL PEAK  7(3Q11.1) WILD-TYPE
  NO                            6                            15
  YES                         124                           317
[1] 2 2
[1] FALSE
D39V11, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  7(3Q11.1) MUTATED    80   3   0   4
  DEL PEAK  7(3Q11.1) WILD-TYPE 238   8   4  15
D39V12, multiclass
    clus
vv   DEL PEAK  7(3Q11.1) MUTATED DEL PEAK  7(3Q11.1) WILD-TYPE
  R0                          80                           238
  R1                           3                             8
  R2                           0                             4
  RX                           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                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  7(3Q11.1) MUTATED                                  0     1
  DEL PEAK  7(3Q11.1) WILD-TYPE                                1     5
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(3Q11.1) MUTATED                           8   105
  DEL PEAK  7(3Q11.1) WILD-TYPE                        18   257
D39V13, multiclass
                                  clus
vv                                 DEL PEAK  7(3Q11.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  8
  WHITE                                                    105
                                  clus
vv                                 DEL PEAK  7(3Q11.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                   18
  WHITE                                                      257
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V14, binary
                               cls
clus                              0   1
  DEL PEAK  7(3Q11.1) MUTATED     1  97
  DEL PEAK  7(3Q11.1) WILD-TYPE   6 235
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3Q11.1) MUTATED      1   97
  DEL PEAK  7(3Q11.1) WILD-TYPE    6  235
                        clus
vv                       DEL PEAK  7(3Q11.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          97
                        clus
vv                       DEL PEAK  7(3Q11.1) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           235
[1] 2 2
[1] FALSE

Clustering(40) Variable = DEL PEAK  8(3Q29) MUTATION ANALYSIS
D40V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  8(3Q29) MUTATED    89  24
  DEL PEAK  8(3Q29) WILD-TYPE 232  58
  DEL PEAK  8(3Q29) MUTATED DEL PEAK  8(3Q29) WILD-TYPE 
                        113                         290 
  DEL PEAK  8(3Q29) MUTATED DEL PEAK  8(3Q29) WILD-TYPE 
                         24                          58 
$`DEL PEAK  8(3Q29) MUTATED`
TCGA-05-4249 TCGA-05-4390 TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4422 
        1523         1126          610         1997          455          365 
TCGA-05-5420 TCGA-05-5715 TCGA-38-4631 TCGA-44-2656 TCGA-44-5644 TCGA-44-6144 
         457           62          354         1429          863          723 
TCGA-44-6774 TCGA-44-6776 TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
         658         1938         1970          535          719          385 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A47F TCGA-49-4506 TCGA-49-4510 TCGA-49-6742 
          99          260          337          999          896          445 
TCGA-50-5068 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-53-7626 TCGA-55-5899 
        1499         1091          653         1015         1971           87 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6972 TCGA-55-6983 TCGA-55-7283 TCGA-55-7573 
         993           24         1475         1826           35            4 
TCGA-55-7725 TCGA-55-7727 TCGA-55-7815 TCGA-55-7910 TCGA-55-8090 TCGA-55-8094 
          39           34           54          197            6            4 
TCGA-55-8206 TCGA-55-8507 TCGA-55-8508 TCGA-55-8514 TCGA-55-8615 TCGA-55-8616 
          46            8           15          202           15           48 
TCGA-55-A48Z TCGA-55-A492 TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
          29            1          162         1216         1289         1970 
TCGA-62-8399 TCGA-62-8402 TCGA-64-1677 TCGA-64-1678 TCGA-64-5774 TCGA-67-3770 
        2696         1445          628         1189         1959           31 
TCGA-67-3772 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 TCGA-69-8253 
         573          690          414          165          184          100 
TCGA-69-8255 TCGA-73-4659 TCGA-73-4662 TCGA-73-4675 TCGA-73-7498 TCGA-75-7027 
         129          711          912           40          621         1956 
TCGA-75-7031 TCGA-78-7147 TCGA-78-7148 TCGA-78-7160 TCGA-78-7161 TCGA-78-7166 
        1965         1950         1944          678          215         1934 
TCGA-78-7167 TCGA-78-7535 TCGA-78-7539 TCGA-78-8660 TCGA-80-5608 TCGA-86-7701 
        1937         1972          327         1954         1972           11 
TCGA-86-7713 TCGA-86-8054 TCGA-86-8055 TCGA-86-8075 TCGA-86-8280 TCGA-91-6828 
         422          745           10          479           16          323 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6847 TCGA-91-7771 TCGA-91-8497 TCGA-95-7567 
          79          417          842          492          174          568 
TCGA-95-7948 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7554 TCGA-97-7937 TCGA-97-8172 
         476          121          964          775          181          182 
TCGA-97-8174 TCGA-97-8177 TCGA-99-7458 TCGA-99-8032 TCGA-J2-8192 TCGA-J2-8194 
        1965          147          392           44          154          114 
TCGA-J2-A4AG TCGA-L9-A443 TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-MP-A4TI 
         238          116         1957         1944         1955 

$`DEL PEAK  8(3Q29) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4396 TCGA-05-4398 TCGA-05-4403 
         607          426         1369         1947         1431          578 
TCGA-05-4410 TCGA-05-4420 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 
        1958          912          913          669          791          791 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
         761          761          730          151          882          670 
TCGA-05-5429 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
          30           14          225          182          264         1952 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4632 
        1962         1147         1492          864         1073         1357 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2657 TCGA-44-2659 
         448         1971          133         1324          400         1367 
TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 
         741         1280         1301           97          246         1130 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 
        1163         1036          190          722         1013          383 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6775 TCGA-44-6777 
         328          302          845          704          705         1942 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
        1864         1978          444          592          366          218 
TCGA-44-7667 TCGA-44-7670 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G 
         557          882          486          466          287          351 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
         415           76         1932         1081         1421          428 
TCGA-49-4507 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
         268          157         1700          369          890          522 
TCGA-49-6761 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
         354         2174         2146          455          785          944 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5941 TCGA-50-5942 
         246          282          267         2370          567          883 
TCGA-50-5944 TCGA-50-5946 TCGA-50-7109 TCGA-50-8460 TCGA-53-7624 TCGA-53-7813 
         764          686          255          105         1986          424 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-6543 
         280          701         1178         1479         1375            2 
TCGA-55-6969 TCGA-55-6971 TCGA-55-6980 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
        1239           25           67         1233         2151         1170 
TCGA-55-7281 TCGA-55-7284 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
          18          121            6           95           40         1958 
TCGA-55-7726 TCGA-55-7728 TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 TCGA-55-7914 
          39           24           19           16           21            3 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8091 
          31            5           33           21          100           43 
TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8207 TCGA-55-8299 
          26           47           15           33           66          216 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8510 TCGA-55-8511 
          44           23           29           11          228            9 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
           3          146          536           49           66          106 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A490 TCGA-55-A491 TCGA-55-A493 TCGA-55-A494 
          33           42           48         1952           28            5 
TCGA-55-A4DF TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
          47         2067         2199         1246          910         1728 
TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
        1686         1126         1968           62         1305          864 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 
        1559          866          610          427          385          174 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7973 TCGA-69-7978 
         141          422          202          186          230           70 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8254 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 
          89          382           77          214           61         1600 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 
         800          467          131          164           38          519 
TCGA-75-6214 TCGA-75-7025 TCGA-78-7145 TCGA-78-7146 TCGA-78-7149 TCGA-78-7150 
        1970         1967         1973         1988         1093         1963 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
        1202          760         1948         1957         1961         1963 
TCGA-78-7159 TCGA-78-7162 TCGA-78-7163 TCGA-78-7220 TCGA-78-7536 TCGA-78-7537 
        1221         1940         1950         1965         1949         1944 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
         881         1952          994         1949         1971         1981 
TCGA-78-8662 TCGA-80-5607 TCGA-83-5908 TCGA-86-6851 TCGA-86-7711 TCGA-86-7714 
        1964         1965          824         1959          630         1968 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
         591         1963          508         1963           13           24 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8281 TCGA-86-8358 TCGA-86-8359 
         489          476          482         1955           19           26 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
          35           45           34           18           15          455 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 
         405           10           30           14           39         1940 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6840 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 
          60          310          372          224           35          197 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
          36           44          218          297          127          186 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7944 TCGA-95-7947 TCGA-97-7547 TCGA-97-7552 
          34            2          377          477         1965         1932 
TCGA-97-7553 TCGA-97-7941 TCGA-97-8171 TCGA-97-8175 TCGA-97-8179 TCGA-97-8547 
        1332           22          107           87           15          148 
TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-8025 TCGA-99-8028 TCGA-99-8033 
         115          197          271          427          459          170 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A444 TCGA-MN-A4N1 
         287          282          578          435            6          285 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 
         622          353         1946         1967         1951         1954 
TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
        1954         1980         1951         1970         1970          142 
TCGA-MP-A4TK TCGA-MP-A5C7 
        1971         1490 

  DEL PEAK  8(3Q29) MUTATED DEL PEAK  8(3Q29) WILD-TYPE 
                          1                           2 
  DEL PEAK  8(3Q29) MUTATED DEL PEAK  8(3Q29) WILD-TYPE 
                       2696                        2370 
  DEL PEAK  8(3Q29) MUTATED DEL PEAK  8(3Q29) WILD-TYPE 
                      476.0                       462.5 
[1] "1.0 - 2696.0 (476.0)" "2.0 - 2370.0 (462.5)"
[1] "hr=" "1.2"
D40V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK  8(3Q29) MUTATED         0       28       36        14        22
  DEL PEAK  8(3Q29) WILD-TYPE       4       85       95        29        47
                             vv
clus                          STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK  8(3Q29) MUTATED           19          2        5
  DEL PEAK  8(3Q29) WILD-TYPE         48          9       18
D40V3, multiclass
            clus
vv           DEL PEAK  8(3Q29) MUTATED DEL PEAK  8(3Q29) WILD-TYPE
  STAGE I                            0                           4
  STAGE IA                          28                          85
  STAGE IB                          36                          95
  STAGE IIA                         14                          29
  STAGE IIB                         22                          47
  STAGE IIIA                        19                          48
  STAGE IIIB                         2                           9
  STAGE IV                           5                          18
[1] 8 2
[1] TRUE
[1] "dimension of 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(3Q29) MUTATED    36  77   9   4
  DEL PEAK  8(3Q29) WILD-TYPE 107 182  31  14
D40V4, multiclass
    clus
vv   DEL PEAK  8(3Q29) MUTATED DEL PEAK  8(3Q29) WILD-TYPE
  T1                        36                         107
  T2                        77                         182
  T3                         9                          31
  T4                         4                          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  8(3Q29) MUTATED    80  26    20
  DEL PEAK  8(3Q29) WILD-TYPE 215  59    52
D40V5, multiclass
       clus
vv      DEL PEAK  8(3Q29) MUTATED DEL PEAK  8(3Q29) WILD-TYPE
  N0                           80                         215
  N1                           26                          59
  N2+N3                        20                          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"
                             vv
clus                           M0  M1 M1A M1B  MX
  DEL PEAK  8(3Q29) MUTATED    90   3   0   1  31
  DEL PEAK  8(3Q29) WILD-TYPE 227  15   1   2  88
D40V6, multiclass
     clus
vv    DEL PEAK  8(3Q29) MUTATED DEL PEAK  8(3Q29) WILD-TYPE
  M0                         90                         227
  M1                          3                          15
  M1A                         0                           1
  M1B                         1                           2
  MX                         31                          88
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V7, binary
                             cls
clus                            0   1
  DEL PEAK  8(3Q29) MUTATED    65  61
  DEL PEAK  8(3Q29) WILD-TYPE 183 153
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  8(3Q29) MUTATED     65   61
  DEL PEAK  8(3Q29) WILD-TYPE  183  153
        clus
vv       DEL PEAK  8(3Q29) MUTATED DEL PEAK  8(3Q29) WILD-TYPE
  FEMALE                        65                         183
  MALE                          61                         153
[1] 2 2
[1] FALSE
D40V8, continuous
                             vv
clus                          LUNG ACINAR ADENOCARCINOMA
  DEL PEAK  8(3Q29) MUTATED                            4
  DEL PEAK  8(3Q29) WILD-TYPE                          9
                             vv
clus                          LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK  8(3Q29) MUTATED                                  30
  DEL PEAK  8(3Q29) WILD-TYPE                                63
                             vv
clus                          LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  8(3Q29) MUTATED                                                   76
  DEL PEAK  8(3Q29) WILD-TYPE                                                218
                             vv
clus                          LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK  8(3Q29) MUTATED                                            0
  DEL PEAK  8(3Q29) WILD-TYPE                                          4
                             vv
clus                          LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK  8(3Q29) MUTATED                                               4
  DEL PEAK  8(3Q29) WILD-TYPE                                            15
                             vv
clus                          LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK  8(3Q29) MUTATED                                0
  DEL PEAK  8(3Q29) WILD-TYPE                              2
                             vv
clus                          LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK  8(3Q29) MUTATED                                    1
  DEL PEAK  8(3Q29) WILD-TYPE                                  3
                             vv
clus                          LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK  8(3Q29) MUTATED                              0
  DEL PEAK  8(3Q29) WILD-TYPE                            2
                             vv
clus                          LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK  8(3Q29) MUTATED                               5
  DEL PEAK  8(3Q29) WILD-TYPE                            14
                             vv
clus                          LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK  8(3Q29) MUTATED                                 1
  DEL PEAK  8(3Q29) WILD-TYPE                               0
                             vv
clus                          LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK  8(3Q29) MUTATED                                               2
  DEL PEAK  8(3Q29) WILD-TYPE                                             2
                             vv
clus                          MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK  8(3Q29) MUTATED                              3
  DEL PEAK  8(3Q29) WILD-TYPE                            4
D40V9, multiclass
                                                    clus
vv                                                   DEL PEAK  8(3Q29) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                 4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                         30
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                        76
  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                                               3
                                                    clus
vv                                                   DEL PEAK  8(3Q29) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                   9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           63
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         218
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                   4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                               15
  LUNG CLEAR CELL ADENOCARCINOMA                                               2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                           3
  LUNG MUCINOUS ADENOCARCINOMA                                                 2
  LUNG PAPILLARY ADENOCARCINOMA                                               14
  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"
D40V10, binary
                             cls
clus                            0   1
  DEL PEAK  8(3Q29) MUTATED     4 122
  DEL PEAK  8(3Q29) WILD-TYPE  17 319
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  8(3Q29) MUTATED      4  122
  DEL PEAK  8(3Q29) WILD-TYPE   17  319
     clus
vv    DEL PEAK  8(3Q29) MUTATED DEL PEAK  8(3Q29) WILD-TYPE
  NO                          4                          17
  YES                       122                         319
[1] 2 2
[1] FALSE
D40V11, continuous
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK  8(3Q29) MUTATED    84   2   0   3
  DEL PEAK  8(3Q29) WILD-TYPE 234   9   4  16
D40V12, multiclass
    clus
vv   DEL PEAK  8(3Q29) MUTATED DEL PEAK  8(3Q29) WILD-TYPE
  R0                        84                         234
  R1                         2                           9
  R2                         0                           4
  RX                         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                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  8(3Q29) MUTATED                                  0     0
  DEL PEAK  8(3Q29) WILD-TYPE                                1     6
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(3Q29) MUTATED                           9    99
  DEL PEAK  8(3Q29) WILD-TYPE                        17   263
D40V13, multiclass
                                  clus
vv                                 DEL PEAK  8(3Q29) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    0
  BLACK OR AFRICAN AMERICAN                                9
  WHITE                                                   99
                                  clus
vv                                 DEL PEAK  8(3Q29) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      6
  BLACK OR AFRICAN AMERICAN                                 17
  WHITE                                                    263
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V14, binary
                             cls
clus                            0   1
  DEL PEAK  8(3Q29) MUTATED     1  94
  DEL PEAK  8(3Q29) WILD-TYPE   6 238
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  8(3Q29) MUTATED      1   94
  DEL PEAK  8(3Q29) WILD-TYPE    6  238
                        clus
vv                       DEL PEAK  8(3Q29) MUTATED DEL PEAK  8(3Q29) WILD-TYPE
  HISPANIC OR LATINO                             1                           6
  NOT HISPANIC OR LATINO                        94                         238
[1] 2 2
[1] FALSE

Clustering(41) Variable = DEL PEAK  9(4P16.3) MUTATION ANALYSIS
D41V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  9(4P16.3) MUTATED    87  14
  DEL PEAK  9(4P16.3) WILD-TYPE 234  68
  DEL PEAK  9(4P16.3) MUTATED DEL PEAK  9(4P16.3) WILD-TYPE 
                          101                           302 
  DEL PEAK  9(4P16.3) MUTATED DEL PEAK  9(4P16.3) WILD-TYPE 
                           14                            68 
$`DEL PEAK  9(4P16.3) MUTATED`
TCGA-05-4249 TCGA-05-4398 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 
        1523         1431          610         1958         1997          455 
TCGA-05-4420 TCGA-05-4424 TCGA-05-5420 TCGA-05-5425 TCGA-35-4123 TCGA-35-5375 
         912          913          457          882          182          264 
TCGA-38-4625 TCGA-38-4632 TCGA-44-2659 TCGA-44-3918 TCGA-44-5643 TCGA-44-5644 
        1952         1357         1367         1036         1013          863 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6778 TCGA-44-7660 
         723          328          302          845         1864          592 
TCGA-44-7667 TCGA-44-7670 TCGA-44-8117 TCGA-44-A479 TCGA-49-4501 TCGA-49-4506 
         557          882          385          486         1421          999 
TCGA-49-4510 TCGA-49-6742 TCGA-49-6743 TCGA-50-5049 TCGA-50-5051 TCGA-50-5066 
         896          445          369         2146          455          944 
TCGA-50-5946 TCGA-50-7109 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6969 
         686          255         1971          280           87         1239 
TCGA-55-6971 TCGA-55-6985 TCGA-55-7574 TCGA-55-7724 TCGA-55-7726 TCGA-55-7815 
          25         1233           95         1958           39           54 
TCGA-55-7903 TCGA-55-7910 TCGA-55-7995 TCGA-55-8096 TCGA-55-8505 TCGA-55-8507 
          19          197            5           47           29            8 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Z 
         202          536           15           48           66           29 
TCGA-55-A491 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8398 TCGA-62-A46V TCGA-62-A472 
        1952           47          162         1970         2199          910 
TCGA-64-1677 TCGA-64-5774 TCGA-64-5779 TCGA-64-5815 TCGA-67-3771 TCGA-69-7760 
         628         1959          864          866          610          202 
TCGA-69-7763 TCGA-69-7973 TCGA-69-7979 TCGA-71-6725 TCGA-73-4659 TCGA-73-4670 
         690          230           89           61          711          131 
TCGA-73-4675 TCGA-78-7159 TCGA-78-7536 TCGA-78-8640 TCGA-78-8662 TCGA-86-7713 
          40         1221         1949         1949         1964          422 
TCGA-86-8055 TCGA-86-8074 TCGA-86-8075 TCGA-91-6830 TCGA-91-6840 TCGA-91-6848 
          10           24          479           60          372          224 
TCGA-91-7771 TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 TCGA-97-8547 TCGA-99-8025 
         492            2          568          377          148          427 
TCGA-99-8033 TCGA-J2-A4AD TCGA-L4-A4E5 TCGA-MN-A4N4 TCGA-MP-A4T4 
         170          287          578          622         1954 

$`DEL PEAK  9(4P16.3) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 TCGA-05-4403 
         607          426         1369         1126         1947          578 
TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
         365          669          791          791          761          761 
TCGA-05-4433 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
         730          151          670           30           62           14 
TCGA-35-4122 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 
         225         1962         1147         1492          864         1073 
TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 
         354          448         1971          133         1324         1429 
TCGA-44-2657 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
         400          741         1280         1301           97          246 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5645 TCGA-44-6148 
        1130         1163          190          722          383          704 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 
         658          705         1938         1942         1978          444 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-8119 
         366          218         1970          535          719           99 
TCGA-44-8120 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
         260          466          287          337          351          415 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 TCGA-49-4505 TCGA-49-4507 TCGA-49-4512 
          76         1932         1081          428          268          157 
TCGA-49-4514 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-50-5045 TCGA-50-5055 
        1700          890          522          354         2174          785 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
        1499          246          282          267         1091         2370 
TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-6597 TCGA-50-8460 
         653          567          883          764         1015          105 
TCGA-53-7624 TCGA-53-7813 TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 
        1986          424          701         1178         1479         1375 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6972 TCGA-55-6980 TCGA-55-6983 
           2          993           24         1475           67         1826 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
        2151         1170           18           35          121            6 
TCGA-55-7573 TCGA-55-7576 TCGA-55-7725 TCGA-55-7727 TCGA-55-7728 TCGA-55-7907 
           4           40           39           34           24           16 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
          21            3           31           33           21          100 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8097 TCGA-55-8205 
           6           43           26            4           15           33 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 
          46           66          216           44           23           11 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8619 
          15          228            9            3          146           49 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A490 TCGA-55-A492 TCGA-55-A493 
         106           33           42           48            1           28 
TCGA-55-A494 TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46U 
           5         1216         1289         2696         1445         2067 
TCGA-62-A471 TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 
        1246         1728         1189         1686         1126         1968 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5781 TCGA-67-3770 TCGA-67-3772 TCGA-67-3773 
          62         1305         1559           31          573          427 
TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7761 TCGA-69-7764 
         385          174          141          422          186          414 
TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
         165          184           70          382          100           77 
TCGA-69-8255 TCGA-69-A59K TCGA-73-4658 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
         129          214         1600          912          800          467 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-75-6214 TCGA-75-7025 
         164           38          621          519         1970         1967 
TCGA-75-7027 TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
        1956         1965         1973         1988         1950         1944 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
        1093         1963         1202          760         1948         1957 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        1961         1963          678          215         1940         1950 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 
        1934         1937         1965         1972         1944          327 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
         881         1952          994         1971         1981         1954 
TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
        1965         1972          824         1959           11          630 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8056 
        1968          591         1963          508          745         1963 
TCGA-86-8073 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8281 
          13          489          476          482           16         1955 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
          19           26           35           45           34           18 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 
          15          455          405           10           30           14 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
          39          323         1940          310           79          417 
TCGA-91-6847 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
         842           35          197          174           36           44 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7947 
         218          297          127          186           34          477 
TCGA-95-7948 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
         476          121          964         1965         1932         1332 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
         775          181           22          107          182         1965 
TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 
          87          147           15          115          197          271 
TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE 
         392          459           44          154          114          282 
TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N5 
         238          435          116            6          285          353 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
        1946         1967         1951         1954         1957         1980 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        1951         1944         1970         1970          142         1955 
TCGA-MP-A4TK TCGA-MP-A5C7 
        1971         1490 

  DEL PEAK  9(4P16.3) MUTATED DEL PEAK  9(4P16.3) WILD-TYPE 
                            2                             1 
  DEL PEAK  9(4P16.3) MUTATED DEL PEAK  9(4P16.3) WILD-TYPE 
                         2199                          2696 
  DEL PEAK  9(4P16.3) MUTATED DEL PEAK  9(4P16.3) WILD-TYPE 
                        492.0                         451.5 
[1] "2.0 - 2199.0 (492.0)" "1.0 - 2696.0 (451.5)"
[1] "hr=" "1.3"
D41V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK  9(4P16.3) MUTATED         2       27       35         9        16
  DEL PEAK  9(4P16.3) WILD-TYPE       2       86       96        34        53
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK  9(4P16.3) MUTATED           18          4        6
  DEL PEAK  9(4P16.3) WILD-TYPE         49          7       17
D41V3, multiclass
            clus
vv           DEL PEAK  9(4P16.3) MUTATED DEL PEAK  9(4P16.3) WILD-TYPE
  STAGE I                              2                             2
  STAGE IA                            27                            86
  STAGE IB                            35                            96
  STAGE IIA                            9                            34
  STAGE IIB                           16                            53
  STAGE IIIA                          18                            49
  STAGE IIIB                           4                             7
  STAGE IV                             6                            17
[1] 8 2
[1] TRUE
[1] "dimension of 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(4P16.3) MUTATED    38  63  11   3
  DEL PEAK  9(4P16.3) WILD-TYPE 105 196  29  15
D41V4, multiclass
    clus
vv   DEL PEAK  9(4P16.3) MUTATED DEL PEAK  9(4P16.3) WILD-TYPE
  T1                          38                           105
  T2                          63                           196
  T3                          11                            29
  T4                           3                            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  9(4P16.3) MUTATED    72  20    21
  DEL PEAK  9(4P16.3) WILD-TYPE 223  65    51
D41V5, multiclass
       clus
vv      DEL PEAK  9(4P16.3) MUTATED DEL PEAK  9(4P16.3) WILD-TYPE
  N0                             72                           223
  N1                             20                            65
  N2+N3                          21                            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"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK  9(4P16.3) MUTATED    78   5   0   1  32
  DEL PEAK  9(4P16.3) WILD-TYPE 239  13   1   2  87
D41V6, multiclass
     clus
vv    DEL PEAK  9(4P16.3) MUTATED DEL PEAK  9(4P16.3) WILD-TYPE
  M0                           78                           239
  M1                            5                            13
  M1A                           0                             1
  M1B                           1                             2
  MX                           32                            87
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V7, binary
                               cls
clus                              0   1
  DEL PEAK  9(4P16.3) MUTATED    62  55
  DEL PEAK  9(4P16.3) WILD-TYPE 186 159
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4P16.3) MUTATED     62   55
  DEL PEAK  9(4P16.3) WILD-TYPE  186  159
        clus
vv       DEL PEAK  9(4P16.3) MUTATED DEL PEAK  9(4P16.3) WILD-TYPE
  FEMALE                          62                           186
  MALE                            55                           159
[1] 2 2
[1] FALSE
D41V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  DEL PEAK  9(4P16.3) MUTATED                            4
  DEL PEAK  9(4P16.3) WILD-TYPE                          9
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK  9(4P16.3) MUTATED                                  22
  DEL PEAK  9(4P16.3) WILD-TYPE                                71
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  9(4P16.3) MUTATED                                                   82
  DEL PEAK  9(4P16.3) WILD-TYPE                                                212
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK  9(4P16.3) MUTATED                                            0
  DEL PEAK  9(4P16.3) WILD-TYPE                                          4
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK  9(4P16.3) MUTATED                                               1
  DEL PEAK  9(4P16.3) WILD-TYPE                                            18
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK  9(4P16.3) MUTATED                                1
  DEL PEAK  9(4P16.3) WILD-TYPE                              1
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK  9(4P16.3) MUTATED                                    1
  DEL PEAK  9(4P16.3) WILD-TYPE                                  3
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK  9(4P16.3) MUTATED                              1
  DEL PEAK  9(4P16.3) WILD-TYPE                            1
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK  9(4P16.3) MUTATED                               2
  DEL PEAK  9(4P16.3) WILD-TYPE                            17
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK  9(4P16.3) MUTATED                                 1
  DEL PEAK  9(4P16.3) WILD-TYPE                               0
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK  9(4P16.3) MUTATED                                               1
  DEL PEAK  9(4P16.3) WILD-TYPE                                             3
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK  9(4P16.3) MUTATED                              1
  DEL PEAK  9(4P16.3) WILD-TYPE                            6
D41V9, multiclass
                                                    clus
vv                                                   DEL PEAK  9(4P16.3) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           22
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          82
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                   0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                1
  LUNG CLEAR CELL ADENOCARCINOMA                                               1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                           1
  LUNG MUCINOUS ADENOCARCINOMA                                                 1
  LUNG PAPILLARY ADENOCARCINOMA                                                2
  LUNG SIGNET RING ADENOCARCINOMA                                              1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                1
  MUCINOUS (COLLOID) CARCINOMA                                                 1
                                                    clus
vv                                                   DEL PEAK  9(4P16.3) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             71
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           212
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 18
  LUNG CLEAR CELL ADENOCARCINOMA                                                 1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             3
  LUNG MUCINOUS ADENOCARCINOMA                                                   1
  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"
D41V10, binary
                               cls
clus                              0   1
  DEL PEAK  9(4P16.3) MUTATED     5 112
  DEL PEAK  9(4P16.3) WILD-TYPE  16 329
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4P16.3) MUTATED      5  112
  DEL PEAK  9(4P16.3) WILD-TYPE   16  329
     clus
vv    DEL PEAK  9(4P16.3) MUTATED DEL PEAK  9(4P16.3) WILD-TYPE
  NO                            5                            16
  YES                         112                           329
[1] 2 2
[1] FALSE
D41V11, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  9(4P16.3) MUTATED    77   3   2   7
  DEL PEAK  9(4P16.3) WILD-TYPE 241   8   2  12
D41V12, multiclass
    clus
vv   DEL PEAK  9(4P16.3) MUTATED DEL PEAK  9(4P16.3) WILD-TYPE
  R0                          77                           241
  R1                           3                             8
  R2                           2                             2
  RX                           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                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  9(4P16.3) MUTATED                                  0     1
  DEL PEAK  9(4P16.3) WILD-TYPE                                1     5
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(4P16.3) MUTATED                          10    85
  DEL PEAK  9(4P16.3) WILD-TYPE                        16   277
D41V13, multiclass
                                  clus
vv                                 DEL PEAK  9(4P16.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                 10
  WHITE                                                     85
                                  clus
vv                                 DEL PEAK  9(4P16.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                   16
  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"
D41V14, binary
                               cls
clus                              0   1
  DEL PEAK  9(4P16.3) MUTATED     2  82
  DEL PEAK  9(4P16.3) WILD-TYPE   5 250
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4P16.3) MUTATED      2   82
  DEL PEAK  9(4P16.3) WILD-TYPE    5  250
                        clus
vv                       DEL PEAK  9(4P16.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          82
                        clus
vv                       DEL PEAK  9(4P16.3) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           250
[1] 2 2
[1] FALSE

Clustering(42) Variable = DEL PEAK 10(4Q22.1) MUTATION ANALYSIS
D42V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 10(4Q22.1) MUTATED    98  25
  DEL PEAK 10(4Q22.1) WILD-TYPE 223  57
  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                          123                           280 
  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                           25                            57 
$`DEL PEAK 10(4Q22.1) MUTATED`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4390 TCGA-05-4398 TCGA-05-4405 TCGA-05-4415 
        1523          607         1126         1431          610         1997 
TCGA-05-4424 TCGA-05-5420 TCGA-05-5425 TCGA-35-4123 TCGA-35-5375 TCGA-38-4628 
         913          457          882          182          264         1492 
TCGA-38-4630 TCGA-38-6178 TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 TCGA-44-6145 
        1073          448         1013          863          723          328 
TCGA-44-6147 TCGA-44-6778 TCGA-44-7660 TCGA-44-7667 TCGA-44-A479 TCGA-44-A4SU 
         845         1864          592          557          486           76 
TCGA-49-4501 TCGA-49-4506 TCGA-49-4507 TCGA-49-6743 TCGA-50-5049 TCGA-50-5051 
        1421          999          268          369         2146          455 
TCGA-50-5066 TCGA-50-5072 TCGA-50-5946 TCGA-50-7109 TCGA-53-A4EZ TCGA-55-1592 
         944          246          686          255          280          701 
TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-6969 TCGA-55-6971 TCGA-55-6985 
        1178         1479         1375         1239           25         1233 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7724 TCGA-55-7726 TCGA-55-7815 TCGA-55-7910 
           4           95         1958           39           54          197 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8301 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 
          26            4           44           29            8           15 
TCGA-55-8514 TCGA-55-8616 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 
         202           48           42           29         1952            1 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-A46U TCGA-62-A46V TCGA-62-A472 TCGA-64-1677 
          47          162         2067         2199          910          628 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5778 TCGA-64-5779 TCGA-67-3771 TCGA-69-7763 
        1686         1968         1305          864          610          690 
TCGA-69-7764 TCGA-69-7973 TCGA-69-8255 TCGA-71-6725 TCGA-73-4659 TCGA-73-4662 
         414          230          129           61          711          912 
TCGA-73-4670 TCGA-73-4675 TCGA-75-6214 TCGA-75-7027 TCGA-75-7031 TCGA-78-7146 
         131           40         1970         1956         1965         1988 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7154 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
        1950         1944         1948         1937         1965         1972 
TCGA-78-7536 TCGA-78-7539 TCGA-78-8640 TCGA-86-7713 TCGA-86-7954 TCGA-86-8054 
        1949          327         1949          422         1963          745 
TCGA-86-8055 TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 TCGA-86-8358 TCGA-86-8669 
          10           24          479          482           19           34 
TCGA-86-8672 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6840 TCGA-91-6847 
          15         1940           60          310          372          842 
TCGA-91-A4BC TCGA-93-8067 TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 TCGA-97-7937 
          44          186            2          568          377          181 
TCGA-97-8547 TCGA-99-8025 TCGA-99-8028 TCGA-99-8033 TCGA-J2-A4AD TCGA-L4-A4E5 
         148          427          459          170          287          578 
TCGA-MN-A4N4 TCGA-MP-A4TA TCGA-MP-A4TF 
         622         1951         1970 

$`DEL PEAK 10(4Q22.1) WILD-TYPE`
TCGA-05-4384 TCGA-05-4389 TCGA-05-4396 TCGA-05-4403 TCGA-05-4410 TCGA-05-4417 
         426         1369         1947          578         1958          455 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 
         912          365          669          791          791          761 
TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
         761          730          151          670           30           62 
TCGA-35-3615 TCGA-35-4122 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4629 
          14          225         1952         1962         1147          864 
TCGA-38-4631 TCGA-38-4632 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 
         354         1357         1971          133         1324         1429 
TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 
         400         1367          741         1280         1301           97 
TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
         246         1130         1163         1036          190          722 
TCGA-44-5645 TCGA-44-6146 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
         383          302          704          658          705         1938 
TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 TCGA-44-7661 TCGA-44-7662 TCGA-44-7669 
        1942         1978          444          366          218         1970 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
         882          535          719          385           99          260 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 
         466          287          337          351          415         1932 
TCGA-49-4494 TCGA-49-4505 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 
        1081          428          896          157         1700          445 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-50-5045 TCGA-50-5055 TCGA-50-5068 
         890          522          354         2174          785         1499 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 
         282          267         1091         2370          653          567 
TCGA-50-5942 TCGA-50-5944 TCGA-50-6597 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
         883          764         1015          105         1986         1971 
TCGA-53-7813 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6972 
         424           87            2          993           24         1475 
TCGA-55-6980 TCGA-55-6983 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 
          67         1826         2151         1170           18           35 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7576 TCGA-55-7725 TCGA-55-7727 TCGA-55-7728 
         121            6           40           39           34           24 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
          19           16           21            3           31            5 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8096 
          33           21          100            6           43           47 
TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8302 
          15           33           46           66          216           23 
TCGA-55-8506 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 
          11          228            9            3          146          536 
TCGA-55-8615 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A490 
          15           49           66          106           33           48 
TCGA-55-A493 TCGA-55-A494 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
          28            5         1216         1289         1970         2696 
TCGA-62-8402 TCGA-62-A471 TCGA-64-1676 TCGA-64-1678 TCGA-64-1680 TCGA-64-5774 
        1445         1246         1728         1189         1126         1959 
TCGA-64-5775 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3772 TCGA-67-3773 
          62         1559          866           31          573          427 
TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
         385          174          141          422          202          186 
TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
         165          184           70           89          382          100 
TCGA-69-8254 TCGA-69-A59K TCGA-73-4658 TCGA-73-4666 TCGA-73-4668 TCGA-73-4676 
          77          214         1600          800          467          164 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-75-7025 TCGA-78-7145 TCGA-78-7149 
          38          621          519         1967         1973         1093 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
        1963         1202          760         1957         1961         1963 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
        1221          678          215         1940         1950         1934 
TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 
        1944          881         1952          994         1971         1981 
TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 
        1954         1964         1965         1972          824         1959 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 TCGA-86-7953 TCGA-86-7955 TCGA-86-8056 
          11          630         1968          591          508         1963 
TCGA-86-8073 TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8281 TCGA-86-8359 
          13          489          476           16         1955           26 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
          35           45           18          455          405           10 
TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6835 TCGA-91-6836 
          30           14           39          323           79          417 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
         224           35          492          197          174           36 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-95-7039 TCGA-95-7947 TCGA-95-7948 
         218          297          127           34          477          476 
TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
         121          964         1965         1932         1332          775 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 
          22          107          182         1965           87          147 
TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8032 
          15          115          197          271          392           44 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 
         154          114          282          238          435          116 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 
           6          285          353         1946         1967         1951 
TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TC TCGA-MP-A4TE 
        1954         1954         1957         1980         1944         1970 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
         142         1955         1971         1490 

  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                            1                             2 
  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                         2199                          2696 
  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                        568.0                         439.5 
[1] "1.0 - 2199.0 (568.0)" "2.0 - 2696.0 (439.5)"
[1] "hr=" "1.1"
D42V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 10(4Q22.1) MUTATED         2       34       38        13        16
  DEL PEAK 10(4Q22.1) WILD-TYPE       2       79       93        30        53
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 10(4Q22.1) MUTATED           26          5        8
  DEL PEAK 10(4Q22.1) WILD-TYPE         41          6       15
D42V3, multiclass
            clus
vv           DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE
  STAGE I                              2                             2
  STAGE IA                            34                            79
  STAGE IB                            38                            93
  STAGE IIA                           13                            30
  STAGE IIB                           16                            53
  STAGE IIIA                          26                            41
  STAGE IIIB                           5                             6
  STAGE IV                             8                            15
[1] 8 2
[1] TRUE
[1] "dimension of 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(4Q22.1) MUTATED    41  84  10   5
  DEL PEAK 10(4Q22.1) WILD-TYPE 102 175  30  13
D42V4, multiclass
    clus
vv   DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE
  T1                          41                           102
  T2                          84                           175
  T3                          10                            30
  T4                           5                            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(4Q22.1) MUTATED    89  20    30
  DEL PEAK 10(4Q22.1) WILD-TYPE 206  65    42
D42V5, multiclass
       clus
vv      DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE
  N0                             89                           206
  N1                             20                            65
  N2+N3                          30                            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"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK 10(4Q22.1) MUTATED    95   7   0   1  37
  DEL PEAK 10(4Q22.1) WILD-TYPE 222  11   1   2  82
D42V6, multiclass
     clus
vv    DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE
  M0                           95                           222
  M1                            7                            11
  M1A                           0                             1
  M1B                           1                             2
  MX                           37                            82
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V7, binary
                               cls
clus                              0   1
  DEL PEAK 10(4Q22.1) MUTATED    73  69
  DEL PEAK 10(4Q22.1) WILD-TYPE 175 145
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q22.1) MUTATED     73   69
  DEL PEAK 10(4Q22.1) WILD-TYPE  175  145
        clus
vv       DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE
  FEMALE                          73                           175
  MALE                            69                           145
[1] 2 2
[1] FALSE
D42V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 10(4Q22.1) MUTATED                            3
  DEL PEAK 10(4Q22.1) WILD-TYPE                         10
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 10(4Q22.1) MUTATED                                  27
  DEL PEAK 10(4Q22.1) WILD-TYPE                                66
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 10(4Q22.1) MUTATED                                                   98
  DEL PEAK 10(4Q22.1) WILD-TYPE                                                196
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 10(4Q22.1) MUTATED                                            0
  DEL PEAK 10(4Q22.1) WILD-TYPE                                          4
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 10(4Q22.1) MUTATED                                               3
  DEL PEAK 10(4Q22.1) WILD-TYPE                                            16
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 10(4Q22.1) MUTATED                                2
  DEL PEAK 10(4Q22.1) WILD-TYPE                              0
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 10(4Q22.1) MUTATED                                    2
  DEL PEAK 10(4Q22.1) WILD-TYPE                                  2
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 10(4Q22.1) MUTATED                              0
  DEL PEAK 10(4Q22.1) WILD-TYPE                            2
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 10(4Q22.1) MUTATED                               3
  DEL PEAK 10(4Q22.1) WILD-TYPE                            16
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 10(4Q22.1) MUTATED                                 1
  DEL PEAK 10(4Q22.1) WILD-TYPE                               0
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 10(4Q22.1) MUTATED                                               1
  DEL PEAK 10(4Q22.1) WILD-TYPE                                             3
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 10(4Q22.1) MUTATED                              2
  DEL PEAK 10(4Q22.1) WILD-TYPE                            5
D42V9, multiclass
                                                    clus
vv                                                   DEL PEAK 10(4Q22.1) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           27
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          98
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                   0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                3
  LUNG CLEAR CELL ADENOCARCINOMA                                               2
  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                                                 2
                                                    clus
vv                                                   DEL PEAK 10(4Q22.1) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                    10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             66
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           196
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 16
  LUNG CLEAR CELL ADENOCARCINOMA                                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             2
  LUNG MUCINOUS ADENOCARCINOMA                                                   2
  LUNG PAPILLARY ADENOCARCINOMA                                                 16
  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"
D42V10, binary
                               cls
clus                              0   1
  DEL PEAK 10(4Q22.1) MUTATED     8 134
  DEL PEAK 10(4Q22.1) WILD-TYPE  13 307
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q22.1) MUTATED      8  134
  DEL PEAK 10(4Q22.1) WILD-TYPE   13  307
     clus
vv    DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE
  NO                            8                            13
  YES                         134                           307
[1] 2 2
[1] FALSE
D42V11, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 10(4Q22.1) MUTATED    97   5   2   8
  DEL PEAK 10(4Q22.1) WILD-TYPE 221   6   2  11
D42V12, multiclass
    clus
vv   DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE
  R0                          97                           221
  R1                           5                             6
  R2                           2                             2
  RX                           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                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 10(4Q22.1) MUTATED                                  0     4
  DEL PEAK 10(4Q22.1) WILD-TYPE                                1     2
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(4Q22.1) MUTATED                          10   105
  DEL PEAK 10(4Q22.1) WILD-TYPE                        16   257
D42V13, multiclass
                                  clus
vv                                 DEL PEAK 10(4Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 10
  WHITE                                                    105
                                  clus
vv                                 DEL PEAK 10(4Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   16
  WHITE                                                      257
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V14, binary
                               cls
clus                              0   1
  DEL PEAK 10(4Q22.1) MUTATED     2 100
  DEL PEAK 10(4Q22.1) WILD-TYPE   5 232
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q22.1) MUTATED      2  100
  DEL PEAK 10(4Q22.1) WILD-TYPE    5  232
                        clus
vv                       DEL PEAK 10(4Q22.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                         100
                        clus
vv                       DEL PEAK 10(4Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           232
[1] 2 2
[1] FALSE

Clustering(43) Variable = DEL PEAK 11(4Q35.1) MUTATION ANALYSIS
D43V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 11(4Q35.1) MUTATED   118  29
  DEL PEAK 11(4Q35.1) WILD-TYPE 203  53
  DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE 
                          147                           256 
  DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE 
                           29                            53 
$`DEL PEAK 11(4Q35.1) MUTATED`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4389 TCGA-05-4390 TCGA-05-4398 TCGA-05-4405 
        1523          607         1369         1126         1431          610 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4424 TCGA-05-4427 TCGA-05-4432 
        1997          455          912          913          791          761 
TCGA-05-5420 TCGA-05-5425 TCGA-05-5428 TCGA-35-4123 TCGA-35-5375 TCGA-38-6178 
         457          882          670          182          264          448 
TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 TCGA-44-6145 TCGA-44-6147 TCGA-44-6778 
        1013          863          723          328          845         1864 
TCGA-44-7660 TCGA-44-7667 TCGA-44-7670 TCGA-44-A479 TCGA-49-4501 TCGA-49-4506 
         592          557          882          486         1421          999 
TCGA-49-4507 TCGA-49-6743 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5066 
         268          369         2174         2146          455          944 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5941 TCGA-50-7109 TCGA-53-7624 
         246          282          267          567          255         1986 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 
         280          701         1178         1479         1375           87 
TCGA-55-6971 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
          25            6            4           95           40         1958 
TCGA-55-7726 TCGA-55-7815 TCGA-55-7910 TCGA-55-8085 TCGA-55-8092 TCGA-55-8094 
          39           54          197           33           26            4 
TCGA-55-8205 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8512 TCGA-55-8514 
          33           29            8           15            3          202 
TCGA-55-8615 TCGA-55-8616 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
          15           48           42           29           48         1952 
TCGA-55-A492 TCGA-55-A4DF TCGA-62-8398 TCGA-62-8399 TCGA-62-A46U TCGA-62-A472 
           1           47         1970         2696         2067          910 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5778 TCGA-64-5779 TCGA-67-3771 
         628         1686         1968         1305          864          610 
TCGA-67-3773 TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 TCGA-69-7979 TCGA-69-8255 
         427          690          414          230           89          129 
TCGA-71-6725 TCGA-73-4659 TCGA-73-4662 TCGA-73-4670 TCGA-73-4675 TCGA-75-6214 
          61          711          912          131           40         1970 
TCGA-75-7027 TCGA-75-7031 TCGA-78-7147 TCGA-78-7148 TCGA-78-7150 TCGA-78-7152 
        1956         1965         1950         1944         1963         1202 
TCGA-78-7155 TCGA-78-7159 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
        1957         1221         1937         1965         1972         1949 
TCGA-78-7539 TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 TCGA-86-7954 TCGA-86-7955 
         327         1959          630          422         1963          508 
TCGA-86-8055 TCGA-86-8075 TCGA-86-8279 TCGA-86-8669 TCGA-86-8672 TCGA-86-A456 
          10          479          482           34           15           10 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6840 TCGA-91-6847 
         323         1940           60          310          372          842 
TCGA-91-7771 TCGA-91-A4BC TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
         492           44            2          568          377          477 
TCGA-97-7937 TCGA-97-8175 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
         181           87          427          459           44          170 
TCGA-J2-A4AD TCGA-L4-A4E5 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SW 
         287          578          285          622          353         1967 
TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TF 
        1957         1951         1970 

$`DEL PEAK 11(4Q35.1) WILD-TYPE`
TCGA-05-4384 TCGA-05-4396 TCGA-05-4403 TCGA-05-4410 TCGA-05-4422 TCGA-05-4425 
         426         1947          578         1958          365          669 
TCGA-05-4426 TCGA-05-4430 TCGA-05-4433 TCGA-05-5423 TCGA-05-5429 TCGA-05-5715 
         791          761          730          151           30           62 
TCGA-35-3615 TCGA-35-4122 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
          14          225         1952         1962         1147         1492 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-7271 TCGA-38-A44F 
         864         1073          354         1357         1971          133 
TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 
        1324         1429          400         1367          741         1280 
TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 
        1301           97          246         1130         1163         1036 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5645 TCGA-44-6146 TCGA-44-6148 TCGA-44-6774 
         190          722          383          302          704          658 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 TCGA-44-7661 
         705         1938         1942         1978          444          366 
TCGA-44-7662 TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
         218         1970          535          719          385           99 
TCGA-44-8120 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
         260          466          287          337          351          415 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 TCGA-49-4505 TCGA-49-4510 TCGA-49-4512 
          76         1932         1081          428          896          157 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-50-5055 
        1700          445          890          522          354          785 
TCGA-50-5068 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5942 TCGA-50-5944 
        1499         1091         2370          653          883          764 
TCGA-50-5946 TCGA-50-6597 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-55-6543 
         686         1015          105         1971          424            2 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6972 TCGA-55-6980 TCGA-55-6983 
         993           24         1239         1475           67         1826 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
        1233         2151         1170           18           35          121 
TCGA-55-7725 TCGA-55-7727 TCGA-55-7728 TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 
          39           34           24           19           16           21 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
           3           31            5           21          100            6 
TCGA-55-8091 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 
          43           47           15           46           66          216 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8510 TCGA-55-8511 TCGA-55-8513 
          44           23           11          228            9          146 
TCGA-55-8614 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A493 
         536           49           66          106           33           28 
TCGA-55-A494 TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8402 TCGA-62-A46V 
           5          162         1216         1289         1445         2199 
TCGA-62-A471 TCGA-64-1676 TCGA-64-1678 TCGA-64-1680 TCGA-64-5774 TCGA-64-5775 
        1246         1728         1189         1126         1959           62 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3772 TCGA-67-3774 TCGA-67-6215 
        1559          866           31          573          385          174 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7765 TCGA-69-7974 
         141          422          202          186          165          184 
TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-A59K TCGA-73-4658 
          70          382          100           77          214         1600 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
         800          467          164           38          621          519 
TCGA-75-7025 TCGA-78-7145 TCGA-78-7146 TCGA-78-7149 TCGA-78-7153 TCGA-78-7154 
        1967         1973         1988         1093          760         1948 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        1961         1963          678          215         1940         1950 
TCGA-78-7166 TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
        1934         1944          881         1952          994         1949 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 
        1971         1981         1954         1964         1965         1972 
TCGA-83-5908 TCGA-86-7701 TCGA-86-7714 TCGA-86-7953 TCGA-86-8054 TCGA-86-8056 
         824           11         1968          591          745         1963 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8281 
          13           24          489          476           16         1955 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8673 
          19           26           35           45           18          455 
TCGA-86-8674 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6835 TCGA-91-6836 
         405           30           14           39           79          417 
TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD 
         224           35          197          174           36          218 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7948 TCGA-95-A4VK 
         297          127          186           34          476          121 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7941 
         964         1965         1932         1332          775           22 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
         107          182         1965          147           15          148 
TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 TCGA-J2-8192 TCGA-J2-8194 
         115          197          271          392          154          114 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MP-A4SV 
         282          238          435          116            6         1946 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TC TCGA-MP-A4TE 
        1951         1954         1954         1980         1944         1970 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
         142         1955         1971         1490 

  DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE 
                            1                             2 
  DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE 
                         2696                          2370 
  DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE 
                        492.0                         431.5 
[1] "1.0 - 2696.0 (492.0)" "2.0 - 2370.0 (431.5)"
[1] "hr=" "1.2"
D43V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 11(4Q35.1) MUTATED         2       42       45        17        19
  DEL PEAK 11(4Q35.1) WILD-TYPE       2       71       86        26        50
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 11(4Q35.1) MUTATED           29          5       10
  DEL PEAK 11(4Q35.1) WILD-TYPE         38          6       13
D43V3, multiclass
            clus
vv           DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE
  STAGE I                              2                             2
  STAGE IA                            42                            71
  STAGE IB                            45                            86
  STAGE IIA                           17                            26
  STAGE IIB                           19                            50
  STAGE IIIA                          29                            38
  STAGE IIIB                           5                             6
  STAGE IV                            10                            13
[1] 8 2
[1] TRUE
[1] "dimension of 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(4Q35.1) MUTATED    50 101  11   5
  DEL PEAK 11(4Q35.1) WILD-TYPE  93 158  29  13
D43V4, multiclass
    clus
vv   DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE
  T1                          50                            93
  T2                         101                           158
  T3                          11                            29
  T4                           5                            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(4Q35.1) MUTATED   105  27    33
  DEL PEAK 11(4Q35.1) WILD-TYPE 190  58    39
D43V5, multiclass
       clus
vv      DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE
  N0                            105                           190
  N1                             27                            58
  N2+N3                          33                            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"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK 11(4Q35.1) MUTATED   122   8   0   2  35
  DEL PEAK 11(4Q35.1) WILD-TYPE 195  10   1   1  84
D43V6, multiclass
     clus
vv    DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE
  M0                          122                           195
  M1                            8                            10
  M1A                           0                             1
  M1B                           2                             1
  MX                           35                            84
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V7, binary
                               cls
clus                              0   1
  DEL PEAK 11(4Q35.1) MUTATED    81  88
  DEL PEAK 11(4Q35.1) WILD-TYPE 167 126
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4Q35.1) MUTATED     81   88
  DEL PEAK 11(4Q35.1) WILD-TYPE  167  126
        clus
vv       DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE
  FEMALE                          81                           167
  MALE                            88                           126
[1] 2 2
[1] FALSE
D43V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 11(4Q35.1) MUTATED                            4
  DEL PEAK 11(4Q35.1) WILD-TYPE                          9
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 11(4Q35.1) MUTATED                                  37
  DEL PEAK 11(4Q35.1) WILD-TYPE                                56
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 11(4Q35.1) MUTATED                                                  110
  DEL PEAK 11(4Q35.1) WILD-TYPE                                                184
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 11(4Q35.1) MUTATED                                            0
  DEL PEAK 11(4Q35.1) WILD-TYPE                                          4
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 11(4Q35.1) MUTATED                                               4
  DEL PEAK 11(4Q35.1) WILD-TYPE                                            15
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 11(4Q35.1) MUTATED                                2
  DEL PEAK 11(4Q35.1) WILD-TYPE                              0
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 11(4Q35.1) MUTATED                                    1
  DEL PEAK 11(4Q35.1) WILD-TYPE                                  3
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 11(4Q35.1) MUTATED                              0
  DEL PEAK 11(4Q35.1) WILD-TYPE                            2
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 11(4Q35.1) MUTATED                               5
  DEL PEAK 11(4Q35.1) WILD-TYPE                            14
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 11(4Q35.1) MUTATED                                 1
  DEL PEAK 11(4Q35.1) WILD-TYPE                               0
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 11(4Q35.1) MUTATED                                               3
  DEL PEAK 11(4Q35.1) WILD-TYPE                                             1
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 11(4Q35.1) MUTATED                              2
  DEL PEAK 11(4Q35.1) WILD-TYPE                            5
D43V9, multiclass
                                                    clus
vv                                                   DEL PEAK 11(4Q35.1) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           37
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         110
  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                                                5
  LUNG SIGNET RING ADENOCARCINOMA                                              1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                3
  MUCINOUS (COLLOID) CARCINOMA                                                 2
                                                    clus
vv                                                   DEL PEAK 11(4Q35.1) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             56
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           184
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 15
  LUNG CLEAR CELL ADENOCARCINOMA                                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             3
  LUNG MUCINOUS ADENOCARCINOMA                                                   2
  LUNG PAPILLARY ADENOCARCINOMA                                                 14
  LUNG SIGNET RING ADENOCARCINOMA                                                0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                  1
  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"
D43V10, binary
                               cls
clus                              0   1
  DEL PEAK 11(4Q35.1) MUTATED    10 159
  DEL PEAK 11(4Q35.1) WILD-TYPE  11 282
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4Q35.1) MUTATED     10  159
  DEL PEAK 11(4Q35.1) WILD-TYPE   11  282
     clus
vv    DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE
  NO                           10                            11
  YES                         159                           282
[1] 2 2
[1] FALSE
D43V11, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 11(4Q35.1) MUTATED   118   4   2   8
  DEL PEAK 11(4Q35.1) WILD-TYPE 200   7   2  11
D43V12, multiclass
    clus
vv   DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE
  R0                         118                           200
  R1                           4                             7
  R2                           2                             2
  RX                           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                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 11(4Q35.1) MUTATED                                  0     4
  DEL PEAK 11(4Q35.1) WILD-TYPE                                1     2
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(4Q35.1) MUTATED                          14   124
  DEL PEAK 11(4Q35.1) WILD-TYPE                        12   238
D43V13, multiclass
                                  clus
vv                                 DEL PEAK 11(4Q35.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 14
  WHITE                                                    124
                                  clus
vv                                 DEL PEAK 11(4Q35.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   12
  WHITE                                                      238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V14, binary
                               cls
clus                              0   1
  DEL PEAK 11(4Q35.1) MUTATED     5 119
  DEL PEAK 11(4Q35.1) WILD-TYPE   2 213
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4Q35.1) MUTATED      5  119
  DEL PEAK 11(4Q35.1) WILD-TYPE    2  213
                        clus
vv                       DEL PEAK 11(4Q35.1) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         119
                        clus
vv                       DEL PEAK 11(4Q35.1) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           213
[1] 2 2
[1] FALSE

Clustering(44) Variable = DEL PEAK 12(5Q11.2) MUTATION ANALYSIS
D44V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 12(5Q11.2) MUTATED   121  28
  DEL PEAK 12(5Q11.2) WILD-TYPE 200  54
  DEL PEAK 12(5Q11.2) MUTATED DEL PEAK 12(5Q11.2) WILD-TYPE 
                          149                           254 
  DEL PEAK 12(5Q11.2) MUTATED DEL PEAK 12(5Q11.2) WILD-TYPE 
                           28                            54 
$`DEL PEAK 12(5Q11.2) MUTATED`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4389 TCGA-05-4396 TCGA-05-4398 TCGA-05-4405 
        1523          607         1369         1947         1431          610 
TCGA-05-4410 TCGA-05-4417 TCGA-05-4424 TCGA-05-4427 TCGA-05-4432 TCGA-05-5425 
        1958          455          913          791          761          882 
TCGA-05-5428 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 TCGA-38-4628 
         670           62          225          182         1952         1492 
TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-44-2657 TCGA-44-2659 TCGA-44-3918 
        1073          354         1357          400         1367         1036 
TCGA-44-3919 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6774 
         190          723          328          302          845          658 
TCGA-44-6775 TCGA-44-6778 TCGA-44-7660 TCGA-44-7662 TCGA-44-7670 TCGA-44-8120 
         705         1864          592          218          882          260 
TCGA-44-A4SS TCGA-49-4505 TCGA-49-4507 TCGA-49-6742 TCGA-50-5045 TCGA-50-5049 
         415          428          268          445         2174         2146 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5944 TCGA-50-5946 TCGA-53-7624 TCGA-53-7626 
         944         1499          764          686         1986         1971 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6969 
         280          701         1178         1375           87         1239 
TCGA-55-6972 TCGA-55-6985 TCGA-55-7570 TCGA-55-7724 TCGA-55-7726 TCGA-55-7727 
        1475         1233            6         1958           39           34 
TCGA-55-7910 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8094 TCGA-55-8505 
         197            3           31            5            4           29 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 TCGA-55-8511 TCGA-55-8514 TCGA-55-8614 
          11            8          228            9          202          536 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A491 TCGA-55-A492 
          15           48           66           42         1952            1 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A471 TCGA-64-1676 TCGA-64-1678 
        1970         2696         1445         1246         1728         1189 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5778 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 
        1686         1968         1305           31          610          573 
TCGA-69-7765 TCGA-69-7979 TCGA-69-7980 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
         165           89          382          129          214           61 
TCGA-73-4668 TCGA-73-4670 TCGA-75-6214 TCGA-75-7027 TCGA-75-7031 TCGA-78-7149 
         467          131         1970         1956         1965         1093 
TCGA-78-7150 TCGA-78-7154 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7220 
        1963         1948         1221          678          215         1965 
TCGA-78-7535 TCGA-78-7536 TCGA-78-8640 TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 
        1972         1949         1949         1972          824         1959 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-7955 TCGA-86-8074 TCGA-86-8279 
         630          422          591          508           24          482 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8672 TCGA-91-6829 TCGA-91-6840 TCGA-91-8499 
          26           35           15         1940          372           36 
TCGA-93-7348 TCGA-93-8067 TCGA-95-7043 TCGA-95-7567 TCGA-95-7947 TCGA-95-7948 
         127          186            2          568          477          476 
TCGA-97-7937 TCGA-97-8172 TCGA-97-8175 TCGA-99-8033 TCGA-J2-A4AD TCGA-L4-A4E5 
         181          182           87          170          287          578 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T4 
           6          285          622         1946         1967         1954 
TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TK TCGA-MP-A5C7 
        1957         1944         1970         1971         1490 

$`DEL PEAK 12(5Q11.2) WILD-TYPE`
TCGA-05-4384 TCGA-05-4390 TCGA-05-4403 TCGA-05-4415 TCGA-05-4420 TCGA-05-4422 
         426         1126          578         1997          912          365 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 
         669          791          761          730          457          151 
TCGA-05-5429 TCGA-35-3615 TCGA-35-5375 TCGA-38-4626 TCGA-38-4627 TCGA-38-4629 
          30           14          264         1962         1147          864 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2661 
         448         1971          133         1324         1429          741 
TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 
        1280         1301           97          246         1130         1163 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6148 TCGA-44-6776 
         722         1013          863          383          704         1938 
TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 TCGA-44-7661 TCGA-44-7667 TCGA-44-7669 
        1942         1978          444          366          557         1970 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A 
         535          719          385           99          486          466 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 
         287          337          351           76         1932         1081 
TCGA-49-4501 TCGA-49-4506 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 
        1421          999          896          157         1700          369 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-50-5051 TCGA-50-5055 TCGA-50-5072 
         890          522          354          455          785          246 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 
         282          267         1091         2370          653          567 
TCGA-50-5942 TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 TCGA-53-7813 TCGA-55-1595 
         883         1015          255          105          424         1479 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6971 TCGA-55-6980 TCGA-55-6983 
           2          993           24           25           67         1826 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7573 
        2151         1170           18           35          121            4 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7725 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 
          95           40           39           24           54           19 
TCGA-55-7907 TCGA-55-7911 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
          16           21           33           21          100            6 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 
          43           26           47           15           33           46 
TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8508 TCGA-55-8512 
          66          216           44           23           15            3 
TCGA-55-8513 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Z TCGA-55-A490 
         146           49          106           33           29           48 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 
          28            5           47          162         1216         1289 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A472 TCGA-64-1677 TCGA-64-1680 TCGA-64-5774 
        2067         2199          910          628         1126         1959 
TCGA-64-5775 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3773 TCGA-67-3774 
          62          864         1559          866          427          385 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
         174          141          422          202          186          690 
TCGA-69-7764 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-8253 TCGA-69-8254 
         414          230          184           70          100           77 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4675 TCGA-73-4676 
        1600          711          912          800           40          164 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-75-7025 TCGA-78-7145 TCGA-78-7146 
          38          621          519         1967         1973         1988 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7152 TCGA-78-7153 TCGA-78-7155 TCGA-78-7156 
        1950         1944         1202          760         1957         1961 
TCGA-78-7158 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7537 
        1963         1940         1950         1934         1937         1944 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 
         327          881         1952          994         1971         1981 
TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 TCGA-86-7701 TCGA-86-7714 TCGA-86-7954 
        1954         1964         1965           11         1968         1963 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 TCGA-86-8076 
         745           10         1963           13          479          489 
TCGA-86-8278 TCGA-86-8280 TCGA-86-8281 TCGA-86-8358 TCGA-86-8668 TCGA-86-8669 
         476           16         1955           19           45           34 
TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 
          18          455          405           10           30           14 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
          39          323           60          310           79          417 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
         842          224           35          492          197          174 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-95-7039 TCGA-95-7944 TCGA-95-A4VK 
          44          218          297           34          377          121 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7941 
         964         1965         1932         1332          775           22 
TCGA-97-8171 TCGA-97-8174 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
         107         1965          147           15          148          115 
TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
         197          271          392          427          459           44 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 
         154          114          282          238          435          116 
TCGA-MN-A4N5 TCGA-MP-A4T2 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TF 
         353         1951         1954         1980         1951         1970 
TCGA-MP-A4TH TCGA-MP-A4TI 
         142         1955 

  DEL PEAK 12(5Q11.2) MUTATED DEL PEAK 12(5Q11.2) WILD-TYPE 
                            1                             2 
  DEL PEAK 12(5Q11.2) MUTATED DEL PEAK 12(5Q11.2) WILD-TYPE 
                         2696                          2370 
  DEL PEAK 12(5Q11.2) MUTATED DEL PEAK 12(5Q11.2) WILD-TYPE 
                        610.0                         419.5 
[1] "1.0 - 2696.0 (610.0)" "2.0 - 2370.0 (419.5)"
[1] "hr=" "1.4"
D44V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 12(5Q11.2) MUTATED         2       39       48        17        27
  DEL PEAK 12(5Q11.2) WILD-TYPE       2       74       83        26        42
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 12(5Q11.2) MUTATED           20          4        9
  DEL PEAK 12(5Q11.2) WILD-TYPE         47          7       14
D44V3, multiclass
            clus
vv           DEL PEAK 12(5Q11.2) MUTATED DEL PEAK 12(5Q11.2) WILD-TYPE
  STAGE I                              2                             2
  STAGE IA                            39                            74
  STAGE IB                            48                            83
  STAGE IIA                           17                            26
  STAGE IIB                           27                            42
  STAGE IIIA                          20                            47
  STAGE IIIB                           4                             7
  STAGE IV                             9                            14
[1] 8 2
[1] TRUE
[1] "dimension of 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(5Q11.2) MUTATED    53  93  12   6
  DEL PEAK 12(5Q11.2) WILD-TYPE  90 166  28  12
D44V4, multiclass
    clus
vv   DEL PEAK 12(5Q11.2) MUTATED DEL PEAK 12(5Q11.2) WILD-TYPE
  T1                          53                            90
  T2                          93                           166
  T3                          12                            28
  T4                           6                            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(5Q11.2) MUTATED   101  38    22
  DEL PEAK 12(5Q11.2) WILD-TYPE 194  47    50
D44V5, multiclass
       clus
vv      DEL PEAK 12(5Q11.2) MUTATED DEL PEAK 12(5Q11.2) WILD-TYPE
  N0                            101                           194
  N1                             38                            47
  N2+N3                          22                            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"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK 12(5Q11.2) MUTATED   120   6   0   2  38
  DEL PEAK 12(5Q11.2) WILD-TYPE 197  12   1   1  81
D44V6, multiclass
     clus
vv    DEL PEAK 12(5Q11.2) MUTATED DEL PEAK 12(5Q11.2) WILD-TYPE
  M0                          120                           197
  M1                            6                            12
  M1A                           0                             1
  M1B                           2                             1
  MX                           38                            81
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V7, binary
                               cls
clus                              0   1
  DEL PEAK 12(5Q11.2) MUTATED    85  81
  DEL PEAK 12(5Q11.2) WILD-TYPE 163 133
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(5Q11.2) MUTATED     85   81
  DEL PEAK 12(5Q11.2) WILD-TYPE  163  133
        clus
vv       DEL PEAK 12(5Q11.2) MUTATED DEL PEAK 12(5Q11.2) WILD-TYPE
  FEMALE                          85                           163
  MALE                            81                           133
[1] 2 2
[1] FALSE
D44V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 12(5Q11.2) MUTATED                            5
  DEL PEAK 12(5Q11.2) WILD-TYPE                          8
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 12(5Q11.2) MUTATED                                  33
  DEL PEAK 12(5Q11.2) WILD-TYPE                                60
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 12(5Q11.2) MUTATED                                                  114
  DEL PEAK 12(5Q11.2) WILD-TYPE                                                180
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 12(5Q11.2) MUTATED                                            0
  DEL PEAK 12(5Q11.2) WILD-TYPE                                          4
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 12(5Q11.2) MUTATED                                               2
  DEL PEAK 12(5Q11.2) WILD-TYPE                                            17
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 12(5Q11.2) MUTATED                                0
  DEL PEAK 12(5Q11.2) WILD-TYPE                              2
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 12(5Q11.2) MUTATED                                    2
  DEL PEAK 12(5Q11.2) WILD-TYPE                                  2
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 12(5Q11.2) MUTATED                              1
  DEL PEAK 12(5Q11.2) WILD-TYPE                            1
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 12(5Q11.2) MUTATED                               4
  DEL PEAK 12(5Q11.2) WILD-TYPE                            15
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 12(5Q11.2) MUTATED                                 0
  DEL PEAK 12(5Q11.2) WILD-TYPE                               1
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 12(5Q11.2) MUTATED                                               4
  DEL PEAK 12(5Q11.2) WILD-TYPE                                             0
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 12(5Q11.2) MUTATED                              1
  DEL PEAK 12(5Q11.2) WILD-TYPE                            6
D44V9, multiclass
                                                    clus
vv                                                   DEL PEAK 12(5Q11.2) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           33
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         114
  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                                                4
  LUNG SIGNET RING ADENOCARCINOMA                                              0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                4
  MUCINOUS (COLLOID) CARCINOMA                                                 1
                                                    clus
vv                                                   DEL PEAK 12(5Q11.2) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             60
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           180
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 17
  LUNG CLEAR CELL ADENOCARCINOMA                                                 2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             2
  LUNG MUCINOUS ADENOCARCINOMA                                                   1
  LUNG PAPILLARY ADENOCARCINOMA                                                 15
  LUNG SIGNET RING ADENOCARCINOMA                                                1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                  0
  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"
D44V10, binary
                               cls
clus                              0   1
  DEL PEAK 12(5Q11.2) MUTATED     6 160
  DEL PEAK 12(5Q11.2) WILD-TYPE  15 281
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(5Q11.2) MUTATED      6  160
  DEL PEAK 12(5Q11.2) WILD-TYPE   15  281
     clus
vv    DEL PEAK 12(5Q11.2) MUTATED DEL PEAK 12(5Q11.2) WILD-TYPE
  NO                            6                            15
  YES                         160                           281
[1] 2 2
[1] FALSE
D44V11, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 12(5Q11.2) MUTATED   121   3   1  10
  DEL PEAK 12(5Q11.2) WILD-TYPE 197   8   3   9
D44V12, multiclass
    clus
vv   DEL PEAK 12(5Q11.2) MUTATED DEL PEAK 12(5Q11.2) WILD-TYPE
  R0                         121                           197
  R1                           3                             8
  R2                           1                             3
  RX                          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                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 12(5Q11.2) MUTATED                                  1     3
  DEL PEAK 12(5Q11.2) WILD-TYPE                                0     3
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(5Q11.2) MUTATED                          12   121
  DEL PEAK 12(5Q11.2) WILD-TYPE                        14   241
D44V13, multiclass
                                  clus
vv                                 DEL PEAK 12(5Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 12
  WHITE                                                    121
                                  clus
vv                                 DEL PEAK 12(5Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        3
  BLACK OR AFRICAN AMERICAN                                   14
  WHITE                                                      241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V14, binary
                               cls
clus                              0   1
  DEL PEAK 12(5Q11.2) MUTATED     6 114
  DEL PEAK 12(5Q11.2) WILD-TYPE   1 218
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(5Q11.2) MUTATED      6  114
  DEL PEAK 12(5Q11.2) WILD-TYPE    1  218
                        clus
vv                       DEL PEAK 12(5Q11.2) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                         114
                        clus
vv                       DEL PEAK 12(5Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                           218
[1] 2 2
[1] FALSE

Clustering(45) Variable = DEL PEAK 13(5Q31.1) MUTATION ANALYSIS
D45V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 13(5Q31.1) MUTATED   141  32
  DEL PEAK 13(5Q31.1) WILD-TYPE 180  50
  DEL PEAK 13(5Q31.1) MUTATED DEL PEAK 13(5Q31.1) WILD-TYPE 
                          173                           230 
  DEL PEAK 13(5Q31.1) MUTATED DEL PEAK 13(5Q31.1) WILD-TYPE 
                           32                            50 
$`DEL PEAK 13(5Q31.1) MUTATED`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4389 TCGA-05-4396 TCGA-05-4398 TCGA-05-4405 
        1523          607         1369         1947         1431          610 
TCGA-05-4410 TCGA-05-4417 TCGA-05-4420 TCGA-05-4424 TCGA-05-4427 TCGA-05-4430 
        1958          455          912          913          791          761 
TCGA-05-4432 TCGA-05-5425 TCGA-05-5428 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 
         761          882          670           62          225          182 
TCGA-38-4625 TCGA-38-4628 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-7271 
        1952         1492         1073          354         1357         1971 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 
        1429          400         1367         1013          863          723 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6774 TCGA-44-6778 TCGA-44-6779 
         328          302          845          658         1864         1978 
TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7670 TCGA-44-8117 TCGA-44-8120 
         592          218          557          882          385          260 
TCGA-44-A4SS TCGA-49-4505 TCGA-49-4507 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
         415          428          268         1700          445          369 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5066 TCGA-50-5068 TCGA-50-5941 TCGA-50-5944 
        2174         2146          944         1499          567          764 
TCGA-50-5946 TCGA-50-7109 TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1592 
         686          255         1986         1971          280          701 
TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6969 TCGA-55-6972 TCGA-55-6985 
        1178         1375           87         1239         1475         1233 
TCGA-55-7281 TCGA-55-7570 TCGA-55-7576 TCGA-55-7724 TCGA-55-7726 TCGA-55-7727 
          18            6           40         1958           39           34 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7914 TCGA-55-7994 TCGA-55-8094 TCGA-55-8302 
          16          197            3           31            4           23 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 TCGA-55-8511 TCGA-55-8514 
          29           11            8          228            9          202 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A491 
         536           15           48           66           42         1952 
TCGA-55-A492 TCGA-55-A4DG TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
           1          162         1216         1970         2696         1445 
TCGA-62-A46V TCGA-62-A471 TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 
        2199         1246         1728         1189         1686         1968 
TCGA-64-5778 TCGA-64-5779 TCGA-67-3771 TCGA-67-3772 TCGA-69-7764 TCGA-69-7765 
        1305          864          610          573          414          165 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8255 TCGA-71-6725 TCGA-73-4668 TCGA-73-4670 
          89          382          129           61          467          131 
TCGA-75-6214 TCGA-75-7027 TCGA-78-7146 TCGA-78-7149 TCGA-78-7150 TCGA-78-7159 
        1970         1956         1988         1093         1963         1221 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
         678          215         1937         1965         1972         1949 
TCGA-78-7537 TCGA-78-8640 TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 TCGA-86-7711 
        1944         1949         1972          824         1959          630 
TCGA-86-7713 TCGA-86-7953 TCGA-86-7955 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
         422          591          508         1963           13           24 
TCGA-86-8279 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8672 TCGA-91-6829 
         482           19           26           35           15         1940 
TCGA-91-6831 TCGA-91-6840 TCGA-91-8499 TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 
         310          372           36          127          186           34 
TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK 
           2          568          377          477          476          121 
TCGA-97-7937 TCGA-97-8172 TCGA-97-8175 TCGA-99-8025 TCGA-J2-A4AD TCGA-L4-A4E5 
         181          182           87          427          287          578 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4T4 TCGA-MP-A4T7 
           6          285          622         1946         1954         1954 
TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TK TCGA-MP-A5C7 
        1957         1944         1970         1971         1490 

$`DEL PEAK 13(5Q31.1) WILD-TYPE`
TCGA-05-4384 TCGA-05-4390 TCGA-05-4403 TCGA-05-4415 TCGA-05-4422 TCGA-05-4425 
         426         1126          578         1997          365          669 
TCGA-05-4426 TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5429 TCGA-35-3615 
         791          730          457          151           30           14 
TCGA-35-5375 TCGA-38-4626 TCGA-38-4627 TCGA-38-4629 TCGA-38-6178 TCGA-38-A44F 
         264         1962         1147          864          448          133 
TCGA-44-2655 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
        1324          741         1280         1301           97          246 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5645 
        1130         1163         1036          190          722          383 
TCGA-44-6148 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-7659 TCGA-44-7661 
         704          705         1938         1942          444          366 
TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A 
        1970          535          719           99          486          466 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 
         287          337          351           76         1932         1081 
TCGA-49-4501 TCGA-49-4506 TCGA-49-4510 TCGA-49-4512 TCGA-49-6744 TCGA-49-6745 
        1421          999          896          157          890          522 
TCGA-49-6761 TCGA-50-5051 TCGA-50-5055 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
         354          455          785          246          282          267 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5942 TCGA-50-6597 TCGA-50-8460 
        1091         2370          653          883         1015          105 
TCGA-53-7813 TCGA-55-1595 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6971 
         424         1479            2          993           24           25 
TCGA-55-6980 TCGA-55-6983 TCGA-55-6986 TCGA-55-6987 TCGA-55-7283 TCGA-55-7284 
          67         1826         2151         1170           35          121 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7725 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 
           4           95           39           24           54           19 
TCGA-55-7911 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
          21            5           33           21          100            6 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 
          43           26           47           15           33           46 
TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 
          66          216           44           15            3          146 
TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 
          49          106           33           29           48           28 
TCGA-55-A494 TCGA-55-A4DF TCGA-62-8397 TCGA-62-A46U TCGA-62-A472 TCGA-64-1677 
           5           47         1289         2067          910          628 
TCGA-64-1680 TCGA-64-5774 TCGA-64-5775 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 
        1126         1959           62         1559          866           31 
TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
         427          385          174          141          422          202 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-8253 
         186          690          230          184           70          100 
TCGA-69-8254 TCGA-69-A59K TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
          77          214         1600          711          912          800 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-75-7025 
          40          164           38          621          519         1967 
TCGA-75-7031 TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 TCGA-78-7152 TCGA-78-7153 
        1965         1973         1950         1944         1202          760 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7162 TCGA-78-7163 
        1948         1957         1961         1963         1940         1950 
TCGA-78-7166 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 
        1934          327          881         1952          994         1971 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 TCGA-86-7701 TCGA-86-7714 
        1981         1954         1964         1965           11         1968 
TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        1963          745           10          479          489          476 
TCGA-86-8280 TCGA-86-8281 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 
          16         1955           45           34           18          455 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
         405           10           30           14           39          323 
TCGA-91-6830 TCGA-91-6835 TCGA-91-6836 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
          60           79          417          842          224           35 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
         492          197          174           44          218          297 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7941 
         964         1965         1932         1332          775           22 
TCGA-97-8171 TCGA-97-8174 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
         107         1965          147           15          148          115 
TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
         197          271          392          459           44          170 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 
         154          114          282          238          435          116 
TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TF 
         353         1967         1951         1980         1951         1970 
TCGA-MP-A4TH TCGA-MP-A4TI 
         142         1955 

  DEL PEAK 13(5Q31.1) MUTATED DEL PEAK 13(5Q31.1) WILD-TYPE 
                            1                             2 
  DEL PEAK 13(5Q31.1) MUTATED DEL PEAK 13(5Q31.1) WILD-TYPE 
                         2696                          2370 
  DEL PEAK 13(5Q31.1) MUTATED DEL PEAK 13(5Q31.1) WILD-TYPE 
                        607.0                         398.5 
[1] "1.0 - 2696.0 (607.0)" "2.0 - 2370.0 (398.5)"
[1] "hr=" "1.6"
D45V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 13(5Q31.1) MUTATED         3       42       57        18        30
  DEL PEAK 13(5Q31.1) WILD-TYPE       1       71       74        25        39
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 13(5Q31.1) MUTATED           27          4       11
  DEL PEAK 13(5Q31.1) WILD-TYPE         40          7       12
D45V3, multiclass
            clus
vv           DEL PEAK 13(5Q31.1) MUTATED DEL PEAK 13(5Q31.1) WILD-TYPE
  STAGE I                              3                             1
  STAGE IA                            42                            71
  STAGE IB                            57                            74
  STAGE IIA                           18                            25
  STAGE IIB                           30                            39
  STAGE IIIA                          27                            40
  STAGE IIIB                           4                             7
  STAGE IV                            11                            12
[1] 8 2
[1] TRUE
[1] "dimension of 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(5Q31.1) MUTATED    59 110  15   7
  DEL PEAK 13(5Q31.1) WILD-TYPE  84 149  25  11
D45V4, multiclass
    clus
vv   DEL PEAK 13(5Q31.1) MUTATED DEL PEAK 13(5Q31.1) WILD-TYPE
  T1                          59                            84
  T2                         110                           149
  T3                          15                            25
  T4                           7                            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 13(5Q31.1) MUTATED   121  39    28
  DEL PEAK 13(5Q31.1) WILD-TYPE 174  46    44
D45V5, multiclass
       clus
vv      DEL PEAK 13(5Q31.1) MUTATED DEL PEAK 13(5Q31.1) WILD-TYPE
  N0                            121                           174
  N1                             39                            46
  N2+N3                          28                            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"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK 13(5Q31.1) MUTATED   133   8   0   2  48
  DEL PEAK 13(5Q31.1) WILD-TYPE 184  10   1   1  71
D45V6, multiclass
     clus
vv    DEL PEAK 13(5Q31.1) MUTATED DEL PEAK 13(5Q31.1) WILD-TYPE
  M0                          133                           184
  M1                            8                            10
  M1A                           0                             1
  M1B                           2                             1
  MX                           48                            71
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V7, binary
                               cls
clus                              0   1
  DEL PEAK 13(5Q31.1) MUTATED    97  95
  DEL PEAK 13(5Q31.1) WILD-TYPE 151 119
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(5Q31.1) MUTATED     97   95
  DEL PEAK 13(5Q31.1) WILD-TYPE  151  119
        clus
vv       DEL PEAK 13(5Q31.1) MUTATED DEL PEAK 13(5Q31.1) WILD-TYPE
  FEMALE                          97                           151
  MALE                            95                           119
[1] 2 2
[1] FALSE
D45V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 13(5Q31.1) MUTATED                            6
  DEL PEAK 13(5Q31.1) WILD-TYPE                          7
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 13(5Q31.1) MUTATED                                  43
  DEL PEAK 13(5Q31.1) WILD-TYPE                                50
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 13(5Q31.1) MUTATED                                                  126
  DEL PEAK 13(5Q31.1) WILD-TYPE                                                168
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 13(5Q31.1) MUTATED                                            0
  DEL PEAK 13(5Q31.1) WILD-TYPE                                          4
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 13(5Q31.1) MUTATED                                               3
  DEL PEAK 13(5Q31.1) WILD-TYPE                                            16
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 13(5Q31.1) MUTATED                                1
  DEL PEAK 13(5Q31.1) WILD-TYPE                              1
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 13(5Q31.1) MUTATED                                    2
  DEL PEAK 13(5Q31.1) WILD-TYPE                                  2
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 13(5Q31.1) MUTATED                              1
  DEL PEAK 13(5Q31.1) WILD-TYPE                            1
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 13(5Q31.1) MUTATED                               6
  DEL PEAK 13(5Q31.1) WILD-TYPE                            13
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 13(5Q31.1) MUTATED                                 0
  DEL PEAK 13(5Q31.1) WILD-TYPE                               1
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 13(5Q31.1) MUTATED                                               3
  DEL PEAK 13(5Q31.1) WILD-TYPE                                             1
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 13(5Q31.1) MUTATED                              1
  DEL PEAK 13(5Q31.1) WILD-TYPE                            6
D45V9, multiclass
                                                    clus
vv                                                   DEL PEAK 13(5Q31.1) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           43
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         126
  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                                                6
  LUNG SIGNET RING ADENOCARCINOMA                                              0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                3
  MUCINOUS (COLLOID) CARCINOMA                                                 1
                                                    clus
vv                                                   DEL PEAK 13(5Q31.1) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             50
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           168
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 16
  LUNG CLEAR CELL ADENOCARCINOMA                                                 1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             2
  LUNG MUCINOUS ADENOCARCINOMA                                                   1
  LUNG PAPILLARY ADENOCARCINOMA                                                 13
  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"
D45V10, binary
                               cls
clus                              0   1
  DEL PEAK 13(5Q31.1) MUTATED     9 183
  DEL PEAK 13(5Q31.1) WILD-TYPE  12 258
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(5Q31.1) MUTATED      9  183
  DEL PEAK 13(5Q31.1) WILD-TYPE   12  258
     clus
vv    DEL PEAK 13(5Q31.1) MUTATED DEL PEAK 13(5Q31.1) WILD-TYPE
  NO                            9                            12
  YES                         183                           258
[1] 2 2
[1] FALSE
D45V11, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 13(5Q31.1) MUTATED   134   3   1  10
  DEL PEAK 13(5Q31.1) WILD-TYPE 184   8   3   9
D45V12, multiclass
    clus
vv   DEL PEAK 13(5Q31.1) MUTATED DEL PEAK 13(5Q31.1) WILD-TYPE
  R0                         134                           184
  R1                           3                             8
  R2                           1                             3
  RX                          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                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 13(5Q31.1) MUTATED                                  1     3
  DEL PEAK 13(5Q31.1) WILD-TYPE                                0     3
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(5Q31.1) MUTATED                          14   143
  DEL PEAK 13(5Q31.1) WILD-TYPE                        12   219
D45V13, multiclass
                                  clus
vv                                 DEL PEAK 13(5Q31.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 14
  WHITE                                                    143
                                  clus
vv                                 DEL PEAK 13(5Q31.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        3
  BLACK OR AFRICAN AMERICAN                                   12
  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"
D45V14, binary
                               cls
clus                              0   1
  DEL PEAK 13(5Q31.1) MUTATED     5 132
  DEL PEAK 13(5Q31.1) WILD-TYPE   2 200
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(5Q31.1) MUTATED      5  132
  DEL PEAK 13(5Q31.1) WILD-TYPE    2  200
                        clus
vv                       DEL PEAK 13(5Q31.1) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         132
                        clus
vv                       DEL PEAK 13(5Q31.1) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           200
[1] 2 2
[1] FALSE

Clustering(46) Variable = DEL PEAK 14(6Q12) MUTATION ANALYSIS
D46V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 14(6Q12) MUTATED   109  36
  DEL PEAK 14(6Q12) WILD-TYPE 212  46
  DEL PEAK 14(6Q12) MUTATED DEL PEAK 14(6Q12) WILD-TYPE 
                        145                         258 
  DEL PEAK 14(6Q12) MUTATED DEL PEAK 14(6Q12) WILD-TYPE 
                         36                          46 
$`DEL PEAK 14(6Q12) MUTATED`
TCGA-05-4389 TCGA-05-4390 TCGA-05-4405 TCGA-05-4415 TCGA-05-4425 TCGA-05-4430 
        1369         1126          610         1997          669          761 
TCGA-35-3615 TCGA-35-4123 TCGA-38-4631 TCGA-38-4632 TCGA-44-2656 TCGA-44-2659 
          14          182          354         1357         1429         1367 
TCGA-44-2666 TCGA-44-2668 TCGA-44-5644 TCGA-44-6147 TCGA-44-6775 TCGA-44-6776 
          97          246          863          845          705         1938 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7671 TCGA-44-8120 TCGA-44-A47F 
        1942         1864         1978          535          260          337 
TCGA-49-4494 TCGA-49-4507 TCGA-49-4514 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
        1081          268         1700          890          522          354 
TCGA-50-5051 TCGA-50-5066 TCGA-50-5068 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
         455          944         1499         1091         2370          653 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5946 TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ 
         567          883          686         1986         1971          280 
TCGA-55-1595 TCGA-55-1596 TCGA-55-6543 TCGA-55-6971 TCGA-55-6972 TCGA-55-6983 
        1479         1375            2           25         1475         1826 
TCGA-55-6985 TCGA-55-7283 TCGA-55-7724 TCGA-55-7815 TCGA-55-7903 TCGA-55-7914 
        1233           35         1958           54           19            3 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8094 TCGA-55-8207 TCGA-55-8302 
         100            6           43            4           66           23 
TCGA-55-8506 TCGA-55-8508 TCGA-55-8511 TCGA-55-8512 TCGA-55-8615 TCGA-55-A48X 
          11           15            9            3           15           33 
TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-62-8398 TCGA-62-8402 TCGA-62-A46U 
          48           28            5         1970         1445         2067 
TCGA-62-A472 TCGA-64-1677 TCGA-64-1678 TCGA-64-5774 TCGA-64-5779 TCGA-64-5781 
         910          628         1189         1959          864         1559 
TCGA-67-6216 TCGA-69-7974 TCGA-69-8253 TCGA-69-8254 TCGA-69-A59K TCGA-73-4659 
         141          184          100           77          214          711 
TCGA-73-4666 TCGA-73-4675 TCGA-73-4677 TCGA-73-7499 TCGA-75-6214 TCGA-75-7025 
         800           40           38          519         1970         1967 
TCGA-75-7027 TCGA-78-7146 TCGA-78-7152 TCGA-78-7153 TCGA-78-7156 TCGA-78-7158 
        1956         1988         1202          760         1961         1963 
TCGA-78-7159 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 
        1221         1965         1972         1949         1944          881 
TCGA-78-7542 TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 TCGA-86-7701 TCGA-86-7713 
        1952         1965         1972          824           11          422 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7955 TCGA-86-8074 TCGA-86-8280 TCGA-86-8359 
        1968          591          508           24           16           26 
TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 TCGA-91-6831 TCGA-91-6849 TCGA-93-7347 
          15          405           10          310           35          297 
TCGA-93-7348 TCGA-93-8067 TCGA-95-7567 TCGA-95-7944 TCGA-95-7948 TCGA-97-7547 
         127          186          568          377          476         1965 
TCGA-97-7552 TCGA-97-7554 TCGA-97-8174 TCGA-97-8177 TCGA-97-8547 TCGA-99-7458 
        1932          775         1965          147          148          392 
TCGA-99-8025 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 TCGA-MN-A4N1 TCGA-MN-A4N4 
         427          154          114          116          285          622 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4T2 TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TF 
         353         1946         1951         1944         1970         1970 
TCGA-MP-A5C7 
        1490 

$`DEL PEAK 14(6Q12) WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4398 TCGA-05-4403 
        1523          607          426         1947         1431          578 
TCGA-05-4410 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4426 
        1958          455          912          365          913          791 
TCGA-05-4427 TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 
         791          761          730          457          151          882 
TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-5375 TCGA-38-4625 
         670           30           62          225          264         1952 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-6178 
        1962         1147         1492          864         1073          448 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2657 TCGA-44-2661 TCGA-44-2662 
        1971          133         1324          400          741         1280 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
        1301         1130         1163         1036          190          722 
TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6148 
        1013          383          723          328          302          704 
TCGA-44-6774 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
         658          444          592          366          218          557 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-A479 
        1970          882          719          385           99          486 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
         466          287          351          415           76         1932 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4510 TCGA-49-4512 TCGA-49-6742 
        1421          428          999          896          157          445 
TCGA-49-6743 TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5072 TCGA-50-5930 
         369         2174         2146          785          246          282 
TCGA-50-5931 TCGA-50-5944 TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 TCGA-53-7813 
         267          764         1015          255          105          424 
TCGA-55-1592 TCGA-55-1594 TCGA-55-5899 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 
         701         1178           87          993           24         1239 
TCGA-55-6980 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7284 TCGA-55-7570 
          67         2151         1170           18          121            6 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
           4           95           40           39           39           34 
TCGA-55-7728 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7994 TCGA-55-7995 
          24           16          197           21           31            5 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 
          33           21           26           47           15           33 
TCGA-55-8206 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8507 TCGA-55-8510 
          46          216           44           29            8          228 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
         146          202          536           48           49           66 
TCGA-55-8621 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF 
         106           42           29         1952            1           47 
TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 TCGA-62-A46V TCGA-62-A471 
         162         1216         1289         2696         2199         1246 
TCGA-64-1676 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5775 TCGA-64-5778 
        1728         1686         1126         1968           62         1305 
TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 
         866           31          610          573          427          385 
TCGA-67-6215 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
         174          422          202          186          690          414 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8255 
         165          230           70           89          382          129 
TCGA-71-6725 TCGA-73-4658 TCGA-73-4662 TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 
          61         1600          912          467          131          164 
TCGA-73-7498 TCGA-75-7031 TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
         621         1965         1973         1950         1944         1093 
TCGA-78-7150 TCGA-78-7154 TCGA-78-7155 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
        1963         1948         1957          678          215         1940 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7539 TCGA-78-7633 TCGA-78-8640 
        1950         1934         1937          327          994         1949 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-86-6851 TCGA-86-7711 
        1971         1981         1954         1964         1959          630 
TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 
        1963          745           10         1963           13          479 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8281 TCGA-86-8358 TCGA-86-8585 
         489          476          482         1955           19           35 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 TCGA-86-A4D0 TCGA-86-A4P7 
          45           34           18          455           30           14 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 TCGA-91-6836 
          39          323         1940           60           79          417 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
         372          842          224          492          197          174 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-95-7039 TCGA-95-7043 TCGA-95-7947 
          36           44          218           34            2          477 
TCGA-95-A4VK TCGA-97-7546 TCGA-97-7553 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 
         121          964         1332          181           22          107 
TCGA-97-8172 TCGA-97-8175 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 
         182           87           15          115          197          271 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
         459           44          170          287          282          238 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A444 TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4T7 
         578          435            6         1967         1954         1954 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
        1957         1980         1951          142         1955         1971 

  DEL PEAK 14(6Q12) MUTATED DEL PEAK 14(6Q12) WILD-TYPE 
                          2                           1 
  DEL PEAK 14(6Q12) MUTATED DEL PEAK 14(6Q12) WILD-TYPE 
                       2370                        2696 
  DEL PEAK 14(6Q12) MUTATED DEL PEAK 14(6Q12) WILD-TYPE 
                      628.0                       426.5 
[1] "2.0 - 2370.0 (628.0)" "1.0 - 2696.0 (426.5)"
[1] "hr=" "1"  
D46V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 14(6Q12) MUTATED         0       29       52        18        18
  DEL PEAK 14(6Q12) WILD-TYPE       4       84       79        25        51
                             vv
clus                          STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 14(6Q12) MUTATED           34          4       10
  DEL PEAK 14(6Q12) WILD-TYPE         33          7       13
D46V3, multiclass
            clus
vv           DEL PEAK 14(6Q12) MUTATED DEL PEAK 14(6Q12) WILD-TYPE
  STAGE I                            0                           4
  STAGE IA                          29                          84
  STAGE IB                          52                          79
  STAGE IIA                         18                          25
  STAGE IIB                         18                          51
  STAGE IIIA                        34                          33
  STAGE IIIB                         4                           7
  STAGE IV                          10                          13
[1] 8 2
[1] TRUE
[1] "dimension of 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(6Q12) MUTATED    43 103  14   6
  DEL PEAK 14(6Q12) WILD-TYPE 100 156  26  12
D46V4, multiclass
    clus
vv   DEL PEAK 14(6Q12) MUTATED DEL PEAK 14(6Q12) WILD-TYPE
  T1                        43                         100
  T2                       103                         156
  T3                        14                          26
  T4                         6                          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 14(6Q12) MUTATED    97  30    35
  DEL PEAK 14(6Q12) WILD-TYPE 198  55    37
D46V5, multiclass
       clus
vv      DEL PEAK 14(6Q12) MUTATED DEL PEAK 14(6Q12) WILD-TYPE
  N0                           97                         198
  N1                           30                          55
  N2+N3                        35                          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"
                             vv
clus                           M0  M1 M1A M1B  MX
  DEL PEAK 14(6Q12) MUTATED   111   8   0   2  43
  DEL PEAK 14(6Q12) WILD-TYPE 206  10   1   1  76
D46V6, multiclass
     clus
vv    DEL PEAK 14(6Q12) MUTATED DEL PEAK 14(6Q12) WILD-TYPE
  M0                        111                         206
  M1                          8                          10
  M1A                         0                           1
  M1B                         2                           1
  MX                         43                          76
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V7, binary
                             cls
clus                            0   1
  DEL PEAK 14(6Q12) MUTATED    87  79
  DEL PEAK 14(6Q12) WILD-TYPE 161 135
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 14(6Q12) MUTATED     87   79
  DEL PEAK 14(6Q12) WILD-TYPE  161  135
        clus
vv       DEL PEAK 14(6Q12) MUTATED DEL PEAK 14(6Q12) WILD-TYPE
  FEMALE                        87                         161
  MALE                          79                         135
[1] 2 2
[1] FALSE
D46V8, continuous
                             vv
clus                          LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 14(6Q12) MUTATED                            3
  DEL PEAK 14(6Q12) WILD-TYPE                         10
                             vv
clus                          LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 14(6Q12) MUTATED                                  38
  DEL PEAK 14(6Q12) WILD-TYPE                                55
                             vv
clus                          LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 14(6Q12) MUTATED                                                  106
  DEL PEAK 14(6Q12) WILD-TYPE                                                188
                             vv
clus                          LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 14(6Q12) MUTATED                                            3
  DEL PEAK 14(6Q12) WILD-TYPE                                          1
                             vv
clus                          LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 14(6Q12) MUTATED                                               4
  DEL PEAK 14(6Q12) WILD-TYPE                                            15
                             vv
clus                          LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 14(6Q12) MUTATED                                1
  DEL PEAK 14(6Q12) WILD-TYPE                              1
                             vv
clus                          LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 14(6Q12) MUTATED                                    1
  DEL PEAK 14(6Q12) WILD-TYPE                                  3
                             vv
clus                          LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 14(6Q12) MUTATED                              0
  DEL PEAK 14(6Q12) WILD-TYPE                            2
                             vv
clus                          LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 14(6Q12) MUTATED                               8
  DEL PEAK 14(6Q12) WILD-TYPE                            11
                             vv
clus                          LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 14(6Q12) MUTATED                                 0
  DEL PEAK 14(6Q12) WILD-TYPE                               1
                             vv
clus                          LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 14(6Q12) MUTATED                                               0
  DEL PEAK 14(6Q12) WILD-TYPE                                             4
                             vv
clus                          MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 14(6Q12) MUTATED                              2
  DEL PEAK 14(6Q12) WILD-TYPE                            5
D46V9, multiclass
                                                    clus
vv                                                   DEL PEAK 14(6Q12) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                 3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                         38
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                       106
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                 3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                              4
  LUNG CLEAR CELL ADENOCARCINOMA                                             1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                         1
  LUNG MUCINOUS ADENOCARCINOMA                                               0
  LUNG PAPILLARY ADENOCARCINOMA                                              8
  LUNG SIGNET RING ADENOCARCINOMA                                            0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                              0
  MUCINOUS (COLLOID) CARCINOMA                                               2
                                                    clus
vv                                                   DEL PEAK 14(6Q12) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                  10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           55
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         188
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                   1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                               15
  LUNG CLEAR CELL ADENOCARCINOMA                                               1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                           3
  LUNG MUCINOUS ADENOCARCINOMA                                                 2
  LUNG PAPILLARY ADENOCARCINOMA                                               11
  LUNG SIGNET RING ADENOCARCINOMA                                              1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                4
  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"
D46V10, binary
                             cls
clus                            0   1
  DEL PEAK 14(6Q12) MUTATED    10 156
  DEL PEAK 14(6Q12) WILD-TYPE  11 285
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 14(6Q12) MUTATED     10  156
  DEL PEAK 14(6Q12) WILD-TYPE   11  285
     clus
vv    DEL PEAK 14(6Q12) MUTATED DEL PEAK 14(6Q12) WILD-TYPE
  NO                         10                          11
  YES                       156                         285
[1] 2 2
[1] FALSE
D46V11, continuous
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 14(6Q12) MUTATED   115   2   1   9
  DEL PEAK 14(6Q12) WILD-TYPE 203   9   3  10
D46V12, multiclass
    clus
vv   DEL PEAK 14(6Q12) MUTATED DEL PEAK 14(6Q12) WILD-TYPE
  R0                       115                         203
  R1                         2                           9
  R2                         1                           3
  RX                         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                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 14(6Q12) MUTATED                                  0     4
  DEL PEAK 14(6Q12) WILD-TYPE                                1     2
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(6Q12) MUTATED                          13   128
  DEL PEAK 14(6Q12) WILD-TYPE                        13   234
D46V13, multiclass
                                  clus
vv                                 DEL PEAK 14(6Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    4
  BLACK OR AFRICAN AMERICAN                               13
  WHITE                                                  128
                                  clus
vv                                 DEL PEAK 14(6Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 13
  WHITE                                                    234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V14, binary
                             cls
clus                            0   1
  DEL PEAK 14(6Q12) MUTATED     4 116
  DEL PEAK 14(6Q12) WILD-TYPE   3 216
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 14(6Q12) MUTATED      4  116
  DEL PEAK 14(6Q12) WILD-TYPE    3  216
                        clus
vv                       DEL PEAK 14(6Q12) MUTATED DEL PEAK 14(6Q12) WILD-TYPE
  HISPANIC OR LATINO                             4                           3
  NOT HISPANIC OR LATINO                       116                         216
[1] 2 2
[1] FALSE

Clustering(47) Variable = DEL PEAK 15(6Q22.31) MUTATION ANALYSIS
D47V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 15(6Q22.31) MUTATED   155  50
  DEL PEAK 15(6Q22.31) WILD-TYPE 166  32
  DEL PEAK 15(6Q22.31) MUTATED DEL PEAK 15(6Q22.31) WILD-TYPE 
                           205                            198 
  DEL PEAK 15(6Q22.31) MUTATED DEL PEAK 15(6Q22.31) WILD-TYPE 
                            50                             32 
$`DEL PEAK 15(6Q22.31) MUTATED`
TCGA-05-4382 TCGA-05-4390 TCGA-05-4396 TCGA-05-4405 TCGA-05-4415 TCGA-05-4420 
         607         1126         1947          610         1997          912 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
         669          791          761          882          670           30 
TCGA-35-3615 TCGA-35-4123 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-44-2656 
          14          182          354         1357          448         1429 
TCGA-44-2659 TCGA-44-2666 TCGA-44-2668 TCGA-44-3918 TCGA-44-4112 TCGA-44-5644 
        1367           97          246         1036          722          863 
TCGA-44-6147 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
         845          658          705         1938         1942         1864 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7670 TCGA-44-8117 TCGA-44-8120 TCGA-44-A47F 
        1978          444          882          385          260          337 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 TCGA-49-4505 TCGA-49-4507 TCGA-49-4510 
          76         1932         1081          428          268          896 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-50-5051 
         157         1700          890          522          354          455 
TCGA-50-5068 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 
        1499         1091         2370          653          567          883 
TCGA-50-5946 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
         686         1986         1971          424          280          701 
TCGA-55-1595 TCGA-55-1596 TCGA-55-6543 TCGA-55-6642 TCGA-55-6971 TCGA-55-6972 
        1479         1375            2          993           25         1475 
TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 TCGA-55-7283 TCGA-55-7576 TCGA-55-7724 
        1826         1233         2151           35           40         1958 
TCGA-55-7725 TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
          39           54           19           21            3           31 
TCGA-55-8085 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8094 TCGA-55-8097 
          33          100            6           43            4           15 
TCGA-55-8207 TCGA-55-8302 TCGA-55-8506 TCGA-55-8508 TCGA-55-8511 TCGA-55-8512 
          66           23           11           15            9            3 
TCGA-55-8615 TCGA-55-8616 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A490 TCGA-55-A494 
          15           48           33           42           48            5 
TCGA-62-8395 TCGA-62-8398 TCGA-62-8402 TCGA-62-A46U TCGA-62-A46V TCGA-62-A472 
        1216         1970         1445         2067         2199          910 
TCGA-64-1677 TCGA-64-1678 TCGA-64-1680 TCGA-64-5774 TCGA-64-5775 TCGA-64-5779 
         628         1189         1126         1959           62          864 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3773 TCGA-67-6216 TCGA-69-7760 
        1559          866          610          427          141          202 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
         690          414          230          184           70           89 
TCGA-69-8253 TCGA-69-8254 TCGA-69-A59K TCGA-73-4658 TCGA-73-4659 TCGA-73-4666 
         100           77          214         1600          711          800 
TCGA-73-4675 TCGA-73-7498 TCGA-73-7499 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 
          40          621          519         1970         1967         1956 
TCGA-78-7146 TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7156 TCGA-78-7158 
        1988         1093         1202          760         1961         1963 
TCGA-78-7159 TCGA-78-7161 TCGA-78-7162 TCGA-78-7167 TCGA-78-7535 TCGA-78-7536 
        1221          215         1940         1937         1972         1949 
TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8655 TCGA-80-5607 
        1944          881         1952          994         1981         1965 
TCGA-83-5908 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
         824           11          630          422         1968          591 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8075 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
         508          745          479          476          482           16 
TCGA-86-8281 TCGA-86-8358 TCGA-86-8359 TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 
        1955           19           26           15          405           10 
TCGA-91-6831 TCGA-91-7771 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
         310          492          218          297          127          186 
TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 TCGA-95-7948 TCGA-97-7547 TCGA-97-7554 
           2          568          377          476         1965          775 
TCGA-97-7937 TCGA-97-8174 TCGA-97-8547 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 
         181         1965          148          197          271          392 
TCGA-99-8025 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-L4-A4E5 TCGA-L9-A443 
         427          170          154          114          578          116 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
           6          285          622          353         1946         1967 
TCGA-MP-A4T2 TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TK 
        1951         1944         1970         1970         1955         1971 
TCGA-MP-A5C7 
        1490 

$`DEL PEAK 15(6Q22.31) WILD-TYPE`
TCGA-05-4249 TCGA-05-4384 TCGA-05-4389 TCGA-05-4398 TCGA-05-4403 TCGA-05-4410 
        1523          426         1369         1431          578         1958 
TCGA-05-4417 TCGA-05-4422 TCGA-05-4424 TCGA-05-4427 TCGA-05-4432 TCGA-05-4433 
         455          365          913          791          761          730 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5715 TCGA-35-4122 TCGA-35-5375 TCGA-38-4625 
         457          151           62          225          264         1952 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-7271 
        1962         1147         1492          864         1073         1971 
TCGA-38-A44F TCGA-44-2655 TCGA-44-2657 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 
         133         1324          400          741         1280         1301 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 
        1130         1163          190         1013          383          723 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6148 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
         328          302          704          592          366          218 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-8119 TCGA-44-A479 
         557         1970          535          719           99          486 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-49-4501 TCGA-49-4506 
         466          287          351          415         1421          999 
TCGA-49-6742 TCGA-49-6743 TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 
         445          369         2174         2146          785          944 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5944 TCGA-50-6597 TCGA-50-7109 
         246          282          267          764         1015          255 
TCGA-50-8460 TCGA-55-1594 TCGA-55-5899 TCGA-55-6712 TCGA-55-6969 TCGA-55-6980 
         105         1178           87           24         1239           67 
TCGA-55-6987 TCGA-55-7281 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        1170           18          121            6            4           95 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7907 TCGA-55-7910 TCGA-55-7995 
          39           34           24           16          197            5 
TCGA-55-8087 TCGA-55-8092 TCGA-55-8096 TCGA-55-8205 TCGA-55-8206 TCGA-55-8299 
          21           26           47           33           46          216 
TCGA-55-8301 TCGA-55-8505 TCGA-55-8507 TCGA-55-8510 TCGA-55-8513 TCGA-55-8514 
          44           29            8          228          146          202 
TCGA-55-8614 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48Z TCGA-55-A491 
         536           49           66          106           29         1952 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8397 TCGA-62-8399 
           1           28           47          162         1289         2696 
TCGA-62-A471 TCGA-64-1676 TCGA-64-1679 TCGA-64-1681 TCGA-64-5778 TCGA-67-3770 
        1246         1728         1686         1968         1305           31 
TCGA-67-3772 TCGA-67-3774 TCGA-67-6215 TCGA-67-6217 TCGA-69-7761 TCGA-69-7765 
         573          385          174          422          186          165 
TCGA-69-7980 TCGA-69-8255 TCGA-71-6725 TCGA-73-4662 TCGA-73-4668 TCGA-73-4670 
         382          129           61          912          467          131 
TCGA-73-4676 TCGA-73-4677 TCGA-75-7031 TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 
         164           38         1965         1973         1950         1944 
TCGA-78-7150 TCGA-78-7154 TCGA-78-7155 TCGA-78-7160 TCGA-78-7163 TCGA-78-7166 
        1963         1948         1957          678         1950         1934 
TCGA-78-7220 TCGA-78-7539 TCGA-78-8640 TCGA-78-8648 TCGA-78-8660 TCGA-78-8662 
        1965          327         1949         1971         1954         1964 
TCGA-80-5608 TCGA-86-6851 TCGA-86-7954 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
        1972         1959         1963           10         1963           13 
TCGA-86-8074 TCGA-86-8076 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
          24          489           35           45           34           18 
TCGA-86-8673 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
         455           30           14           39          323         1940 
TCGA-91-6830 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
          60           79          417          372          842          224 
TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-95-7039 
          35          197          174           36           44           34 
TCGA-95-7947 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7552 TCGA-97-7553 TCGA-97-7941 
         477          121          964         1932         1332           22 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 
         107          182           87          147           15          115 
TCGA-99-8028 TCGA-99-8032 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 
         459           44          287          282          238          435 
TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TH 
        1954         1954         1957         1980         1951          142 

  DEL PEAK 15(6Q22.31) MUTATED DEL PEAK 15(6Q22.31) WILD-TYPE 
                             2                              1 
  DEL PEAK 15(6Q22.31) MUTATED DEL PEAK 15(6Q22.31) WILD-TYPE 
                          2370                           2696 
  DEL PEAK 15(6Q22.31) MUTATED DEL PEAK 15(6Q22.31) WILD-TYPE 
                         610.0                          382.5 
[1] "2.0 - 2370.0 (610.0)" "1.0 - 2696.0 (382.5)"
[1] "hr=" "1.2"
D47V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 15(6Q22.31) MUTATED         1       49       67        24        31
  DEL PEAK 15(6Q22.31) WILD-TYPE       3       64       64        19        38
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 15(6Q22.31) MUTATED           38          7       13
  DEL PEAK 15(6Q22.31) WILD-TYPE         29          4       10
D47V3, multiclass
            clus
vv           DEL PEAK 15(6Q22.31) MUTATED DEL PEAK 15(6Q22.31) WILD-TYPE
  STAGE I                               1                              3
  STAGE IA                             49                             64
  STAGE IB                             67                             64
  STAGE IIA                            24                             19
  STAGE IIB                            31                             38
  STAGE IIIA                           38                             29
  STAGE IIIB                            7                              4
  STAGE IV                             13                             10
[1] 8 2
[1] TRUE
[1] "dimension of 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(6Q22.31) MUTATED    65 133  21  10
  DEL PEAK 15(6Q22.31) WILD-TYPE  78 126  19   8
D47V4, multiclass
    clus
vv   DEL PEAK 15(6Q22.31) MUTATED DEL PEAK 15(6Q22.31) WILD-TYPE
  T1                           65                             78
  T2                          133                            126
  T3                           21                             19
  T4                           10                              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 15(6Q22.31) MUTATED   142  44    39
  DEL PEAK 15(6Q22.31) WILD-TYPE 153  41    33
D47V5, multiclass
       clus
vv      DEL PEAK 15(6Q22.31) MUTATED DEL PEAK 15(6Q22.31) WILD-TYPE
  N0                             142                            153
  N1                              44                             41
  N2+N3                           39                             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"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 15(6Q22.31) MUTATED   157  11   0   2  58
  DEL PEAK 15(6Q22.31) WILD-TYPE 160   7   1   1  61
D47V6, multiclass
     clus
vv    DEL PEAK 15(6Q22.31) MUTATED DEL PEAK 15(6Q22.31) WILD-TYPE
  M0                           157                            160
  M1                            11                              7
  M1A                            0                              1
  M1B                            2                              1
  MX                            58                             61
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V7, binary
                                cls
clus                               0   1
  DEL PEAK 15(6Q22.31) MUTATED   117 114
  DEL PEAK 15(6Q22.31) WILD-TYPE 131 100
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 15(6Q22.31) MUTATED    117  114
  DEL PEAK 15(6Q22.31) WILD-TYPE  131  100
        clus
vv       DEL PEAK 15(6Q22.31) MUTATED DEL PEAK 15(6Q22.31) WILD-TYPE
  FEMALE                          117                            131
  MALE                            114                            100
[1] 2 2
[1] FALSE
D47V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 15(6Q22.31) MUTATED                            7
  DEL PEAK 15(6Q22.31) WILD-TYPE                          6
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 15(6Q22.31) MUTATED                                  55
  DEL PEAK 15(6Q22.31) WILD-TYPE                                38
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 15(6Q22.31) MUTATED                                                  142
  DEL PEAK 15(6Q22.31) WILD-TYPE                                                152
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 15(6Q22.31) MUTATED                                            2
  DEL PEAK 15(6Q22.31) WILD-TYPE                                          2
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 15(6Q22.31) MUTATED                                               8
  DEL PEAK 15(6Q22.31) WILD-TYPE                                            11
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 15(6Q22.31) MUTATED                                1
  DEL PEAK 15(6Q22.31) WILD-TYPE                              1
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 15(6Q22.31) MUTATED                                    2
  DEL PEAK 15(6Q22.31) WILD-TYPE                                  2
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 15(6Q22.31) MUTATED                              0
  DEL PEAK 15(6Q22.31) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 15(6Q22.31) MUTATED                              10
  DEL PEAK 15(6Q22.31) WILD-TYPE                             9
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 15(6Q22.31) MUTATED                                 1
  DEL PEAK 15(6Q22.31) WILD-TYPE                               0
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 15(6Q22.31) MUTATED                                               1
  DEL PEAK 15(6Q22.31) WILD-TYPE                                             3
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 15(6Q22.31) MUTATED                              2
  DEL PEAK 15(6Q22.31) WILD-TYPE                            5
D47V9, multiclass
                                                    clus
vv                                                   DEL PEAK 15(6Q22.31) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            55
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          142
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 8
  LUNG CLEAR CELL ADENOCARCINOMA                                                1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            2
  LUNG MUCINOUS ADENOCARCINOMA                                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                                10
  LUNG SIGNET RING ADENOCARCINOMA                                               1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 1
  MUCINOUS (COLLOID) CARCINOMA                                                  2
                                                    clus
vv                                                   DEL PEAK 15(6Q22.31) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              38
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            152
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  11
  LUNG CLEAR CELL ADENOCARCINOMA                                                  1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              2
  LUNG MUCINOUS ADENOCARCINOMA                                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                                   9
  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"
D47V10, binary
                                cls
clus                               0   1
  DEL PEAK 15(6Q22.31) MUTATED    11 220
  DEL PEAK 15(6Q22.31) WILD-TYPE  10 221
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 15(6Q22.31) MUTATED     11  220
  DEL PEAK 15(6Q22.31) WILD-TYPE   10  221
     clus
vv    DEL PEAK 15(6Q22.31) MUTATED DEL PEAK 15(6Q22.31) WILD-TYPE
  NO                            11                             10
  YES                          220                            221
[1] 2 2
[1] FALSE
D47V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 15(6Q22.31) MUTATED   166   5   1  10
  DEL PEAK 15(6Q22.31) WILD-TYPE 152   6   3   9
D47V12, multiclass
    clus
vv   DEL PEAK 15(6Q22.31) MUTATED DEL PEAK 15(6Q22.31) WILD-TYPE
  R0                          166                            152
  R1                            5                              6
  R2                            1                              3
  RX                           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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 15(6Q22.31) MUTATED                                  0     4
  DEL PEAK 15(6Q22.31) WILD-TYPE                                1     2
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(6Q22.31) MUTATED                          13   183
  DEL PEAK 15(6Q22.31) WILD-TYPE                        13   179
D47V13, multiclass
                                  clus
vv                                 DEL PEAK 15(6Q22.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  13
  WHITE                                                     183
                                  clus
vv                                 DEL PEAK 15(6Q22.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         2
  BLACK OR AFRICAN AMERICAN                                    13
  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"
D47V14, binary
                                cls
clus                               0   1
  DEL PEAK 15(6Q22.31) MUTATED     6 162
  DEL PEAK 15(6Q22.31) WILD-TYPE   1 170
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 15(6Q22.31) MUTATED      6  162
  DEL PEAK 15(6Q22.31) WILD-TYPE    1  170
                        clus
vv                       DEL PEAK 15(6Q22.31) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          162
                        clus
vv                       DEL PEAK 15(6Q22.31) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                            170
[1] 2 2
[1] FALSE

Clustering(48) Variable = DEL PEAK 16(6Q26) MUTATION ANALYSIS
D48V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 16(6Q26) MUTATED   159  50
  DEL PEAK 16(6Q26) WILD-TYPE 162  32
  DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE 
                        209                         194 
  DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE 
                         50                          32 
$`DEL PEAK 16(6Q26) MUTATED`
TCGA-05-4382 TCGA-05-4389 TCGA-05-4390 TCGA-05-4405 TCGA-05-4415 TCGA-05-4420 
         607         1369         1126          610         1997          912 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
         669          791          761          882          670           30 
TCGA-35-3615 TCGA-35-4123 TCGA-38-4625 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
          14          182         1952          354         1357          448 
TCGA-44-2656 TCGA-44-2659 TCGA-44-2662 TCGA-44-2666 TCGA-44-2668 TCGA-44-3918 
        1429         1367         1280           97          246         1036 
TCGA-44-5644 TCGA-44-6147 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 
         863          845          658          705         1942         1864 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7670 TCGA-44-8117 TCGA-44-8120 TCGA-44-A47F 
        1978          444          882          385          260          337 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 TCGA-49-4505 TCGA-49-4507 TCGA-49-4510 
          76         1932         1081          428          268          896 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-50-5051 
         157         1700          890          522          354          455 
TCGA-50-5068 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 
        1499         1091         2370          653          567          883 
TCGA-50-5946 TCGA-50-7109 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
         686          255         1986         1971          424          280 
TCGA-55-1592 TCGA-55-1595 TCGA-55-1596 TCGA-55-6543 TCGA-55-6642 TCGA-55-6971 
         701         1479         1375            2          993           25 
TCGA-55-6972 TCGA-55-6983 TCGA-55-6985 TCGA-55-7283 TCGA-55-7576 TCGA-55-7724 
        1475         1826         1233           35           40         1958 
TCGA-55-7725 TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
          39           54           19           21            3           31 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
           5           33          100            6           43           26 
TCGA-55-8094 TCGA-55-8097 TCGA-55-8207 TCGA-55-8302 TCGA-55-8506 TCGA-55-8508 
           4           15           66           23           11           15 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8615 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A494 
           9            3           15           33           42            5 
TCGA-62-8395 TCGA-62-8398 TCGA-62-8402 TCGA-62-A46U TCGA-62-A46V TCGA-62-A472 
        1216         1970         1445         2067         2199          910 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-1680 TCGA-64-5774 TCGA-64-5775 
        1728          628         1189         1126         1959           62 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3773 TCGA-67-6216 
         864         1559          866          610          427          141 
TCGA-69-7760 TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
         202          690          414          230          184           70 
TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 
          89          100           77          214           61         1600 
TCGA-73-4659 TCGA-73-4666 TCGA-73-4670 TCGA-73-4675 TCGA-73-7498 TCGA-73-7499 
         711          800          131           40          621          519 
TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7146 TCGA-78-7149 TCGA-78-7152 
        1970         1967         1956         1988         1093         1202 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7162 
         760         1948         1961         1963         1221         1940 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 
        1937         1965         1972         1949         1944          881 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8655 TCGA-80-5607 TCGA-83-5908 TCGA-86-7701 
        1952          994         1981         1965          824           11 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7955 TCGA-86-8054 
         630          422         1968          591          508          745 
TCGA-86-8075 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8281 TCGA-86-8359 
         479          476          482           16         1955           26 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 TCGA-91-6831 TCGA-91-6849 
          18           15          405           10          310           35 
TCGA-91-7771 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-95-7043 
         492           36          218          297          127            2 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7948 TCGA-97-7547 TCGA-97-7554 TCGA-97-7937 
         568          377          476         1965          775          181 
TCGA-97-8174 TCGA-97-8547 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-8025 TCGA-99-8028 
        1965          148          197          271          427          459 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-L4-A4E5 TCGA-L9-A443 TCGA-L9-A444 
         170          154          114          578          116            6 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4TC 
         622          353         1946         1967         1951         1944 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
        1970         1970         1955         1971         1490 

$`DEL PEAK 16(6Q26) WILD-TYPE`
TCGA-05-4249 TCGA-05-4384 TCGA-05-4396 TCGA-05-4398 TCGA-05-4403 TCGA-05-4410 
        1523          426         1947         1431          578         1958 
TCGA-05-4417 TCGA-05-4422 TCGA-05-4424 TCGA-05-4427 TCGA-05-4432 TCGA-05-4433 
         455          365          913          791          761          730 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5715 TCGA-35-4122 TCGA-35-5375 TCGA-38-4626 
         457          151           62          225          264         1962 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-7271 TCGA-38-A44F 
        1147         1492          864         1073         1971          133 
TCGA-44-2655 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 
        1324          400          741         1301         1130         1163 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
         190          722         1013          383          723          328 
TCGA-44-6146 TCGA-44-6148 TCGA-44-6776 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
         302          704         1938          592          366          218 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-8119 TCGA-44-A479 
         557         1970          535          719           99          486 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-49-4501 TCGA-49-4506 
         466          287          351          415         1421          999 
TCGA-49-6742 TCGA-49-6743 TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 
         445          369         2174         2146          785          944 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5944 TCGA-50-6597 TCGA-50-8460 
         246          282          267          764         1015          105 
TCGA-55-1594 TCGA-55-5899 TCGA-55-6712 TCGA-55-6969 TCGA-55-6980 TCGA-55-6986 
        1178           87           24         1239           67         2151 
TCGA-55-6987 TCGA-55-7281 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        1170           18          121            6            4           95 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7907 TCGA-55-7910 TCGA-55-8087 
          39           34           24           16          197           21 
TCGA-55-8096 TCGA-55-8205 TCGA-55-8206 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 
          47           33           46          216           44           29 
TCGA-55-8507 TCGA-55-8510 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 
           8          228          146          202          536           48 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
          49           66          106           29           48         1952 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8397 TCGA-62-8399 
           1           28           47          162         1289         2696 
TCGA-62-A471 TCGA-64-1679 TCGA-64-1681 TCGA-64-5778 TCGA-67-3770 TCGA-67-3772 
        1246         1686         1968         1305           31          573 
TCGA-67-3774 TCGA-67-6215 TCGA-67-6217 TCGA-69-7761 TCGA-69-7765 TCGA-69-7980 
         385          174          422          186          165          382 
TCGA-69-8255 TCGA-73-4662 TCGA-73-4668 TCGA-73-4676 TCGA-73-4677 TCGA-75-7031 
         129          912          467          164           38         1965 
TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 TCGA-78-7150 TCGA-78-7155 TCGA-78-7160 
        1973         1950         1944         1963         1957          678 
TCGA-78-7161 TCGA-78-7163 TCGA-78-7166 TCGA-78-7539 TCGA-78-8640 TCGA-78-8648 
         215         1950         1934          327         1949         1971 
TCGA-78-8660 TCGA-78-8662 TCGA-80-5608 TCGA-86-6851 TCGA-86-7954 TCGA-86-8055 
        1954         1964         1972         1959         1963           10 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8076 TCGA-86-8358 TCGA-86-8585 
        1963           13           24          489           19           35 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8673 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 
          45           34          455           30           14           39 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
         323         1940           60           79          417          372 
TCGA-91-6847 TCGA-91-6848 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC TCGA-93-8067 
         842          224          197          174           44          186 
TCGA-95-7039 TCGA-95-7947 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7552 TCGA-97-7553 
          34          477          121          964         1932         1332 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 
          22          107          182           87          147           15 
TCGA-97-8552 TCGA-99-7458 TCGA-99-8032 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
         115          392           44          287          282          238 
TCGA-L4-A4E6 TCGA-MN-A4N1 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
         435          285         1954         1954         1957         1980 
TCGA-MP-A4TA TCGA-MP-A4TH 
        1951          142 

  DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE 
                          2                           1 
  DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE 
                       2370                        2696 
  DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE 
                      610.0                       382.5 
[1] "2.0 - 2370.0 (610.0)" "1.0 - 2696.0 (382.5)"
[1] "hr=" "1.2"
D48V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 16(6Q26) MUTATED         2       53       64        22        32
  DEL PEAK 16(6Q26) WILD-TYPE       2       60       67        21        37
                             vv
clus                          STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 16(6Q26) MUTATED           38          6       15
  DEL PEAK 16(6Q26) WILD-TYPE         29          5        8
D48V3, multiclass
            clus
vv           DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE
  STAGE I                            2                           2
  STAGE IA                          53                          60
  STAGE IB                          64                          67
  STAGE IIA                         22                          21
  STAGE IIB                         32                          37
  STAGE IIIA                        38                          29
  STAGE IIIB                         6                           5
  STAGE IV                          15                           8
[1] 8 2
[1] TRUE
[1] "dimension of 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(6Q26) MUTATED    69 131  22   9
  DEL PEAK 16(6Q26) WILD-TYPE  74 128  18   9
D48V4, multiclass
    clus
vv   DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE
  T1                        69                          74
  T2                       131                         128
  T3                        22                          18
  T4                         9                           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 16(6Q26) MUTATED   143  44    40
  DEL PEAK 16(6Q26) WILD-TYPE 152  41    32
D48V5, multiclass
       clus
vv      DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE
  N0                          143                         152
  N1                           44                          41
  N2+N3                        40                          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"
                             vv
clus                           M0  M1 M1A M1B  MX
  DEL PEAK 16(6Q26) MUTATED   156  13   0   2  59
  DEL PEAK 16(6Q26) WILD-TYPE 161   5   1   1  60
D48V6, multiclass
     clus
vv    DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE
  M0                        156                         161
  M1                         13                           5
  M1A                         0                           1
  M1B                         2                           1
  MX                         59                          60
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V7, binary
                             cls
clus                            0   1
  DEL PEAK 16(6Q26) MUTATED   120 113
  DEL PEAK 16(6Q26) WILD-TYPE 128 101
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(6Q26) MUTATED    120  113
  DEL PEAK 16(6Q26) WILD-TYPE  128  101
        clus
vv       DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE
  FEMALE                       120                         128
  MALE                         113                         101
[1] 2 2
[1] FALSE
D48V8, continuous
                             vv
clus                          LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 16(6Q26) MUTATED                            7
  DEL PEAK 16(6Q26) WILD-TYPE                          6
                             vv
clus                          LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 16(6Q26) MUTATED                                  54
  DEL PEAK 16(6Q26) WILD-TYPE                                39
                             vv
clus                          LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 16(6Q26) MUTATED                                                  145
  DEL PEAK 16(6Q26) WILD-TYPE                                                149
                             vv
clus                          LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 16(6Q26) MUTATED                                            2
  DEL PEAK 16(6Q26) WILD-TYPE                                          2
                             vv
clus                          LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 16(6Q26) MUTATED                                               6
  DEL PEAK 16(6Q26) WILD-TYPE                                            13
                             vv
clus                          LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 16(6Q26) MUTATED                                1
  DEL PEAK 16(6Q26) WILD-TYPE                              1
                             vv
clus                          LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 16(6Q26) MUTATED                                    2
  DEL PEAK 16(6Q26) WILD-TYPE                                  2
                             vv
clus                          LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 16(6Q26) MUTATED                              0
  DEL PEAK 16(6Q26) WILD-TYPE                            2
                             vv
clus                          LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 16(6Q26) MUTATED                              12
  DEL PEAK 16(6Q26) WILD-TYPE                             7
                             vv
clus                          LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 16(6Q26) MUTATED                                 1
  DEL PEAK 16(6Q26) WILD-TYPE                               0
                             vv
clus                          LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 16(6Q26) MUTATED                                               1
  DEL PEAK 16(6Q26) WILD-TYPE                                             3
                             vv
clus                          MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 16(6Q26) MUTATED                              2
  DEL PEAK 16(6Q26) WILD-TYPE                            5
D48V9, multiclass
                                                    clus
vv                                                   DEL PEAK 16(6Q26) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                 7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                         54
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                       145
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                 2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                              6
  LUNG CLEAR CELL ADENOCARCINOMA                                             1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                         2
  LUNG MUCINOUS ADENOCARCINOMA                                               0
  LUNG PAPILLARY ADENOCARCINOMA                                             12
  LUNG SIGNET RING ADENOCARCINOMA                                            1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                              1
  MUCINOUS (COLLOID) CARCINOMA                                               2
                                                    clus
vv                                                   DEL PEAK 16(6Q26) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                   6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           39
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         149
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                   2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                               13
  LUNG CLEAR CELL ADENOCARCINOMA                                               1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                           2
  LUNG MUCINOUS ADENOCARCINOMA                                                 2
  LUNG PAPILLARY ADENOCARCINOMA                                                7
  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"
D48V10, binary
                             cls
clus                            0   1
  DEL PEAK 16(6Q26) MUTATED    12 221
  DEL PEAK 16(6Q26) WILD-TYPE   9 220
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(6Q26) MUTATED     12  221
  DEL PEAK 16(6Q26) WILD-TYPE    9  220
     clus
vv    DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE
  NO                         12                           9
  YES                       221                         220
[1] 2 2
[1] FALSE
D48V11, continuous
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 16(6Q26) MUTATED   168   4   2   9
  DEL PEAK 16(6Q26) WILD-TYPE 150   7   2  10
D48V12, multiclass
    clus
vv   DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE
  R0                       168                         150
  R1                         4                           7
  R2                         2                           2
  RX                         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                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 16(6Q26) MUTATED                                  0     4
  DEL PEAK 16(6Q26) WILD-TYPE                                1     2
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(6Q26) MUTATED                          14   184
  DEL PEAK 16(6Q26) WILD-TYPE                        12   178
D48V13, multiclass
                                  clus
vv                                 DEL PEAK 16(6Q26) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    4
  BLACK OR AFRICAN AMERICAN                               14
  WHITE                                                  184
                                  clus
vv                                 DEL PEAK 16(6Q26) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 12
  WHITE                                                    178
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V14, binary
                             cls
clus                            0   1
  DEL PEAK 16(6Q26) MUTATED     6 166
  DEL PEAK 16(6Q26) WILD-TYPE   1 166
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(6Q26) MUTATED      6  166
  DEL PEAK 16(6Q26) WILD-TYPE    1  166
                        clus
vv                       DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE
  HISPANIC OR LATINO                             6                           1
  NOT HISPANIC OR LATINO                       166                         166
[1] 2 2
[1] FALSE

Clustering(49) Variable = DEL PEAK 17(8P23.2) MUTATION ANALYSIS
D49V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 17(8P23.2) MUTATED   153  42
  DEL PEAK 17(8P23.2) WILD-TYPE 168  40
  DEL PEAK 17(8P23.2) MUTATED DEL PEAK 17(8P23.2) WILD-TYPE 
                          195                           208 
  DEL PEAK 17(8P23.2) MUTATED DEL PEAK 17(8P23.2) WILD-TYPE 
                           42                            40 
$`DEL PEAK 17(8P23.2) MUTATED`
TCGA-05-4249 TCGA-05-4389 TCGA-05-4390 TCGA-05-4398 TCGA-05-4410 TCGA-05-4420 
        1523         1369         1126         1431         1958          912 
TCGA-05-4425 TCGA-05-4427 TCGA-05-4433 TCGA-05-5425 TCGA-05-5428 TCGA-35-4122 
         669          791          730          882          670          225 
TCGA-35-4123 TCGA-38-4625 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 
         182         1952         1147         1492          864         1073 
TCGA-38-4631 TCGA-38-6178 TCGA-44-2656 TCGA-44-2657 TCGA-44-2662 TCGA-44-2668 
         354          448         1429          400         1280          246 
TCGA-44-3918 TCGA-44-3919 TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 TCGA-44-6145 
        1036          190         1013          863          723          328 
TCGA-44-6147 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6779 TCGA-44-7660 
         845          658          705         1942         1978          592 
TCGA-44-7662 TCGA-44-7670 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
         218          882          719          385           99          260 
TCGA-44-A479 TCGA-49-4501 TCGA-49-4505 TCGA-49-4510 TCGA-49-4512 TCGA-49-6743 
         486         1421          428          896          157          369 
TCGA-49-6761 TCGA-50-5045 TCGA-50-5049 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
         354         2174         2146          944         1499          246 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5941 TCGA-50-6597 
         282          267         1091         2370          567         1015 
TCGA-50-7109 TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 
         255         1986         1971          280          701         1178 
TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6969 TCGA-55-6980 TCGA-55-6985 
        1479         1375           87         1239           67         1233 
TCGA-55-7283 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7726 
          35            6            4           95           40           39 
TCGA-55-7727 TCGA-55-7903 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
          34           19            3           31            5           33 
TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8207 TCGA-55-8301 
          26           47           15           33           66           44 
TCGA-55-8302 TCGA-55-8506 TCGA-55-8510 TCGA-55-8614 TCGA-55-8616 TCGA-55-A48Y 
          23           11          228          536           48           42 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A493 TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 
          48         1952           28          162         1216         1289 
TCGA-62-8402 TCGA-62-A46U TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 
        1445         2067          910         1728          628         1189 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5775 TCGA-64-5778 TCGA-64-5815 TCGA-67-3770 
        1686         1968           62         1305          866           31 
TCGA-67-3771 TCGA-67-3772 TCGA-67-6217 TCGA-69-7760 TCGA-69-7974 TCGA-69-7978 
         610          573          422          202          184           70 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-73-4662 
          89          382          129          214           61          912 
TCGA-73-4668 TCGA-73-4670 TCGA-73-7498 TCGA-73-7499 TCGA-75-6214 TCGA-75-7025 
         467          131          621          519         1970         1967 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7155 TCGA-78-7159 TCGA-78-7167 
        1963         1202          760         1957         1221         1937 
TCGA-78-7536 TCGA-78-7542 TCGA-78-8640 TCGA-78-8660 TCGA-78-8662 TCGA-86-6851 
        1949         1952         1949         1954         1964         1959 
TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 TCGA-86-8074 
         422          591         1963          745           10           24 
TCGA-86-8075 TCGA-86-8279 TCGA-86-8280 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
         479          482           16           35           45           34 
TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-91-6836 TCGA-91-6847 TCGA-91-6848 
          10           30           14          417          842          224 
TCGA-91-8499 TCGA-91-A4BD TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 
          36          218          186           34            2          568 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7554 
         377          477          476          121          964          775 
TCGA-97-7937 TCGA-97-8547 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8032 TCGA-J2-8192 
         181          148          271          392           44          154 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L9-A444 TCGA-MN-A4N4 
         114          287          282          578            6          622 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T9 
         353         1946         1967         1954         1954         1980 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TF 
        1951         1944         1970 

$`DEL PEAK 17(8P23.2) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 
         607          426         1947          578          610         1997 
TCGA-05-4417 TCGA-05-4422 TCGA-05-4424 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 
         455          365          913          791          761          761 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-5375 
         457          151           30           62           14          264 
TCGA-38-4626 TCGA-38-4632 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2659 
        1962         1357         1971          133         1324         1367 
TCGA-44-2661 TCGA-44-2665 TCGA-44-2666 TCGA-44-3396 TCGA-44-3398 TCGA-44-4112 
         741         1301           97         1130         1163          722 
TCGA-44-5645 TCGA-44-6146 TCGA-44-6148 TCGA-44-6776 TCGA-44-6778 TCGA-44-7659 
         383          302          704         1938         1864          444 
TCGA-44-7661 TCGA-44-7667 TCGA-44-7669 TCGA-44-7671 TCGA-44-A47A TCGA-44-A47B 
         366          557         1970          535          466          287 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 
         337          351          415           76         1932         1081 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4514 TCGA-49-6742 TCGA-49-6744 TCGA-49-6745 
         999          268         1700          445          890          522 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5935 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
         455          785          653          883          764          686 
TCGA-50-8460 TCGA-53-7813 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6971 
         105          424            2          993           24           25 
TCGA-55-6972 TCGA-55-6983 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7284 
        1475         1826         2151         1170           18          121 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7728 TCGA-55-7815 TCGA-55-7907 TCGA-55-7910 
        1958           39           24           54           16          197 
TCGA-55-7911 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8094 
          21           21          100            6           43            4 
TCGA-55-8206 TCGA-55-8299 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8511 
          46          216           29            8           15            9 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8615 TCGA-55-8619 TCGA-55-8620 
           3          146          202           15           49           66 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Z TCGA-55-A492 TCGA-55-A494 TCGA-55-A4DF 
         106           33           29            1            5           47 
TCGA-62-8398 TCGA-62-8399 TCGA-62-A46V TCGA-62-A471 TCGA-64-1680 TCGA-64-5774 
        1970         2696         2199         1246         1126         1959 
TCGA-64-5779 TCGA-64-5781 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 
         864         1559          427          385          174          141 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-8253 
         186          690          414          165          230          100 
TCGA-69-8254 TCGA-73-4658 TCGA-73-4659 TCGA-73-4666 TCGA-73-4675 TCGA-73-4676 
          77         1600          711          800           40          164 
TCGA-73-4677 TCGA-75-7027 TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
          38         1956         1965         1973         1988         1950 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 
        1944         1093         1948         1961         1963          678 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7220 TCGA-78-7535 
         215         1940         1950         1934         1965         1972 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 
        1944          327          881          994         1971         1981 
TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 
        1965         1972          824           11          630         1968 
TCGA-86-7955 TCGA-86-8056 TCGA-86-8073 TCGA-86-8076 TCGA-86-8278 TCGA-86-8281 
         508         1963           13          489          476         1955 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
          19           26           18           15          455          405 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
          39          323         1940           60          310           79 
TCGA-91-6840 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC 
         372           35          492          197          174           44 
TCGA-93-7347 TCGA-93-7348 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7941 
         297          127         1965         1932         1332           22 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 
         107          182         1965           87          147           15 
TCGA-97-8552 TCGA-97-A4M2 TCGA-99-8025 TCGA-99-8028 TCGA-99-8033 TCGA-J2-A4AG 
         115          197          427          459          170          238 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-MN-A4N1 TCGA-MP-A4T2 TCGA-MP-A4T8 TCGA-MP-A4TE 
         435          116          285         1951         1957         1970 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
         142         1955         1971         1490 

  DEL PEAK 17(8P23.2) MUTATED DEL PEAK 17(8P23.2) WILD-TYPE 
                            2                             1 
  DEL PEAK 17(8P23.2) MUTATED DEL PEAK 17(8P23.2) WILD-TYPE 
                         2370                          2696 
  DEL PEAK 17(8P23.2) MUTATED DEL PEAK 17(8P23.2) WILD-TYPE 
                        519.0                         444.5 
[1] "2.0 - 2370.0 (519.0)" "1.0 - 2696.0 (444.5)"
[1] "hr=" "1.3"
D49V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 17(8P23.2) MUTATED         3       54       65        22        38
  DEL PEAK 17(8P23.2) WILD-TYPE       1       59       66        21        31
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 17(8P23.2) MUTATED           32          4        9
  DEL PEAK 17(8P23.2) WILD-TYPE         35          7       14
D49V3, multiclass
            clus
vv           DEL PEAK 17(8P23.2) MUTATED DEL PEAK 17(8P23.2) WILD-TYPE
  STAGE I                              3                             1
  STAGE IA                            54                            59
  STAGE IB                            65                            66
  STAGE IIA                           22                            21
  STAGE IIB                           38                            31
  STAGE IIIA                          32                            35
  STAGE IIIB                           4                             7
  STAGE IV                             9                            14
[1] 8 2
[1] TRUE
[1] "dimension of 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(8P23.2) MUTATED    71 131  18   6
  DEL PEAK 17(8P23.2) WILD-TYPE  72 128  22  12
D49V4, multiclass
    clus
vv   DEL PEAK 17(8P23.2) MUTATED DEL PEAK 17(8P23.2) WILD-TYPE
  T1                          71                            72
  T2                         131                           128
  T3                          18                            22
  T4                           6                            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 17(8P23.2) MUTATED   147  40    35
  DEL PEAK 17(8P23.2) WILD-TYPE 148  45    37
D49V5, multiclass
       clus
vv      DEL PEAK 17(8P23.2) MUTATED DEL PEAK 17(8P23.2) WILD-TYPE
  N0                            147                           148
  N1                             40                            45
  N2+N3                          35                            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"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK 17(8P23.2) MUTATED   159   9   0   0  57
  DEL PEAK 17(8P23.2) WILD-TYPE 158   9   1   3  62
D49V6, multiclass
     clus
vv    DEL PEAK 17(8P23.2) MUTATED DEL PEAK 17(8P23.2) WILD-TYPE
  M0                          159                           158
  M1                            9                             9
  M1A                           0                             1
  M1B                           0                             3
  MX                           57                            62
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V7, binary
                               cls
clus                              0   1
  DEL PEAK 17(8P23.2) MUTATED   132  95
  DEL PEAK 17(8P23.2) WILD-TYPE 116 119
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(8P23.2) MUTATED    132   95
  DEL PEAK 17(8P23.2) WILD-TYPE  116  119
        clus
vv       DEL PEAK 17(8P23.2) MUTATED DEL PEAK 17(8P23.2) WILD-TYPE
  FEMALE                         132                           116
  MALE                            95                           119
[1] 2 2
[1] FALSE
D49V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 17(8P23.2) MUTATED                            6
  DEL PEAK 17(8P23.2) WILD-TYPE                          7
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 17(8P23.2) MUTATED                                  40
  DEL PEAK 17(8P23.2) WILD-TYPE                                53
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 17(8P23.2) MUTATED                                                  155
  DEL PEAK 17(8P23.2) WILD-TYPE                                                139
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 17(8P23.2) MUTATED                                            1
  DEL PEAK 17(8P23.2) WILD-TYPE                                          3
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 17(8P23.2) MUTATED                                               8
  DEL PEAK 17(8P23.2) WILD-TYPE                                            11
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 17(8P23.2) MUTATED                                2
  DEL PEAK 17(8P23.2) WILD-TYPE                              0
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 17(8P23.2) MUTATED                                    4
  DEL PEAK 17(8P23.2) WILD-TYPE                                  0
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 17(8P23.2) MUTATED                              0
  DEL PEAK 17(8P23.2) WILD-TYPE                            2
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 17(8P23.2) MUTATED                               7
  DEL PEAK 17(8P23.2) WILD-TYPE                            12
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 17(8P23.2) MUTATED                                 1
  DEL PEAK 17(8P23.2) WILD-TYPE                               0
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 17(8P23.2) MUTATED                                               3
  DEL PEAK 17(8P23.2) WILD-TYPE                                             1
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 17(8P23.2) MUTATED                              0
  DEL PEAK 17(8P23.2) WILD-TYPE                            7
D49V9, multiclass
                                                    clus
vv                                                   DEL PEAK 17(8P23.2) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           40
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         155
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                   1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                8
  LUNG CLEAR CELL ADENOCARCINOMA                                               2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                           4
  LUNG MUCINOUS ADENOCARCINOMA                                                 0
  LUNG PAPILLARY ADENOCARCINOMA                                                7
  LUNG SIGNET RING ADENOCARCINOMA                                              1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                3
  MUCINOUS (COLLOID) CARCINOMA                                                 0
                                                    clus
vv                                                   DEL PEAK 17(8P23.2) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             53
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           139
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 11
  LUNG CLEAR CELL ADENOCARCINOMA                                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             0
  LUNG MUCINOUS ADENOCARCINOMA                                                   2
  LUNG PAPILLARY ADENOCARCINOMA                                                 12
  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"
D49V10, binary
                               cls
clus                              0   1
  DEL PEAK 17(8P23.2) MUTATED    11 216
  DEL PEAK 17(8P23.2) WILD-TYPE  10 225
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(8P23.2) MUTATED     11  216
  DEL PEAK 17(8P23.2) WILD-TYPE   10  225
     clus
vv    DEL PEAK 17(8P23.2) MUTATED DEL PEAK 17(8P23.2) WILD-TYPE
  NO                           11                            10
  YES                         216                           225
[1] 2 2
[1] FALSE
D49V11, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 17(8P23.2) MUTATED   150   5   2  12
  DEL PEAK 17(8P23.2) WILD-TYPE 168   6   2   7
D49V12, multiclass
    clus
vv   DEL PEAK 17(8P23.2) MUTATED DEL PEAK 17(8P23.2) WILD-TYPE
  R0                         150                           168
  R1                           5                             6
  R2                           2                             2
  RX                          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                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 17(8P23.2) MUTATED                                  1     5
  DEL PEAK 17(8P23.2) WILD-TYPE                                0     1
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(8P23.2) MUTATED                          11   179
  DEL PEAK 17(8P23.2) WILD-TYPE                        15   183
D49V13, multiclass
                                  clus
vv                                 DEL PEAK 17(8P23.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      5
  BLACK OR AFRICAN AMERICAN                                 11
  WHITE                                                    179
                                  clus
vv                                 DEL PEAK 17(8P23.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                   15
  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"
D49V14, binary
                               cls
clus                              0   1
  DEL PEAK 17(8P23.2) MUTATED     5 169
  DEL PEAK 17(8P23.2) WILD-TYPE   2 163
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(8P23.2) MUTATED      5  169
  DEL PEAK 17(8P23.2) WILD-TYPE    2  163
                        clus
vv                       DEL PEAK 17(8P23.2) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         169
                        clus
vv                       DEL PEAK 17(8P23.2) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           163
[1] 2 2
[1] FALSE

Clustering(50) Variable = DEL PEAK 18(8P12) MUTATION ANALYSIS
D50V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 18(8P12) MUTATED   140  33
  DEL PEAK 18(8P12) WILD-TYPE 181  49
  DEL PEAK 18(8P12) MUTATED DEL PEAK 18(8P12) WILD-TYPE 
                        173                         230 
  DEL PEAK 18(8P12) MUTATED DEL PEAK 18(8P12) WILD-TYPE 
                         33                          49 
$`DEL PEAK 18(8P12) MUTATED`
TCGA-05-4249 TCGA-05-4390 TCGA-05-4410 TCGA-05-4420 TCGA-05-4425 TCGA-05-4427 
        1523         1126         1958          912          669          791 
TCGA-05-4433 TCGA-05-5425 TCGA-05-5428 TCGA-35-4123 TCGA-38-4625 TCGA-38-4631 
         730          882          670          182         1952          354 
TCGA-38-4632 TCGA-38-6178 TCGA-44-2656 TCGA-44-2657 TCGA-44-2662 TCGA-44-2668 
        1357          448         1429          400         1280          246 
TCGA-44-3918 TCGA-44-3919 TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 TCGA-44-6145 
        1036          190         1013          863          723          328 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-7670 TCGA-44-7672 TCGA-44-8117 
         658          705         1942          882          719          385 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A4SU TCGA-49-4501 TCGA-49-4505 
          99          260          486           76         1421          428 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 
         268          896          157         1700          369          890 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5049 TCGA-50-5066 TCGA-50-5068 TCGA-50-5932 
         522          354         2146          944         1499         1091 
TCGA-50-5933 TCGA-50-5941 TCGA-50-6597 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        2370          567         1015         1971          424          280 
TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6969 TCGA-55-6972 TCGA-55-6980 
        1479         1375           87         1239         1475           67 
TCGA-55-6985 TCGA-55-7283 TCGA-55-7570 TCGA-55-7573 TCGA-55-7726 TCGA-55-7903 
        1233           35            6            4           39           19 
TCGA-55-7914 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8207 
           3           26           47           15           33           66 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8510 TCGA-55-8511 TCGA-55-8614 
          44           23           11          228            9          536 
TCGA-55-8615 TCGA-55-8616 TCGA-55-A490 TCGA-55-A491 TCGA-55-A493 TCGA-55-A4DG 
          15           48           48         1952           28          162 
TCGA-62-8395 TCGA-62-8402 TCGA-62-A46U TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
        1216         1445         2067          910         1728          628 
TCGA-64-1678 TCGA-64-1679 TCGA-64-5778 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 
        1189         1686         1305          866           31          610 
TCGA-67-3772 TCGA-67-6217 TCGA-69-7760 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
         573          422          202           70           89          382 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-73-4662 TCGA-73-4668 TCGA-73-4670 
         129          214           61          912          467          131 
TCGA-73-7498 TCGA-73-7499 TCGA-75-6214 TCGA-75-7025 TCGA-78-7145 TCGA-78-7146 
         621          519         1970         1967         1973         1988 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7155 TCGA-78-7159 TCGA-78-7167 
        1963         1202          760         1957         1221         1937 
TCGA-78-7536 TCGA-78-7542 TCGA-78-8640 TCGA-78-8660 TCGA-78-8662 TCGA-86-6851 
        1949         1952         1949         1954         1964         1959 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-8054 TCGA-86-8055 TCGA-86-8074 
         630          422          591          745           10           24 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
         482           16           26           35           45           34 
TCGA-86-A456 TCGA-86-A4P7 TCGA-91-6831 TCGA-91-6836 TCGA-91-6847 TCGA-91-8499 
          10           14          310          417          842           36 
TCGA-91-A4BD TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 
         218          186           34            2          568          377 
TCGA-95-7947 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7554 TCGA-97-7937 TCGA-97-8171 
         477          121          964          775          181          107 
TCGA-97-8547 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8033 TCGA-J2-8192 
         148          271          392          427          170          154 
TCGA-J2-8194 TCGA-L4-A4E5 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
         114          578          622          353         1946         1967 
TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TC TCGA-MP-A4TF 
        1954         1954         1980         1944         1970 

$`DEL PEAK 18(8P12) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4396 TCGA-05-4398 TCGA-05-4403 
         607          426         1369         1947         1431          578 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4422 TCGA-05-4424 TCGA-05-4426 
         610         1997          455          365          913          791 
TCGA-05-4430 TCGA-05-4432 TCGA-05-5420 TCGA-05-5423 TCGA-05-5429 TCGA-05-5715 
         761          761          457          151           30           62 
TCGA-35-3615 TCGA-35-4122 TCGA-35-5375 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
          14          225          264         1962         1147         1492 
TCGA-38-4629 TCGA-38-4630 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2659 
         864         1073         1971          133         1324         1367 
TCGA-44-2661 TCGA-44-2665 TCGA-44-2666 TCGA-44-3396 TCGA-44-3398 TCGA-44-4112 
         741         1301           97         1130         1163          722 
TCGA-44-5645 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6776 TCGA-44-6778 
         383          302          845          704         1938         1864 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
        1978          444          592          366          218          557 
TCGA-44-7669 TCGA-44-7671 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        1970          535          466          287          337          351 
TCGA-44-A4SS TCGA-49-4486 TCGA-49-4494 TCGA-49-4506 TCGA-49-6742 TCGA-50-5045 
         415         1932         1081          999          445         2174 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5935 
         455          785          246          282          267          653 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-7109 TCGA-50-8460 TCGA-53-7624 
         883          764          686          255          105         1986 
TCGA-55-1592 TCGA-55-1594 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6971 
         701         1178            2          993           24           25 
TCGA-55-6983 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7284 TCGA-55-7574 
        1826         2151         1170           18          121           95 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
          40         1958           39           34           24           54 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
          16          197           21           31            5           33 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8094 TCGA-55-8206 
          21          100            6           43            4           46 
TCGA-55-8299 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 
         216           29            8           15            3          146 
TCGA-55-8514 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
         202           49           66          106           33           42 
TCGA-55-A48Z TCGA-55-A492 TCGA-55-A494 TCGA-55-A4DF TCGA-62-8397 TCGA-62-8398 
          29            1            5           47         1289         1970 
TCGA-62-8399 TCGA-62-A46V TCGA-62-A471 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 
        2696         2199         1246         1126         1968         1959 
TCGA-64-5775 TCGA-64-5779 TCGA-64-5781 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 
          62          864         1559          427          385          174 
TCGA-67-6216 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
         141          186          690          414          165          230 
TCGA-69-7974 TCGA-69-8253 TCGA-69-8254 TCGA-73-4658 TCGA-73-4659 TCGA-73-4666 
         184          100           77         1600          711          800 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-75-7027 TCGA-75-7031 TCGA-78-7147 
          40          164           38         1956         1965         1950 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 
        1944         1093         1948         1961         1963          678 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7220 TCGA-78-7535 
         215         1940         1950         1934         1965         1972 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 
        1944          327          881          994         1971         1981 
TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 TCGA-86-7701 TCGA-86-7714 TCGA-86-7954 
        1965         1972          824           11         1968         1963 
TCGA-86-7955 TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
         508         1963           13          479          489          476 
TCGA-86-8281 TCGA-86-8358 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
        1955           19           18           15          455          405 
TCGA-86-A4D0 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 
          30           39          323         1940           60           79 
TCGA-91-6840 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
         372          224           35          492          197          174 
TCGA-91-A4BC TCGA-93-7347 TCGA-93-7348 TCGA-95-7948 TCGA-97-7547 TCGA-97-7552 
          44          297          127          476         1965         1932 
TCGA-97-7553 TCGA-97-7941 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 
        1332           22          182         1965           87          147 
TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M2 TCGA-99-8028 TCGA-99-8032 TCGA-J2-A4AD 
          15          115          197          459           44          287 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
         282          238          435          116            6          285 
TCGA-MP-A4T2 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TI 
        1951         1957         1951         1970          142         1955 
TCGA-MP-A4TK TCGA-MP-A5C7 
        1971         1490 

  DEL PEAK 18(8P12) MUTATED DEL PEAK 18(8P12) WILD-TYPE 
                          2                           1 
  DEL PEAK 18(8P12) MUTATED DEL PEAK 18(8P12) WILD-TYPE 
                       2370                        2696 
  DEL PEAK 18(8P12) MUTATED DEL PEAK 18(8P12) WILD-TYPE 
                      536.0                       444.5 
[1] "2.0 - 2370.0 (536.0)" "1.0 - 2696.0 (444.5)"
[1] "hr=" "1"  
D50V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 18(8P12) MUTATED         2       43       58        21        33
  DEL PEAK 18(8P12) WILD-TYPE       2       70       73        22        36
                             vv
clus                          STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 18(8P12) MUTATED           29          4       12
  DEL PEAK 18(8P12) WILD-TYPE         38          7       11
D50V3, multiclass
            clus
vv           DEL PEAK 18(8P12) MUTATED DEL PEAK 18(8P12) WILD-TYPE
  STAGE I                            2                           2
  STAGE IA                          43                          70
  STAGE IB                          58                          73
  STAGE IIA                         21                          22
  STAGE IIB                         33                          36
  STAGE IIIA                        29                          38
  STAGE IIIB                         4                           7
  STAGE IV                          12                          11
[1] 8 2
[1] TRUE
[1] "dimension of 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(8P12) MUTATED    58 119  17   6
  DEL PEAK 18(8P12) WILD-TYPE  85 140  23  12
D50V4, multiclass
    clus
vv   DEL PEAK 18(8P12) MUTATED DEL PEAK 18(8P12) WILD-TYPE
  T1                        58                          85
  T2                       119                         140
  T3                        17                          23
  T4                         6                          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 18(8P12) MUTATED   124  41    32
  DEL PEAK 18(8P12) WILD-TYPE 171  44    40
D50V5, multiclass
       clus
vv      DEL PEAK 18(8P12) MUTATED DEL PEAK 18(8P12) WILD-TYPE
  N0                          124                         171
  N1                           41                          44
  N2+N3                        32                          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"
                             vv
clus                           M0  M1 M1A M1B  MX
  DEL PEAK 18(8P12) MUTATED   138  11   1   0  50
  DEL PEAK 18(8P12) WILD-TYPE 179   7   0   3  69
D50V6, multiclass
     clus
vv    DEL PEAK 18(8P12) MUTATED DEL PEAK 18(8P12) WILD-TYPE
  M0                        138                         179
  M1                         11                           7
  M1A                         1                           0
  M1B                         0                           3
  MX                         50                          69
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V7, binary
                             cls
clus                            0   1
  DEL PEAK 18(8P12) MUTATED   118  84
  DEL PEAK 18(8P12) WILD-TYPE 130 130
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 18(8P12) MUTATED    118   84
  DEL PEAK 18(8P12) WILD-TYPE  130  130
        clus
vv       DEL PEAK 18(8P12) MUTATED DEL PEAK 18(8P12) WILD-TYPE
  FEMALE                       118                         130
  MALE                          84                         130
[1] 2 2
[1] FALSE
D50V8, continuous
                             vv
clus                          LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 18(8P12) MUTATED                            6
  DEL PEAK 18(8P12) WILD-TYPE                          7
                             vv
clus                          LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 18(8P12) MUTATED                                  35
  DEL PEAK 18(8P12) WILD-TYPE                                58
                             vv
clus                          LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 18(8P12) MUTATED                                                  135
  DEL PEAK 18(8P12) WILD-TYPE                                                159
                             vv
clus                          LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 18(8P12) MUTATED                                            1
  DEL PEAK 18(8P12) WILD-TYPE                                          3
                             vv
clus                          LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 18(8P12) MUTATED                                               8
  DEL PEAK 18(8P12) WILD-TYPE                                            11
                             vv
clus                          LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 18(8P12) MUTATED                                2
  DEL PEAK 18(8P12) WILD-TYPE                              0
                             vv
clus                          LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 18(8P12) MUTATED                                    4
  DEL PEAK 18(8P12) WILD-TYPE                                  0
                             vv
clus                          LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 18(8P12) MUTATED                              0
  DEL PEAK 18(8P12) WILD-TYPE                            2
                             vv
clus                          LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 18(8P12) MUTATED                               7
  DEL PEAK 18(8P12) WILD-TYPE                            12
                             vv
clus                          LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 18(8P12) MUTATED                                 1
  DEL PEAK 18(8P12) WILD-TYPE                               0
                             vv
clus                          LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 18(8P12) MUTATED                                               3
  DEL PEAK 18(8P12) WILD-TYPE                                             1
                             vv
clus                          MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 18(8P12) MUTATED                              0
  DEL PEAK 18(8P12) WILD-TYPE                            7
D50V9, multiclass
                                                    clus
vv                                                   DEL PEAK 18(8P12) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                 6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                         35
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                       135
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                 1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                              8
  LUNG CLEAR CELL ADENOCARCINOMA                                             2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                         4
  LUNG MUCINOUS ADENOCARCINOMA                                               0
  LUNG PAPILLARY ADENOCARCINOMA                                              7
  LUNG SIGNET RING ADENOCARCINOMA                                            1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                              3
  MUCINOUS (COLLOID) CARCINOMA                                               0
                                                    clus
vv                                                   DEL PEAK 18(8P12) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                   7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           58
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         159
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                   3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                               11
  LUNG CLEAR CELL ADENOCARCINOMA                                               0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                           0
  LUNG MUCINOUS ADENOCARCINOMA                                                 2
  LUNG PAPILLARY ADENOCARCINOMA                                               12
  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"
D50V10, binary
                             cls
clus                            0   1
  DEL PEAK 18(8P12) MUTATED     7 195
  DEL PEAK 18(8P12) WILD-TYPE  14 246
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 18(8P12) MUTATED      7  195
  DEL PEAK 18(8P12) WILD-TYPE   14  246
     clus
vv    DEL PEAK 18(8P12) MUTATED DEL PEAK 18(8P12) WILD-TYPE
  NO                          7                          14
  YES                       195                         246
[1] 2 2
[1] FALSE
D50V11, continuous
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 18(8P12) MUTATED   134   4   1  11
  DEL PEAK 18(8P12) WILD-TYPE 184   7   3   8
D50V12, multiclass
    clus
vv   DEL PEAK 18(8P12) MUTATED DEL PEAK 18(8P12) WILD-TYPE
  R0                       134                         184
  R1                         4                           7
  R2                         1                           3
  RX                        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                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 18(8P12) MUTATED                                  1     6
  DEL PEAK 18(8P12) WILD-TYPE                                0     0
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(8P12) MUTATED                          10   157
  DEL PEAK 18(8P12) WILD-TYPE                        16   205
D50V13, multiclass
                                  clus
vv                                 DEL PEAK 18(8P12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                    6
  BLACK OR AFRICAN AMERICAN                               10
  WHITE                                                  157
                                  clus
vv                                 DEL PEAK 18(8P12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                 16
  WHITE                                                    205
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V14, binary
                             cls
clus                            0   1
  DEL PEAK 18(8P12) MUTATED     5 143
  DEL PEAK 18(8P12) WILD-TYPE   2 189
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 18(8P12) MUTATED      5  143
  DEL PEAK 18(8P12) WILD-TYPE    2  189
                        clus
vv                       DEL PEAK 18(8P12) MUTATED DEL PEAK 18(8P12) WILD-TYPE
  HISPANIC OR LATINO                             5                           2
  NOT HISPANIC OR LATINO                       143                         189
[1] 2 2
[1] FALSE

Clustering(51) Variable = DEL PEAK 19(8P11.21) MUTATION ANALYSIS
D51V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 19(8P11.21) MUTATED    75  15
  DEL PEAK 19(8P11.21) WILD-TYPE 246  67
  DEL PEAK 19(8P11.21) MUTATED DEL PEAK 19(8P11.21) WILD-TYPE 
                            90                            313 
  DEL PEAK 19(8P11.21) MUTATED DEL PEAK 19(8P11.21) WILD-TYPE 
                            15                             67 
$`DEL PEAK 19(8P11.21) MUTATED`
TCGA-05-4249 TCGA-05-4410 TCGA-05-4420 TCGA-05-4425 TCGA-38-4631 TCGA-38-6178 
        1523         1958          912          669          354          448 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2668 TCGA-44-5644 TCGA-44-6144 TCGA-44-6145 
        1429          400          246          863          723          328 
TCGA-44-6775 TCGA-44-6777 TCGA-44-7672 TCGA-44-8120 TCGA-44-A479 TCGA-44-A4SU 
         705         1942          719          260          486           76 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4507 TCGA-49-6743 TCGA-49-6744 TCGA-49-6761 
        1421          428          268          369          890          354 
TCGA-50-5049 TCGA-50-5932 TCGA-50-5933 TCGA-50-6597 TCGA-53-7813 TCGA-55-1595 
        2146         1091         2370         1015          424         1479 
TCGA-55-1596 TCGA-55-6972 TCGA-55-6985 TCGA-55-7283 TCGA-55-7573 TCGA-55-7726 
        1375         1475         1233           35            4           39 
TCGA-55-7994 TCGA-55-8097 TCGA-55-8302 TCGA-55-8506 TCGA-55-8510 TCGA-55-8615 
          31           15           23           11          228           15 
TCGA-55-A490 TCGA-55-A4DG TCGA-62-8402 TCGA-62-A46U TCGA-62-A472 TCGA-64-1678 
          48          162         1445         2067          910         1189 
TCGA-64-1679 TCGA-67-3770 TCGA-67-6217 TCGA-69-7978 TCGA-69-7980 TCGA-69-A59K 
        1686           31          422           70          382          214 
TCGA-71-6725 TCGA-73-4662 TCGA-73-4668 TCGA-73-4670 TCGA-73-7498 TCGA-73-7499 
          61          912          467          131          621          519 
TCGA-75-7025 TCGA-78-7161 TCGA-78-8640 TCGA-86-7711 TCGA-86-7953 TCGA-86-8054 
        1967          215         1949          630          591          745 
TCGA-86-8074 TCGA-86-8280 TCGA-86-8359 TCGA-86-8668 TCGA-86-A456 TCGA-91-6847 
          24           16           26           45           10          842 
TCGA-91-7771 TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-A4VK 
         492           34          568          377          477          121 
TCGA-97-7546 TCGA-97-8547 TCGA-97-A4M7 TCGA-99-8025 TCGA-J2-8192 TCGA-L4-A4E5 
         964          148          271          427          154          578 
TCGA-MN-A4N4 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TC 
         622         1954         1954         1957         1980         1944 

$`DEL PEAK 19(8P11.21) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 TCGA-05-4398 
         607          426         1369         1126         1947         1431 
TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4422 TCGA-05-4424 
         578          610         1997          455          365          913 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 
         791          791          761          761          730          457 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
         151          882          670           30           62           14 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
         225          182          264         1952         1962         1147 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4632 TCGA-38-7271 TCGA-38-A44F 
        1492          864         1073         1357         1971          133 
TCGA-44-2655 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 
        1324         1367          741         1280         1301           97 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
        1130         1163         1036          190          722         1013 
TCGA-44-5645 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6776 
         383          302          845          704          658         1938 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
        1864         1978          444          592          366          218 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-8117 TCGA-44-8119 
         557         1970          882          535          385           99 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 
         466          287          337          351          415         1932 
TCGA-49-4494 TCGA-49-4506 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 
        1081          999          896          157         1700          445 
TCGA-49-6745 TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
         522         2174          455          785          944         1499 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 
         246          282          267          653          567          883 
TCGA-50-5944 TCGA-50-5946 TCGA-50-7109 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
         764          686          255          105         1986         1971 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
         280          701         1178           87            2          993 
TCGA-55-6712 TCGA-55-6969 TCGA-55-6971 TCGA-55-6980 TCGA-55-6983 TCGA-55-6986 
          24         1239           25           67         1826         2151 
TCGA-55-6987 TCGA-55-7281 TCGA-55-7284 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 
        1170           18          121            6           95           40 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 
        1958           39           34           24           54           19 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 
          16          197           21            3            5           33 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
          21          100            6           43           26            4 
TCGA-55-8096 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 
          47           33           46           66          216           44 
TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
          29            8           15            9            3          146 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
         202          536           48           49           66          106 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
          33           42           29         1952            1           28 
TCGA-55-A494 TCGA-55-A4DF TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
           5           47         1216         1289         1970         2696 
TCGA-62-A46V TCGA-62-A471 TCGA-64-1676 TCGA-64-1677 TCGA-64-1680 TCGA-64-1681 
        2199         1246         1728          628         1126         1968 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
        1959           62         1305          864         1559          866 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 
         610          573          427          385          174          141 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
         202          186          690          414          165          230 
TCGA-69-7974 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-73-4658 
         184           89          100           77          129         1600 
TCGA-73-4659 TCGA-73-4666 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-75-6214 
         711          800           40          164           38         1970 
TCGA-75-7027 TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
        1956         1965         1973         1988         1950         1944 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
        1093         1963         1202          760         1948         1957 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7162 TCGA-78-7163 
        1961         1963         1221          678         1940         1950 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        1934         1937         1965         1972         1949         1944 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 
         327          881         1952          994         1971         1981 
TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 
        1954         1964         1965         1972          824         1959 
TCGA-86-7701 TCGA-86-7713 TCGA-86-7714 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 
          11          422         1968         1963          508           10 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
        1963           13          479          489          476          482 
TCGA-86-8281 TCGA-86-8358 TCGA-86-8585 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
        1955           19           35           34           18           15 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
         455          405           30           14           39          323 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
        1940           60          310           79          417          372 
TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
         224           35          197          174           36           44 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7043 TCGA-95-7948 
         218          297          127          186            2          476 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 
        1965         1932         1332          775          181           22 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 
         107          182         1965           87          147           15 
TCGA-97-8552 TCGA-97-A4M2 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
         115          197          392          459           44          170 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 
         114          287          282          238          435          116 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 
           6          285          353         1946         1967         1951 
TCGA-MP-A4TA TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
        1951         1970         1970          142         1955         1971 
TCGA-MP-A5C7 
        1490 

  DEL PEAK 19(8P11.21) MUTATED DEL PEAK 19(8P11.21) WILD-TYPE 
                             4                              1 
  DEL PEAK 19(8P11.21) MUTATED DEL PEAK 19(8P11.21) WILD-TYPE 
                          2370                           2696 
  DEL PEAK 19(8P11.21) MUTATED DEL PEAK 19(8P11.21) WILD-TYPE 
                         481.5                          457.0 
[1] "4.0 - 2370.0 (481.5)" "1.0 - 2696.0 (457.0)"
[1] "hr=" "1.1"
D51V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 19(8P11.21) MUTATED         2       23       26        10        20
  DEL PEAK 19(8P11.21) WILD-TYPE       2       90      105        33        49
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 19(8P11.21) MUTATED           16          3        5
  DEL PEAK 19(8P11.21) WILD-TYPE         51          8       18
D51V3, multiclass
            clus
vv           DEL PEAK 19(8P11.21) MUTATED DEL PEAK 19(8P11.21) WILD-TYPE
  STAGE I                               2                              2
  STAGE IA                             23                             90
  STAGE IB                             26                            105
  STAGE IIA                            10                             33
  STAGE IIB                            20                             49
  STAGE IIIA                           16                             51
  STAGE IIIB                            3                              8
  STAGE IV                              5                             18
[1] 8 2
[1] TRUE
[1] "dimension of 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(8P11.21) MUTATED    30  58  14   3
  DEL PEAK 19(8P11.21) WILD-TYPE 113 201  26  15
D51V4, multiclass
    clus
vv   DEL PEAK 19(8P11.21) MUTATED DEL PEAK 19(8P11.21) WILD-TYPE
  T1                           30                            113
  T2                           58                            201
  T3                           14                             26
  T4                            3                             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 19(8P11.21) MUTATED    65  20    17
  DEL PEAK 19(8P11.21) WILD-TYPE 230  65    55
D51V5, multiclass
       clus
vv      DEL PEAK 19(8P11.21) MUTATED DEL PEAK 19(8P11.21) WILD-TYPE
  N0                              65                            230
  N1                              20                             65
  N2+N3                           17                             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"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 19(8P11.21) MUTATED    70   5   0   0  28
  DEL PEAK 19(8P11.21) WILD-TYPE 247  13   1   3  91
D51V6, multiclass
     clus
vv    DEL PEAK 19(8P11.21) MUTATED DEL PEAK 19(8P11.21) WILD-TYPE
  M0                            70                            247
  M1                             5                             13
  M1A                            0                              1
  M1B                            0                              3
  MX                            28                             91
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V7, binary
                                cls
clus                               0   1
  DEL PEAK 19(8P11.21) MUTATED    69  36
  DEL PEAK 19(8P11.21) WILD-TYPE 179 178
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(8P11.21) MUTATED     69   36
  DEL PEAK 19(8P11.21) WILD-TYPE  179  178
        clus
vv       DEL PEAK 19(8P11.21) MUTATED DEL PEAK 19(8P11.21) WILD-TYPE
  FEMALE                           69                            179
  MALE                             36                            178
[1] 2 2
[1] FALSE
D51V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 19(8P11.21) MUTATED                            2
  DEL PEAK 19(8P11.21) WILD-TYPE                         11
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 19(8P11.21) MUTATED                                  20
  DEL PEAK 19(8P11.21) WILD-TYPE                                73
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 19(8P11.21) MUTATED                                                   69
  DEL PEAK 19(8P11.21) WILD-TYPE                                                225
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 19(8P11.21) MUTATED                                            1
  DEL PEAK 19(8P11.21) WILD-TYPE                                          3
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 19(8P11.21) MUTATED                                               5
  DEL PEAK 19(8P11.21) WILD-TYPE                                            14
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 19(8P11.21) MUTATED                                2
  DEL PEAK 19(8P11.21) WILD-TYPE                              0
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 19(8P11.21) MUTATED                                    3
  DEL PEAK 19(8P11.21) WILD-TYPE                                  1
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 19(8P11.21) MUTATED                              0
  DEL PEAK 19(8P11.21) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 19(8P11.21) MUTATED                               3
  DEL PEAK 19(8P11.21) WILD-TYPE                            16
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 19(8P11.21) MUTATED                                 0
  DEL PEAK 19(8P11.21) WILD-TYPE                               1
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 19(8P11.21) MUTATED                                               0
  DEL PEAK 19(8P11.21) WILD-TYPE                                             4
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 19(8P11.21) MUTATED                              0
  DEL PEAK 19(8P11.21) WILD-TYPE                            7
D51V9, multiclass
                                                    clus
vv                                                   DEL PEAK 19(8P11.21) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            20
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           69
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 5
  LUNG CLEAR CELL ADENOCARCINOMA                                                2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            3
  LUNG MUCINOUS ADENOCARCINOMA                                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                                 3
  LUNG SIGNET RING ADENOCARCINOMA                                               0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 0
  MUCINOUS (COLLOID) CARCINOMA                                                  0
                                                    clus
vv                                                   DEL PEAK 19(8P11.21) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              73
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            225
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  14
  LUNG CLEAR CELL ADENOCARCINOMA                                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              1
  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"
D51V10, binary
                                cls
clus                               0   1
  DEL PEAK 19(8P11.21) MUTATED     4 101
  DEL PEAK 19(8P11.21) WILD-TYPE  17 340
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(8P11.21) MUTATED      4  101
  DEL PEAK 19(8P11.21) WILD-TYPE   17  340
     clus
vv    DEL PEAK 19(8P11.21) MUTATED DEL PEAK 19(8P11.21) WILD-TYPE
  NO                             4                             17
  YES                          101                            340
[1] 2 2
[1] FALSE
D51V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 19(8P11.21) MUTATED    66   3   1   7
  DEL PEAK 19(8P11.21) WILD-TYPE 252   8   3  12
D51V12, multiclass
    clus
vv   DEL PEAK 19(8P11.21) MUTATED DEL PEAK 19(8P11.21) WILD-TYPE
  R0                           66                            252
  R1                            3                              8
  R2                            1                              3
  RX                            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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 19(8P11.21) MUTATED                                  1     4
  DEL PEAK 19(8P11.21) WILD-TYPE                                0     2
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 19(8P11.21) MUTATED                           4    83
  DEL PEAK 19(8P11.21) WILD-TYPE                        22   279
D51V13, multiclass
                                  clus
vv                                 DEL PEAK 19(8P11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                   4
  WHITE                                                      83
                                  clus
vv                                 DEL PEAK 19(8P11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         2
  BLACK OR AFRICAN AMERICAN                                    22
  WHITE                                                       279
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V14, binary
                                cls
clus                               0   1
  DEL PEAK 19(8P11.21) MUTATED     2  82
  DEL PEAK 19(8P11.21) WILD-TYPE   5 250
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(8P11.21) MUTATED      2   82
  DEL PEAK 19(8P11.21) WILD-TYPE    5  250
                        clus
vv                       DEL PEAK 19(8P11.21) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           82
                        clus
vv                       DEL PEAK 19(8P11.21) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            250
[1] 2 2
[1] FALSE

Clustering(52) Variable = DEL PEAK 20(8Q11.21) MUTATION ANALYSIS
D52V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 20(8Q11.21) MUTATED    38   8
  DEL PEAK 20(8Q11.21) WILD-TYPE 283  74
  DEL PEAK 20(8Q11.21) MUTATED DEL PEAK 20(8Q11.21) WILD-TYPE 
                            46                            357 
  DEL PEAK 20(8Q11.21) MUTATED DEL PEAK 20(8Q11.21) WILD-TYPE 
                             8                             74 
$`DEL PEAK 20(8Q11.21) MUTATED`
TCGA-05-4249 TCGA-44-2657 TCGA-44-6144 TCGA-44-6145 TCGA-44-6775 TCGA-44-7660 
        1523          400          723          328          705          592 
TCGA-44-A479 TCGA-44-A47F TCGA-49-6743 TCGA-49-6744 TCGA-50-6597 TCGA-55-5899 
         486          337          369          890         1015           87 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7726 TCGA-55-8506 TCGA-64-1678 TCGA-64-1679 
           6            4           39           11         1189         1686 
TCGA-64-5774 TCGA-67-6217 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-A59K 
        1959          422           70           89          382          214 
TCGA-73-4662 TCGA-73-4668 TCGA-75-7025 TCGA-78-7147 TCGA-78-7150 TCGA-78-7153 
         912          467         1967         1950         1963          760 
TCGA-78-7167 TCGA-78-8640 TCGA-86-8055 TCGA-86-A456 TCGA-95-7567 TCGA-95-7944 
        1937         1949           10           10          568          377 
TCGA-95-7948 TCGA-97-7546 TCGA-97-8547 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-A4AE 
         476          964          148          271          154          282 
TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
        1954         1954         1957         1980 

$`DEL PEAK 20(8Q11.21) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 TCGA-05-4398 
         607          426         1369         1126         1947         1431 
TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 
         578          610         1958         1997          455          912 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 
         365          913          669          791          791          761 
TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
         761          730          457          151          882          670 
TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 
          30           62           14          225          182          264 
TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 
        1952         1962         1147         1492          864         1073 
TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 
         354         1357          448         1971          133         1324 
TCGA-44-2656 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 
        1429         1367          741         1280         1301           97 
TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
         246         1130         1163         1036          190          722 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
        1013          863          383          302          845          704 
TCGA-44-6774 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
         658         1938         1942         1864         1978          444 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 
         366          218          557         1970          882          535 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A47A TCGA-44-A47B 
         719          385           99          260          466          287 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 
         351          415           76         1932         1081         1421 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
         428          999          268          896          157         1700 
TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
         445          522          354         2174         2146          455 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
         785          944         1499          246          282          267 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
        1091         2370          653          567          883          764 
TCGA-50-5946 TCGA-50-7109 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
         686          255          105         1986         1971          424 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-6543 
         280          701         1178         1479         1375            2 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 
         993           24         1239           25         1475           67 
TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 
        1826         1233         2151         1170           18           35 
TCGA-55-7284 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7727 
         121           95           40         1958           39           34 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
          24           54           19           16          197           21 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
           3           31            5           33           21          100 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
           6           43           26            4           47           15 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
          33           46           66          216           44           23 
TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
          29            8           15          228            9            3 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
         146          202          536           15           48           49 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
          66          106           33           42           29           48 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
        1952            1           28            5           47          162 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46U 
        1216         1289         1970         2696         1445         2067 
TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1680 
        2199         1246          910         1728          628         1126 
TCGA-64-1681 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
        1968           62         1305          864         1559          866 
TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 
          31          610          573          427          385          174 
TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
         141          202          186          690          414          165 
TCGA-69-7973 TCGA-69-7974 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-71-6725 
         230          184          100           77          129           61 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4666 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
        1600          711          800          131           40          164 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-75-6214 TCGA-75-7027 TCGA-75-7031 
          38          621          519         1970         1956         1965 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 TCGA-78-7154 
        1973         1988         1944         1093         1202         1948 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
        1957         1961         1963         1221          678          215 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
        1940         1950         1934         1965         1972         1949 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 
        1944          327          881         1952          994         1971 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 
        1981         1954         1964         1965         1972          824 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        1959           11          630          422         1968          591 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
        1963          508          745         1963           13           24 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8281 
         479          489          476          482           16         1955 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
          19           26           35           45           34           18 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 
          15          455          405           30           14           39 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
         323         1940           60          310           79          417 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
         372          842          224           35          492          197 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
         174           36           44          218          297          127 
TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-95-7947 TCGA-95-A4VK TCGA-97-7547 
         186           34            2          477          121         1965 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 
        1932         1332          775          181           22          107 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 
         182         1965           87          147           15          115 
TCGA-97-A4M2 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
         197          392          427          459           44          170 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
         114          287          238          578          435          116 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
           6          285          622          353         1946         1967 
TCGA-MP-A4T2 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
        1951         1951         1944         1970         1970          142 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
        1955         1971         1490 

  DEL PEAK 20(8Q11.21) MUTATED DEL PEAK 20(8Q11.21) WILD-TYPE 
                             4                              1 
  DEL PEAK 20(8Q11.21) MUTATED DEL PEAK 20(8Q11.21) WILD-TYPE 
                          1980                           2696 
  DEL PEAK 20(8Q11.21) MUTATED DEL PEAK 20(8Q11.21) WILD-TYPE 
                           481                            457 
[1] "4.0 - 1980.0 (481.0)" "1.0 - 2696.0 (457.0)"
[1] "hr=" "1"  
D52V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 20(8Q11.21) MUTATED         1       13       16         7        12
  DEL PEAK 20(8Q11.21) WILD-TYPE       3      100      115        36        57
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 20(8Q11.21) MUTATED            6          1        3
  DEL PEAK 20(8Q11.21) WILD-TYPE         61         10       20
D52V3, multiclass
            clus
vv           DEL PEAK 20(8Q11.21) MUTATED DEL PEAK 20(8Q11.21) WILD-TYPE
  STAGE I                               1                              3
  STAGE IA                             13                            100
  STAGE IB                             16                            115
  STAGE IIA                             7                             36
  STAGE IIB                            12                             57
  STAGE IIIA                            6                             61
  STAGE IIIB                            1                             10
  STAGE IV                              3                             20
[1] 8 2
[1] TRUE
[1] "dimension of 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(8Q11.21) MUTATED    17  37   4   1
  DEL PEAK 20(8Q11.21) WILD-TYPE 126 222  36  17
D52V4, multiclass
    clus
vv   DEL PEAK 20(8Q11.21) MUTATED DEL PEAK 20(8Q11.21) WILD-TYPE
  T1                           17                            126
  T2                           37                            222
  T3                            4                             36
  T4                            1                             17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1 N2+N3
  DEL PEAK 20(8Q11.21) MUTATED    34  16     7
  DEL PEAK 20(8Q11.21) WILD-TYPE 261  69    65
D52V5, multiclass
       clus
vv      DEL PEAK 20(8Q11.21) MUTATED DEL PEAK 20(8Q11.21) WILD-TYPE
  N0                              34                            261
  N1                              16                             69
  N2+N3                            7                             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 20(8Q11.21) MUTATED    40   3   0   0  16
  DEL PEAK 20(8Q11.21) WILD-TYPE 277  15   1   3 103
D52V6, multiclass
     clus
vv    DEL PEAK 20(8Q11.21) MUTATED DEL PEAK 20(8Q11.21) WILD-TYPE
  M0                            40                            277
  M1                             3                             15
  M1A                            0                              1
  M1B                            0                              3
  MX                            16                            103
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V7, binary
                                cls
clus                               0   1
  DEL PEAK 20(8Q11.21) MUTATED    37  22
  DEL PEAK 20(8Q11.21) WILD-TYPE 211 192
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(8Q11.21) MUTATED     37   22
  DEL PEAK 20(8Q11.21) WILD-TYPE  211  192
        clus
vv       DEL PEAK 20(8Q11.21) MUTATED DEL PEAK 20(8Q11.21) WILD-TYPE
  FEMALE                           37                            211
  MALE                             22                            192
[1] 2 2
[1] FALSE
D52V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 20(8Q11.21) MUTATED                            2
  DEL PEAK 20(8Q11.21) WILD-TYPE                         11
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 20(8Q11.21) MUTATED                                  11
  DEL PEAK 20(8Q11.21) WILD-TYPE                                82
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 20(8Q11.21) MUTATED                                                   38
  DEL PEAK 20(8Q11.21) WILD-TYPE                                                256
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 20(8Q11.21) MUTATED                                            0
  DEL PEAK 20(8Q11.21) WILD-TYPE                                          4
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 20(8Q11.21) MUTATED                                               0
  DEL PEAK 20(8Q11.21) WILD-TYPE                                            19
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 20(8Q11.21) MUTATED                                1
  DEL PEAK 20(8Q11.21) WILD-TYPE                              1
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 20(8Q11.21) MUTATED                                    3
  DEL PEAK 20(8Q11.21) WILD-TYPE                                  1
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 20(8Q11.21) MUTATED                              0
  DEL PEAK 20(8Q11.21) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 20(8Q11.21) MUTATED                               3
  DEL PEAK 20(8Q11.21) WILD-TYPE                            16
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 20(8Q11.21) MUTATED                                 0
  DEL PEAK 20(8Q11.21) WILD-TYPE                               1
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 20(8Q11.21) MUTATED                                               1
  DEL PEAK 20(8Q11.21) WILD-TYPE                                             3
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 20(8Q11.21) MUTATED                              0
  DEL PEAK 20(8Q11.21) WILD-TYPE                            7
D52V9, multiclass
                                                    clus
vv                                                   DEL PEAK 20(8Q11.21) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            11
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           38
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                                1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            3
  LUNG MUCINOUS ADENOCARCINOMA                                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                                 3
  LUNG SIGNET RING ADENOCARCINOMA                                               0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 1
  MUCINOUS (COLLOID) CARCINOMA                                                  0
                                                    clus
vv                                                   DEL PEAK 20(8Q11.21) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              82
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            256
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                                  1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              1
  LUNG MUCINOUS ADENOCARCINOMA                                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                                  16
  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"
D52V10, binary
                                cls
clus                               0   1
  DEL PEAK 20(8Q11.21) MUTATED     0  59
  DEL PEAK 20(8Q11.21) WILD-TYPE  21 382
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(8Q11.21) MUTATED      0   59
  DEL PEAK 20(8Q11.21) WILD-TYPE   21  382
     clus
vv    DEL PEAK 20(8Q11.21) MUTATED DEL PEAK 20(8Q11.21) WILD-TYPE
  NO                             0                             21
  YES                           59                            382
[1] 2 2
[1] FALSE
D52V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 20(8Q11.21) MUTATED    39   0   1   3
  DEL PEAK 20(8Q11.21) WILD-TYPE 279  11   3  16
D52V12, multiclass
    clus
vv   DEL PEAK 20(8Q11.21) MUTATED DEL PEAK 20(8Q11.21) WILD-TYPE
  R0                           39                            279
  R1                            0                             11
  R2                            1                              3
  RX                            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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 20(8Q11.21) MUTATED                                  1     1
  DEL PEAK 20(8Q11.21) WILD-TYPE                                0     5
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(8Q11.21) MUTATED                           3    43
  DEL PEAK 20(8Q11.21) WILD-TYPE                        23   319
D52V13, multiclass
                                  clus
vv                                 DEL PEAK 20(8Q11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   3
  WHITE                                                      43
                                  clus
vv                                 DEL PEAK 20(8Q11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         5
  BLACK OR AFRICAN AMERICAN                                    23
  WHITE                                                       319
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V14, binary
                                cls
clus                               0   1
  DEL PEAK 20(8Q11.21) MUTATED     1  39
  DEL PEAK 20(8Q11.21) WILD-TYPE   6 293
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(8Q11.21) MUTATED      1   39
  DEL PEAK 20(8Q11.21) WILD-TYPE    6  293
                        clus
vv                       DEL PEAK 20(8Q11.21) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           39
                        clus
vv                       DEL PEAK 20(8Q11.21) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            293
[1] 2 2
[1] FALSE

Clustering(53) Variable = DEL PEAK 21(9P23) MUTATION ANALYSIS
D53V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 21(9P23) MUTATED   169  54
  DEL PEAK 21(9P23) WILD-TYPE 152  28
  DEL PEAK 21(9P23) MUTATED DEL PEAK 21(9P23) WILD-TYPE 
                        223                         180 
  DEL PEAK 21(9P23) MUTATED DEL PEAK 21(9P23) WILD-TYPE 
                         54                          28 
$`DEL PEAK 21(9P23) MUTATED`
TCGA-05-4249 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 TCGA-05-4405 
        1523          426         1369         1126         1947          610 
TCGA-05-4415 TCGA-05-4420 TCGA-05-4424 TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 
        1997          912          913          761          730          457 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-38-4627 
         151          882           30           62          225         1147 
TCGA-38-4628 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-A44F 
        1492         1073          354         1357          448          133 
TCGA-44-2655 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 
        1324          400         1367          741         1280         1301 
TCGA-44-2668 TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 TCGA-44-6146 TCGA-44-6777 
         246         1013          863          723          302         1942 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
        1864         1978          218          557         1970          882 
TCGA-44-7671 TCGA-44-8117 TCGA-44-8120 TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
         535          385          260          415           76         1932 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4507 TCGA-49-4510 TCGA-49-4514 
        1081         1421          428          268          896         1700 
TCGA-49-6742 TCGA-49-6743 TCGA-50-5055 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
         445          369          785         1499          246          282 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5944 TCGA-50-5946 
         267         1091         2370          653          764          686 
TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        1015          255          105         1971          424          280 
TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6642 TCGA-55-6712 
         701         1178         1375           87          993           24 
TCGA-55-6971 TCGA-55-6980 TCGA-55-6985 TCGA-55-6986 TCGA-55-7281 TCGA-55-7283 
          25           67         1233         2151           18           35 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7576 TCGA-55-7724 TCGA-55-7726 TCGA-55-7907 
           6            4           40         1958           39           16 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8097 
         100            6           43           26            4           15 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 
          46           66           29           11            8          228 
TCGA-55-8512 TCGA-55-8614 TCGA-55-8615 TCGA-55-A48X TCGA-55-A490 TCGA-55-A492 
           3          536           15           33           48            1 
TCGA-55-A493 TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
          28          162         1216         1289         1970         2696 
TCGA-62-8402 TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 TCGA-64-1678 TCGA-64-1679 
        1445         2199         1246          910         1189         1686 
TCGA-64-1680 TCGA-64-1681 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 
        1126         1968         1559          866           31          610 
TCGA-67-3772 TCGA-67-3774 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
         573          385          141          422          202          186 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7974 TCGA-69-8254 TCGA-69-8255 TCGA-73-4662 
         690          414          184           77          129          912 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-7499 TCGA-75-7025 
         800          467          131           40          519         1967 
TCGA-75-7027 TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
        1956         1965         1973         1988         1950         1944 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7156 TCGA-78-7160 TCGA-78-7161 TCGA-78-7166 
        1093         1963         1961          678          215         1934 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
        1937         1965          881         1952          994         1949 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 
        1981         1954         1964         1959          630          422 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
         591         1963          508          745           10         1963 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8585 
          24          479          482           16           19           35 
TCGA-86-8668 TCGA-86-8672 TCGA-86-A456 TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 
          45           15           10         1940           60           79 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8497 
         417          372          842          224           35          174 
TCGA-91-8499 TCGA-93-7348 TCGA-93-8067 TCGA-95-7567 TCGA-95-A4VK TCGA-97-7937 
          36          127          186          568          121          181 
TCGA-97-7941 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
          22         1965           87          147           15          148 
TCGA-97-8552 TCGA-97-A4M7 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-A4AD 
         115          271           44          170          154          287 
TCGA-J2-A4AG TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
         238          285          622          353         1946         1967 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TE TCGA-MP-A4TK 
        1954         1957         1980         1951         1970         1971 
TCGA-MP-A5C7 
        1490 

$`DEL PEAK 21(9P23) WILD-TYPE`
TCGA-05-4382 TCGA-05-4398 TCGA-05-4403 TCGA-05-4410 TCGA-05-4417 TCGA-05-4422 
         607         1431          578         1958          455          365 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-5428 TCGA-35-3615 
         669          791          791          761          670           14 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4629 TCGA-38-7271 
         182          264         1952         1962          864         1971 
TCGA-44-2656 TCGA-44-2666 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
        1429           97         1130         1163         1036          190 
TCGA-44-4112 TCGA-44-5645 TCGA-44-6145 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
         722          383          328          845          704          658 
TCGA-44-6775 TCGA-44-6776 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7672 
         705         1938          444          592          366          719 
TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
          99          486          466          287          337          351 
TCGA-49-4506 TCGA-49-4512 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-50-5045 
         999          157          890          522          354         2174 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5066 TCGA-50-5941 TCGA-50-5942 TCGA-53-7624 
        2146          455          944          567          883         1986 
TCGA-55-1595 TCGA-55-6543 TCGA-55-6969 TCGA-55-6972 TCGA-55-6983 TCGA-55-6987 
        1479            2         1239         1475         1826         1170 
TCGA-55-7284 TCGA-55-7574 TCGA-55-7725 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
         121           95           39           34           24           54 
TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
          19          197           21            3           31            5 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8096 TCGA-55-8205 TCGA-55-8299 TCGA-55-8301 
          33           21           47           33          216           44 
TCGA-55-8302 TCGA-55-8508 TCGA-55-8511 TCGA-55-8513 TCGA-55-8514 TCGA-55-8616 
          23           15            9          146          202           48 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 
          49           66          106           42           29         1952 
TCGA-55-A494 TCGA-55-A4DF TCGA-62-A46U TCGA-64-1676 TCGA-64-1677 TCGA-64-5774 
           5           47         2067         1728          628         1959 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-67-3773 TCGA-67-6215 TCGA-69-7765 
          62         1305          864          427          174          165 
TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-A59K 
         230           70           89          382          100          214 
TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
          61         1600          711          164           38          621 
TCGA-75-6214 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7158 
        1970         1202          760         1948         1957         1963 
TCGA-78-7159 TCGA-78-7162 TCGA-78-7163 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        1221         1940         1950         1972         1949         1944 
TCGA-78-7539 TCGA-78-8648 TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 TCGA-86-7701 
         327         1971         1965         1972          824           11 
TCGA-86-7714 TCGA-86-8073 TCGA-86-8076 TCGA-86-8278 TCGA-86-8281 TCGA-86-8359 
        1968           13          489          476         1955           26 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4D0 TCGA-86-A4P7 
          34           18          455          405           30           14 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6831 TCGA-91-7771 TCGA-91-8496 TCGA-91-A4BC 
          39          323          310          492          197           44 
TCGA-91-A4BD TCGA-93-7347 TCGA-95-7039 TCGA-95-7043 TCGA-95-7944 TCGA-95-7947 
         218          297           34            2          377          477 
TCGA-95-7948 TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
         476          964         1965         1932         1332          775 
TCGA-97-8171 TCGA-97-8172 TCGA-97-A4M2 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
         107          182          197          392          427          459 
TCGA-J2-8194 TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
         114          282          578          435          116            6 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4TC TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        1951         1954         1944         1970          142         1955 

  DEL PEAK 21(9P23) MUTATED DEL PEAK 21(9P23) WILD-TYPE 
                          1                           2 
  DEL PEAK 21(9P23) MUTATED DEL PEAK 21(9P23) WILD-TYPE 
                       2696                        2174 
  DEL PEAK 21(9P23) MUTATED DEL PEAK 21(9P23) WILD-TYPE 
                      535.0                       439.5 
[1] "1.0 - 2696.0 (535.0)" "2.0 - 2174.0 (439.5)"
[1] "hr=" "1.3"
D53V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 21(9P23) MUTATED         2       58       67        26        40
  DEL PEAK 21(9P23) WILD-TYPE       2       55       64        17        29
                             vv
clus                          STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 21(9P23) MUTATED           38          7       14
  DEL PEAK 21(9P23) WILD-TYPE         29          4        9
D53V3, multiclass
            clus
vv           DEL PEAK 21(9P23) MUTATED DEL PEAK 21(9P23) WILD-TYPE
  STAGE I                            2                           2
  STAGE IA                          58                          55
  STAGE IB                          67                          64
  STAGE IIA                         26                          17
  STAGE IIB                         40                          29
  STAGE IIIA                        38                          29
  STAGE IIIB                         7                           4
  STAGE IV                          14                           9
[1] 8 2
[1] TRUE
[1] "dimension of 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(9P23) MUTATED    77 143  21  11
  DEL PEAK 21(9P23) WILD-TYPE  66 116  19   7
D53V4, multiclass
    clus
vv   DEL PEAK 21(9P23) MUTATED DEL PEAK 21(9P23) WILD-TYPE
  T1                        77                          66
  T2                       143                         116
  T3                        21                          19
  T4                        11                           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 21(9P23) MUTATED   150  58    40
  DEL PEAK 21(9P23) WILD-TYPE 145  27    32
D53V5, multiclass
       clus
vv      DEL PEAK 21(9P23) MUTATED DEL PEAK 21(9P23) WILD-TYPE
  N0                          150                         145
  N1                           58                          27
  N2+N3                        40                          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"
                             vv
clus                           M0  M1 M1A M1B  MX
  DEL PEAK 21(9P23) MUTATED   175  12   0   2  61
  DEL PEAK 21(9P23) WILD-TYPE 142   6   1   1  58
D53V6, multiclass
     clus
vv    DEL PEAK 21(9P23) MUTATED DEL PEAK 21(9P23) WILD-TYPE
  M0                        175                         142
  M1                         12                           6
  M1A                         0                           1
  M1B                         2                           1
  MX                         61                          58
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V7, binary
                             cls
clus                            0   1
  DEL PEAK 21(9P23) MUTATED   131 122
  DEL PEAK 21(9P23) WILD-TYPE 117  92
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 21(9P23) MUTATED    131  122
  DEL PEAK 21(9P23) WILD-TYPE  117   92
        clus
vv       DEL PEAK 21(9P23) MUTATED DEL PEAK 21(9P23) WILD-TYPE
  FEMALE                       131                         117
  MALE                         122                          92
[1] 2 2
[1] FALSE
D53V8, continuous
                             vv
clus                          LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 21(9P23) MUTATED                            8
  DEL PEAK 21(9P23) WILD-TYPE                          5
                             vv
clus                          LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 21(9P23) MUTATED                                  53
  DEL PEAK 21(9P23) WILD-TYPE                                40
                             vv
clus                          LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 21(9P23) MUTATED                                                  161
  DEL PEAK 21(9P23) WILD-TYPE                                                133
                             vv
clus                          LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 21(9P23) MUTATED                                            2
  DEL PEAK 21(9P23) WILD-TYPE                                          2
                             vv
clus                          LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 21(9P23) MUTATED                                              11
  DEL PEAK 21(9P23) WILD-TYPE                                             8
                             vv
clus                          LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 21(9P23) MUTATED                                1
  DEL PEAK 21(9P23) WILD-TYPE                              1
                             vv
clus                          LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 21(9P23) MUTATED                                    4
  DEL PEAK 21(9P23) WILD-TYPE                                  0
                             vv
clus                          LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 21(9P23) MUTATED                              1
  DEL PEAK 21(9P23) WILD-TYPE                            1
                             vv
clus                          LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 21(9P23) MUTATED                               7
  DEL PEAK 21(9P23) WILD-TYPE                            12
                             vv
clus                          LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 21(9P23) MUTATED                                 0
  DEL PEAK 21(9P23) WILD-TYPE                               1
                             vv
clus                          LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 21(9P23) MUTATED                                               3
  DEL PEAK 21(9P23) WILD-TYPE                                             1
                             vv
clus                          MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 21(9P23) MUTATED                              2
  DEL PEAK 21(9P23) WILD-TYPE                            5
D53V9, multiclass
                                                    clus
vv                                                   DEL PEAK 21(9P23) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                 8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                         53
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                       161
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                 2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                             11
  LUNG CLEAR CELL ADENOCARCINOMA                                             1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                         4
  LUNG MUCINOUS ADENOCARCINOMA                                               1
  LUNG PAPILLARY ADENOCARCINOMA                                              7
  LUNG SIGNET RING ADENOCARCINOMA                                            0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                              3
  MUCINOUS (COLLOID) CARCINOMA                                               2
                                                    clus
vv                                                   DEL PEAK 21(9P23) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                   5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           40
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         133
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                   2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                8
  LUNG CLEAR CELL ADENOCARCINOMA                                               1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                           0
  LUNG MUCINOUS ADENOCARCINOMA                                                 1
  LUNG PAPILLARY ADENOCARCINOMA                                               12
  LUNG SIGNET RING ADENOCARCINOMA                                              1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                1
  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"
D53V10, binary
                             cls
clus                            0   1
  DEL PEAK 21(9P23) MUTATED    12 241
  DEL PEAK 21(9P23) WILD-TYPE   9 200
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 21(9P23) MUTATED     12  241
  DEL PEAK 21(9P23) WILD-TYPE    9  200
     clus
vv    DEL PEAK 21(9P23) MUTATED DEL PEAK 21(9P23) WILD-TYPE
  NO                         12                           9
  YES                       241                         200
[1] 2 2
[1] FALSE
D53V11, continuous
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 21(9P23) MUTATED   172   5   2  14
  DEL PEAK 21(9P23) WILD-TYPE 146   6   2   5
D53V12, multiclass
    clus
vv   DEL PEAK 21(9P23) MUTATED DEL PEAK 21(9P23) WILD-TYPE
  R0                       172                         146
  R1                         5                           6
  R2                         2                           2
  RX                        14                           5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 21(9P23) MUTATED                                  1     3
  DEL PEAK 21(9P23) WILD-TYPE                                0     3
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(9P23) MUTATED                          12   199
  DEL PEAK 21(9P23) WILD-TYPE                        14   163
D53V13, multiclass
                                  clus
vv                                 DEL PEAK 21(9P23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                    3
  BLACK OR AFRICAN AMERICAN                               12
  WHITE                                                  199
                                  clus
vv                                 DEL PEAK 21(9P23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 14
  WHITE                                                    163
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V14, binary
                             cls
clus                            0   1
  DEL PEAK 21(9P23) MUTATED     4 176
  DEL PEAK 21(9P23) WILD-TYPE   3 156
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 21(9P23) MUTATED      4  176
  DEL PEAK 21(9P23) WILD-TYPE    3  156
                        clus
vv                       DEL PEAK 21(9P23) MUTATED DEL PEAK 21(9P23) WILD-TYPE
  HISPANIC OR LATINO                             4                           3
  NOT HISPANIC OR LATINO                       176                         156
[1] 2 2
[1] FALSE

Clustering(54) Variable = DEL PEAK 22(9P21.3) MUTATION ANALYSIS
D54V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 22(9P21.3) MUTATED   174  55
  DEL PEAK 22(9P21.3) WILD-TYPE 147  27
  DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE 
                          229                           174 
  DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE 
                           55                            27 
$`DEL PEAK 22(9P21.3) MUTATED`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4396 TCGA-05-4403 
        1523          607          426         1369         1947          578 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4420 TCGA-05-4424 TCGA-05-4432 TCGA-05-4433 
         610         1997          912          913          761          730 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 
         457          151          882           30           62          225 
TCGA-38-4625 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4631 TCGA-38-4632 
        1952         1147         1492          864          354         1357 
TCGA-38-6178 TCGA-38-A44F TCGA-44-2655 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 
         448          133         1324          400         1367          741 
TCGA-44-2662 TCGA-44-2665 TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 TCGA-44-6146 
        1280         1301         1013          863          723          302 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
        1942         1864         1978          218          557         1970 
TCGA-44-7670 TCGA-44-7671 TCGA-44-8117 TCGA-44-8120 TCGA-44-A4SS TCGA-44-A4SU 
         882          535          385          260          415           76 
TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
        1932         1081         1421          428          999          268 
TCGA-49-4510 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6745 TCGA-50-5055 
         896         1700          445          369          522          785 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
        1499          246          282          267         1091         2370 
TCGA-50-5935 TCGA-50-5944 TCGA-50-5946 TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 
         653          764          686         1015          255          105 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 
        1986         1971          424          701         1178         1375 
TCGA-55-5899 TCGA-55-6642 TCGA-55-6712 TCGA-55-6971 TCGA-55-6980 TCGA-55-6985 
          87          993           24           25           67         1233 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
        2151         1170           18           35          121            6 
TCGA-55-7573 TCGA-55-7576 TCGA-55-7724 TCGA-55-7726 TCGA-55-7907 TCGA-55-7914 
           4           40         1958           39           16            3 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8097 
         100            6           43           26            4           15 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 
          46           66           29           11            8          228 
TCGA-55-8512 TCGA-55-8614 TCGA-55-A48X TCGA-55-A490 TCGA-55-A492 TCGA-55-A493 
           3          536           33           48            1           28 
TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
         162         1216         1289         1970         2696         1445 
TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 
        2199         1246          910         1728         1189         1686 
TCGA-64-1680 TCGA-64-1681 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 
        1126         1968         1559          866           31          610 
TCGA-67-3772 TCGA-67-3774 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
         573          385          141          422          202          186 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7974 TCGA-69-7980 TCGA-69-8255 TCGA-73-4662 
         690          414          184          382          129          912 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-7499 TCGA-75-6214 TCGA-75-7025 
         467          131           40          519         1970         1967 
TCGA-75-7027 TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
        1956         1965         1973         1988         1950         1944 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7156 TCGA-78-7160 TCGA-78-7161 TCGA-78-7166 
        1093         1963         1961          678          215         1934 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
        1937         1965          881         1952          994         1949 
TCGA-78-8655 TCGA-78-8660 TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 TCGA-86-7954 
        1981         1954         1959          630          422         1963 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 TCGA-86-8075 
         508          745           10         1963           24          479 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8585 TCGA-86-8668 TCGA-86-8672 
         482           16           19           35           45           15 
TCGA-86-A456 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 
          10         1940           60          310           79          372 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8497 TCGA-91-8499 TCGA-93-7348 
         842          224           35          174           36          127 
TCGA-93-8067 TCGA-95-7567 TCGA-95-A4VK TCGA-97-7547 TCGA-97-7552 TCGA-97-7937 
         186          568          121         1965         1932          181 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
        1965           87          147           15          148          115 
TCGA-97-A4M7 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-A4AD TCGA-J2-A4AG 
         271           44          170          154          287          238 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T7 
         285          622          353         1946         1967         1954 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TK 
        1957         1980         1951         1970         1970         1971 
TCGA-MP-A5C7 
        1490 

$`DEL PEAK 22(9P21.3) WILD-TYPE`
TCGA-05-4390 TCGA-05-4398 TCGA-05-4410 TCGA-05-4417 TCGA-05-4422 TCGA-05-4425 
        1126         1431         1958          455          365          669 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-5428 TCGA-35-3615 TCGA-35-4123 
         791          791          761          670           14          182 
TCGA-35-5375 TCGA-38-4626 TCGA-38-4630 TCGA-38-7271 TCGA-44-2656 TCGA-44-2666 
         264         1962         1073         1971         1429           97 
TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
         246         1130         1163         1036          190          722 
TCGA-44-5645 TCGA-44-6145 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
         383          328          845          704          658          705 
TCGA-44-6776 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7672 TCGA-44-8119 
        1938          444          592          366          719           99 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-49-4512 
         486          466          287          337          351          157 
TCGA-49-6744 TCGA-49-6761 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5066 
         890          354         2174         2146          455          944 
TCGA-50-5941 TCGA-50-5942 TCGA-53-A4EZ TCGA-55-1595 TCGA-55-6543 TCGA-55-6969 
         567          883          280         1479            2         1239 
TCGA-55-6972 TCGA-55-6983 TCGA-55-7574 TCGA-55-7725 TCGA-55-7727 TCGA-55-7728 
        1475         1826           95           39           34           24 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7994 TCGA-55-7995 
          54           19          197           21           31            5 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8096 TCGA-55-8205 TCGA-55-8299 TCGA-55-8301 
          33           21           47           33          216           44 
TCGA-55-8302 TCGA-55-8508 TCGA-55-8511 TCGA-55-8513 TCGA-55-8514 TCGA-55-8615 
          23           15            9          146          202           15 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48Y TCGA-55-A48Z 
          48           49           66          106           42           29 
TCGA-55-A491 TCGA-55-A494 TCGA-55-A4DF TCGA-62-A46U TCGA-64-1677 TCGA-64-5774 
        1952            5           47         2067          628         1959 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-67-3773 TCGA-67-6215 TCGA-69-7765 
          62         1305          864          427          174          165 
TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-69-A59K 
         230           70           89          100           77          214 
TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4666 TCGA-73-4676 TCGA-73-4677 
          61         1600          711          800          164           38 
TCGA-73-7498 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7158 
         621         1202          760         1948         1957         1963 
TCGA-78-7159 TCGA-78-7162 TCGA-78-7163 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        1221         1940         1950         1972         1949         1944 
TCGA-78-7539 TCGA-78-8648 TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 
         327         1971         1964         1965         1972          824 
TCGA-86-7701 TCGA-86-7714 TCGA-86-7953 TCGA-86-8073 TCGA-86-8076 TCGA-86-8278 
          11         1968          591           13          489          476 
TCGA-86-8281 TCGA-86-8359 TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 
        1955           26           34           18          455          405 
TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6836 TCGA-91-7771 
          30           14           39          323          417          492 
TCGA-91-8496 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-95-7039 TCGA-95-7043 
         197           44          218          297           34            2 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-97-7546 TCGA-97-7553 TCGA-97-7554 
         377          477          476          964         1332          775 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-A4M2 TCGA-99-7458 TCGA-99-8025 
          22          107          182          197          392          427 
TCGA-99-8028 TCGA-J2-8194 TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
         459          114          282          578          435          116 
TCGA-L9-A444 TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4TC TCGA-MP-A4TH TCGA-MP-A4TI 
           6         1951         1954         1944          142         1955 

  DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE 
                            1                             2 
  DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE 
                         2696                          2174 
  DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE 
                        573.0                         398.5 
[1] "1.0 - 2696.0 (573.0)" "2.0 - 2174.0 (398.5)"
[1] "hr=" "1"  
D54V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 22(9P21.3) MUTATED         3       58       68        28        44
  DEL PEAK 22(9P21.3) WILD-TYPE       1       55       63        15        25
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 22(9P21.3) MUTATED           40          6       14
  DEL PEAK 22(9P21.3) WILD-TYPE         27          5        9
D54V3, multiclass
            clus
vv           DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE
  STAGE I                              3                             1
  STAGE IA                            58                            55
  STAGE IB                            68                            63
  STAGE IIA                           28                            15
  STAGE IIB                           44                            25
  STAGE IIIA                          40                            27
  STAGE IIIB                           6                             5
  STAGE IV                            14                             9
[1] 8 2
[1] TRUE
[1] "dimension of 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(9P21.3) MUTATED    78 150  22  10
  DEL PEAK 22(9P21.3) WILD-TYPE  65 109  18   8
D54V4, multiclass
    clus
vv   DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE
  T1                          78                            65
  T2                         150                           109
  T3                          22                            18
  T4                          10                             8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1 N2+N3
  DEL PEAK 22(9P21.3) MUTATED   155  60    42
  DEL PEAK 22(9P21.3) WILD-TYPE 140  25    30
D54V5, multiclass
       clus
vv      DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE
  N0                            155                           140
  N1                             60                            25
  N2+N3                          42                            30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK 22(9P21.3) MUTATED   183  12   0   2  62
  DEL PEAK 22(9P21.3) WILD-TYPE 134   6   1   1  57
D54V6, multiclass
     clus
vv    DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE
  M0                          183                           134
  M1                           12                             6
  M1A                           0                             1
  M1B                           2                             1
  MX                           62                            57
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V7, binary
                               cls
clus                              0   1
  DEL PEAK 22(9P21.3) MUTATED   130 131
  DEL PEAK 22(9P21.3) WILD-TYPE 118  83
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(9P21.3) MUTATED    130  131
  DEL PEAK 22(9P21.3) WILD-TYPE  118   83
        clus
vv       DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE
  FEMALE                         130                           118
  MALE                           131                            83
[1] 2 2
[1] FALSE
D54V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 22(9P21.3) MUTATED                            6
  DEL PEAK 22(9P21.3) WILD-TYPE                          7
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 22(9P21.3) MUTATED                                  53
  DEL PEAK 22(9P21.3) WILD-TYPE                                40
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 22(9P21.3) MUTATED                                                  168
  DEL PEAK 22(9P21.3) WILD-TYPE                                                126
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 22(9P21.3) MUTATED                                            3
  DEL PEAK 22(9P21.3) WILD-TYPE                                          1
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 22(9P21.3) MUTATED                                              12
  DEL PEAK 22(9P21.3) WILD-TYPE                                             7
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 22(9P21.3) MUTATED                                1
  DEL PEAK 22(9P21.3) WILD-TYPE                              1
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 22(9P21.3) MUTATED                                    4
  DEL PEAK 22(9P21.3) WILD-TYPE                                  0
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 22(9P21.3) MUTATED                              1
  DEL PEAK 22(9P21.3) WILD-TYPE                            1
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 22(9P21.3) MUTATED                               7
  DEL PEAK 22(9P21.3) WILD-TYPE                            12
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 22(9P21.3) MUTATED                                 0
  DEL PEAK 22(9P21.3) WILD-TYPE                               1
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 22(9P21.3) MUTATED                                               4
  DEL PEAK 22(9P21.3) WILD-TYPE                                             0
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 22(9P21.3) MUTATED                              2
  DEL PEAK 22(9P21.3) WILD-TYPE                            5
D54V9, multiclass
                                                    clus
vv                                                   DEL PEAK 22(9P21.3) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           53
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         168
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                   3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                               12
  LUNG CLEAR CELL ADENOCARCINOMA                                               1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                           4
  LUNG MUCINOUS ADENOCARCINOMA                                                 1
  LUNG PAPILLARY ADENOCARCINOMA                                                7
  LUNG SIGNET RING ADENOCARCINOMA                                              0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                4
  MUCINOUS (COLLOID) CARCINOMA                                                 2
                                                    clus
vv                                                   DEL PEAK 22(9P21.3) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             40
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           126
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  7
  LUNG CLEAR CELL ADENOCARCINOMA                                                 1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             0
  LUNG MUCINOUS ADENOCARCINOMA                                                   1
  LUNG PAPILLARY ADENOCARCINOMA                                                 12
  LUNG SIGNET RING ADENOCARCINOMA                                                1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                  0
  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"
D54V10, binary
                               cls
clus                              0   1
  DEL PEAK 22(9P21.3) MUTATED    11 250
  DEL PEAK 22(9P21.3) WILD-TYPE  10 191
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(9P21.3) MUTATED     11  250
  DEL PEAK 22(9P21.3) WILD-TYPE   10  191
     clus
vv    DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE
  NO                           11                            10
  YES                         250                           191
[1] 2 2
[1] FALSE
D54V11, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 22(9P21.3) MUTATED   179   5   2  12
  DEL PEAK 22(9P21.3) WILD-TYPE 139   6   2   7
D54V12, multiclass
    clus
vv   DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE
  R0                         179                           139
  R1                           5                             6
  R2                           2                             2
  RX                          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                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 22(9P21.3) MUTATED                                  1     3
  DEL PEAK 22(9P21.3) WILD-TYPE                                0     3
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 22(9P21.3) MUTATED                          12   204
  DEL PEAK 22(9P21.3) WILD-TYPE                        14   158
D54V13, multiclass
                                  clus
vv                                 DEL PEAK 22(9P21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 12
  WHITE                                                    204
                                  clus
vv                                 DEL PEAK 22(9P21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        3
  BLACK OR AFRICAN AMERICAN                                   14
  WHITE                                                      158
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V14, binary
                               cls
clus                              0   1
  DEL PEAK 22(9P21.3) MUTATED     4 180
  DEL PEAK 22(9P21.3) WILD-TYPE   3 152
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(9P21.3) MUTATED      4  180
  DEL PEAK 22(9P21.3) WILD-TYPE    3  152
                        clus
vv                       DEL PEAK 22(9P21.3) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         180
                        clus
vv                       DEL PEAK 22(9P21.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           152
[1] 2 2
[1] FALSE

Clustering(55) Variable = DEL PEAK 23(9Q21.11) MUTATION ANALYSIS
D55V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 23(9Q21.11) MUTATED   156  46
  DEL PEAK 23(9Q21.11) WILD-TYPE 165  36
  DEL PEAK 23(9Q21.11) MUTATED DEL PEAK 23(9Q21.11) WILD-TYPE 
                           202                            201 
  DEL PEAK 23(9Q21.11) MUTATED DEL PEAK 23(9Q21.11) WILD-TYPE 
                            46                             36 
$`DEL PEAK 23(9Q21.11) MUTATED`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4389 TCGA-05-4390 TCGA-05-4415 TCGA-05-4420 
        1523          607         1369         1126         1997          912 
TCGA-05-4424 TCGA-05-4432 TCGA-05-5420 TCGA-05-5425 TCGA-05-5715 TCGA-35-4122 
         913          761          457          882           62          225 
TCGA-35-5375 TCGA-38-4625 TCGA-38-4627 TCGA-38-4628 TCGA-38-4630 TCGA-38-4631 
         264         1952         1147         1492         1073          354 
TCGA-38-4632 TCGA-38-6178 TCGA-38-A44F TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 
        1357          448          133          400         1367          741 
TCGA-44-2662 TCGA-44-3918 TCGA-44-5644 TCGA-44-6144 TCGA-44-6147 TCGA-44-6774 
        1280         1036          863          723          845          658 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 
        1942         1864         1978          592          218          557 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
        1970          882          535          385           99          260 
TCGA-44-A479 TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
         486          415           76         1081         1421          428 
TCGA-49-4506 TCGA-49-4510 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-50-5055 
         999          896         1700          445          369          785 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
        1499          246          267         1091         2370          653 
TCGA-50-5944 TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 TCGA-53-7624 TCGA-53-7813 
         764         1015          255          105         1986          424 
TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6642 TCGA-55-6712 
         701         1178         1375           87          993           24 
TCGA-55-6971 TCGA-55-6980 TCGA-55-6985 TCGA-55-6986 TCGA-55-7283 TCGA-55-7570 
          25           67         1233         2151           35            6 
TCGA-55-7573 TCGA-55-7724 TCGA-55-7726 TCGA-55-7907 TCGA-55-7911 TCGA-55-7914 
           4         1958           39           16           21            3 
TCGA-55-7994 TCGA-55-8085 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8094 
          31           33          100            6           43            4 
TCGA-55-8097 TCGA-55-8206 TCGA-55-8207 TCGA-55-8301 TCGA-55-8505 TCGA-55-8507 
          15           46           66           44           29            8 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
          15          228            3          202          536           15 
TCGA-55-A48X TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
          33            1           28            5           47          162 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46V TCGA-64-1676 
        1289         1970         2696         1445         2199         1728 
TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5779 TCGA-67-3770 
        1189         1686         1968         1959          864           31 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3774 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
         610          573          385          141          422          202 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7973 TCGA-69-7974 TCGA-69-7980 TCGA-69-8255 
         186          690          230          184          382          129 
TCGA-69-A59K TCGA-73-4659 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-75-7025 
         214          711          467          131           40         1967 
TCGA-75-7027 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
        1956         1973         1988         1950         1944         1093 
TCGA-78-7150 TCGA-78-7161 TCGA-78-7167 TCGA-78-7536 TCGA-78-7633 TCGA-78-8640 
        1963          215         1937         1949          994         1949 
TCGA-78-8660 TCGA-80-5608 TCGA-86-7711 TCGA-86-7713 TCGA-86-7954 TCGA-86-7955 
        1954         1972          630          422         1963          508 
TCGA-86-8055 TCGA-86-8075 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8585 
          10          479          482           16           19           35 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8672 TCGA-86-A456 TCGA-91-6829 TCGA-91-6830 
          45           34           15           10         1940           60 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-7771 
         310           79          372          842          224          492 
TCGA-91-8499 TCGA-93-7348 TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-95-7948 
          36          127           34            2          568          476 
TCGA-97-7937 TCGA-97-8174 TCGA-97-8177 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M7 
         181         1965          147          148          115          271 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-A4AD TCGA-J2-A4AG TCGA-MN-A4N1 
          44          170          154          287          238          285 
TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
         622         1946         1967         1954         1957         1980 
TCGA-MP-A4TA TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A5C7 
        1951         1970         1970         1490 

$`DEL PEAK 23(9Q21.11) WILD-TYPE`
TCGA-05-4384 TCGA-05-4396 TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 
         426         1947         1431          578          610         1958 
TCGA-05-4417 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 
         455          365          669          791          791          761 
TCGA-05-4433 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 TCGA-35-3615 TCGA-35-4123 
         730          151          670           30           14          182 
TCGA-38-4626 TCGA-38-4629 TCGA-38-7271 TCGA-44-2655 TCGA-44-2656 TCGA-44-2665 
        1962          864         1971         1324         1429         1301 
TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 
          97          246         1130         1163          190          722 
TCGA-44-5643 TCGA-44-5645 TCGA-44-6145 TCGA-44-6146 TCGA-44-6148 TCGA-44-6775 
        1013          383          328          302          704          705 
TCGA-44-6776 TCGA-44-7659 TCGA-44-7661 TCGA-44-7672 TCGA-44-A47A TCGA-44-A47B 
        1938          444          366          719          466          287 
TCGA-44-A47F TCGA-44-A47G TCGA-49-4486 TCGA-49-4507 TCGA-49-4512 TCGA-49-6744 
         337          351         1932          268          157          890 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5066 
         522          354         2174         2146          455          944 
TCGA-50-5930 TCGA-50-5941 TCGA-50-5942 TCGA-50-5946 TCGA-53-7626 TCGA-53-A4EZ 
         282          567          883          686         1971          280 
TCGA-55-1595 TCGA-55-6543 TCGA-55-6969 TCGA-55-6972 TCGA-55-6983 TCGA-55-6987 
        1479            2         1239         1475         1826         1170 
TCGA-55-7281 TCGA-55-7284 TCGA-55-7574 TCGA-55-7576 TCGA-55-7725 TCGA-55-7727 
          18          121           95           40           39           34 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7910 TCGA-55-7995 TCGA-55-8087 
          24           54           19          197            5           21 
TCGA-55-8092 TCGA-55-8096 TCGA-55-8205 TCGA-55-8299 TCGA-55-8302 TCGA-55-8506 
          26           47           33          216           23           11 
TCGA-55-8511 TCGA-55-8513 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
           9          146           48           49           66          106 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-62-8395 TCGA-62-A46U 
          42           29           48         1952         1216         2067 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1677 TCGA-64-1680 TCGA-64-5775 TCGA-64-5778 
        1246          910          628         1126           62         1305 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3773 TCGA-67-6215 TCGA-69-7764 TCGA-69-7765 
        1559          866          427          174          414          165 
TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-71-6725 TCGA-73-4658 
          70           89          100           77           61         1600 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
         912          800          164           38          621          519 
TCGA-75-6214 TCGA-75-7031 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
        1970         1965         1202          760         1948         1957 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7162 TCGA-78-7163 
        1961         1963         1221          678         1940         1950 
TCGA-78-7166 TCGA-78-7220 TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
        1934         1965         1972         1944          327          881 
TCGA-78-7542 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5607 TCGA-83-5908 
        1952         1971         1981         1964         1965          824 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7714 TCGA-86-7953 TCGA-86-8054 TCGA-86-8056 
        1959           11         1968          591          745         1963 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8076 TCGA-86-8278 TCGA-86-8281 TCGA-86-8359 
          13           24          489          476         1955           26 
TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 
          18          455          405           30           14           39 
TCGA-91-6828 TCGA-91-6836 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC 
         323          417           35          197          174           44 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-8067 TCGA-95-7944 TCGA-95-7947 TCGA-95-A4VK 
         218          297          186          377          477          121 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7941 
         964         1965         1932         1332          775           22 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 TCGA-97-8179 TCGA-97-A4M2 TCGA-99-7458 
         107          182           87           15          197          392 
TCGA-99-8025 TCGA-99-8028 TCGA-J2-8194 TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 
         427          459          114          282          578          435 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N5 TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4TC 
         116            6          353         1951         1954         1944 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
         142         1955         1971 

  DEL PEAK 23(9Q21.11) MUTATED DEL PEAK 23(9Q21.11) WILD-TYPE 
                             1                              2 
  DEL PEAK 23(9Q21.11) MUTATED DEL PEAK 23(9Q21.11) WILD-TYPE 
                          2696                           2174 
  DEL PEAK 23(9Q21.11) MUTATED DEL PEAK 23(9Q21.11) WILD-TYPE 
                         477.5                          455.0 
[1] "1.0 - 2696.0 (477.5)" "2.0 - 2174.0 (455.0)"
[1] "hr=" "1.1"
D55V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 23(9Q21.11) MUTATED         3       56       67        24        34
  DEL PEAK 23(9Q21.11) WILD-TYPE       1       57       64        19        35
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 23(9Q21.11) MUTATED           35          4       10
  DEL PEAK 23(9Q21.11) WILD-TYPE         32          7       13
D55V3, multiclass
            clus
vv           DEL PEAK 23(9Q21.11) MUTATED DEL PEAK 23(9Q21.11) WILD-TYPE
  STAGE I                               3                              1
  STAGE IA                             56                             57
  STAGE IB                             67                             64
  STAGE IIA                            24                             19
  STAGE IIB                            34                             35
  STAGE IIIA                           35                             32
  STAGE IIIB                            4                              7
  STAGE IV                             10                             13
[1] 8 2
[1] TRUE
[1] "dimension of 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(9Q21.11) MUTATED    73 133  20   5
  DEL PEAK 23(9Q21.11) WILD-TYPE  70 126  20  13
D55V4, multiclass
    clus
vv   DEL PEAK 23(9Q21.11) MUTATED DEL PEAK 23(9Q21.11) WILD-TYPE
  T1                           73                             70
  T2                          133                            126
  T3                           20                             20
  T4                            5                             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 23(9Q21.11) MUTATED   147  46    35
  DEL PEAK 23(9Q21.11) WILD-TYPE 148  39    37
D55V5, multiclass
       clus
vv      DEL PEAK 23(9Q21.11) MUTATED DEL PEAK 23(9Q21.11) WILD-TYPE
  N0                             147                            148
  N1                              46                             39
  N2+N3                           35                             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"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 23(9Q21.11) MUTATED   157   8   0   2  64
  DEL PEAK 23(9Q21.11) WILD-TYPE 160  10   1   1  55
D55V6, multiclass
     clus
vv    DEL PEAK 23(9Q21.11) MUTATED DEL PEAK 23(9Q21.11) WILD-TYPE
  M0                           157                            160
  M1                             8                             10
  M1A                            0                              1
  M1B                            2                              1
  MX                            64                             55
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V7, binary
                                cls
clus                               0   1
  DEL PEAK 23(9Q21.11) MUTATED   123 110
  DEL PEAK 23(9Q21.11) WILD-TYPE 125 104
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(9Q21.11) MUTATED    123  110
  DEL PEAK 23(9Q21.11) WILD-TYPE  125  104
        clus
vv       DEL PEAK 23(9Q21.11) MUTATED DEL PEAK 23(9Q21.11) WILD-TYPE
  FEMALE                          123                            125
  MALE                            110                            104
[1] 2 2
[1] FALSE
D55V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 23(9Q21.11) MUTATED                            6
  DEL PEAK 23(9Q21.11) WILD-TYPE                          7
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 23(9Q21.11) MUTATED                                  38
  DEL PEAK 23(9Q21.11) WILD-TYPE                                55
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 23(9Q21.11) MUTATED                                                  158
  DEL PEAK 23(9Q21.11) WILD-TYPE                                                136
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 23(9Q21.11) MUTATED                                            1
  DEL PEAK 23(9Q21.11) WILD-TYPE                                          3
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 23(9Q21.11) MUTATED                                              10
  DEL PEAK 23(9Q21.11) WILD-TYPE                                             9
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 23(9Q21.11) MUTATED                                1
  DEL PEAK 23(9Q21.11) WILD-TYPE                              1
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 23(9Q21.11) MUTATED                                    4
  DEL PEAK 23(9Q21.11) WILD-TYPE                                  0
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 23(9Q21.11) MUTATED                              0
  DEL PEAK 23(9Q21.11) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 23(9Q21.11) MUTATED                               8
  DEL PEAK 23(9Q21.11) WILD-TYPE                            11
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 23(9Q21.11) MUTATED                                 1
  DEL PEAK 23(9Q21.11) WILD-TYPE                               0
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 23(9Q21.11) MUTATED                                               3
  DEL PEAK 23(9Q21.11) WILD-TYPE                                             1
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 23(9Q21.11) MUTATED                              3
  DEL PEAK 23(9Q21.11) WILD-TYPE                            4
D55V9, multiclass
                                                    clus
vv                                                   DEL PEAK 23(9Q21.11) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            38
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          158
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                10
  LUNG CLEAR CELL ADENOCARCINOMA                                                1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            4
  LUNG MUCINOUS ADENOCARCINOMA                                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                                 8
  LUNG SIGNET RING ADENOCARCINOMA                                               1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 3
  MUCINOUS (COLLOID) CARCINOMA                                                  3
                                                    clus
vv                                                   DEL PEAK 23(9Q21.11) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              55
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            136
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                   9
  LUNG CLEAR CELL ADENOCARCINOMA                                                  1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              0
  LUNG MUCINOUS ADENOCARCINOMA                                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                                  11
  LUNG SIGNET RING ADENOCARCINOMA                                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                   1
  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"
D55V10, binary
                                cls
clus                               0   1
  DEL PEAK 23(9Q21.11) MUTATED     8 225
  DEL PEAK 23(9Q21.11) WILD-TYPE  13 216
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(9Q21.11) MUTATED      8  225
  DEL PEAK 23(9Q21.11) WILD-TYPE   13  216
     clus
vv    DEL PEAK 23(9Q21.11) MUTATED DEL PEAK 23(9Q21.11) WILD-TYPE
  NO                             8                             13
  YES                          225                            216
[1] 2 2
[1] FALSE
D55V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 23(9Q21.11) MUTATED   159   6   2   8
  DEL PEAK 23(9Q21.11) WILD-TYPE 159   5   2  11
D55V12, multiclass
    clus
vv   DEL PEAK 23(9Q21.11) MUTATED DEL PEAK 23(9Q21.11) WILD-TYPE
  R0                          159                            159
  R1                            6                              5
  R2                            2                              2
  RX                            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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 23(9Q21.11) MUTATED                                  1     2
  DEL PEAK 23(9Q21.11) WILD-TYPE                                0     4
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 23(9Q21.11) MUTATED                          14   186
  DEL PEAK 23(9Q21.11) WILD-TYPE                        12   176
D55V13, multiclass
                                  clus
vv                                 DEL PEAK 23(9Q21.11) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  14
  WHITE                                                     186
                                  clus
vv                                 DEL PEAK 23(9Q21.11) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    12
  WHITE                                                       176
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V14, binary
                                cls
clus                               0   1
  DEL PEAK 23(9Q21.11) MUTATED     4 171
  DEL PEAK 23(9Q21.11) WILD-TYPE   3 161
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(9Q21.11) MUTATED      4  171
  DEL PEAK 23(9Q21.11) WILD-TYPE    3  161
                        clus
vv                       DEL PEAK 23(9Q21.11) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          171
                        clus
vv                       DEL PEAK 23(9Q21.11) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            161
[1] 2 2
[1] FALSE

Clustering(56) Variable = DEL PEAK 24(10P15.3) MUTATION ANALYSIS
D56V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 24(10P15.3) MUTATED    70  28
  DEL PEAK 24(10P15.3) WILD-TYPE 251  54
  DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE 
                            98                            305 
  DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE 
                            28                             54 
$`DEL PEAK 24(10P15.3) MUTATED`
TCGA-05-5429 TCGA-05-5715 TCGA-38-4627 TCGA-38-4628 TCGA-38-4630 TCGA-38-4631 
          30           62         1147         1492         1073          354 
TCGA-38-6178 TCGA-44-2657 TCGA-44-2662 TCGA-44-3398 TCGA-44-3919 TCGA-44-5644 
         448          400         1280         1163          190          863 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6779 TCGA-44-7660 TCGA-44-7669 TCGA-44-7670 
         705         1938         1978          592         1970          882 
TCGA-44-8119 TCGA-44-A4SU TCGA-49-4501 TCGA-49-4505 TCGA-49-4510 TCGA-49-4512 
          99           76         1421          428          896          157 
TCGA-49-6742 TCGA-50-5931 TCGA-50-6597 TCGA-53-7624 TCGA-53-7626 TCGA-55-6642 
         445          267         1015         1986         1971          993 
TCGA-55-6980 TCGA-55-6986 TCGA-55-7281 TCGA-55-7283 TCGA-55-7726 TCGA-55-7994 
          67         2151           18           35           39           31 
TCGA-55-8091 TCGA-55-8094 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8514 
          43            4           29           11            8          202 
TCGA-55-8614 TCGA-55-A48X TCGA-55-A490 TCGA-55-A4DF TCGA-62-8402 TCGA-64-1679 
         536           33           48           47         1445         1686 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5779 TCGA-67-3771 TCGA-67-3772 
        1968         1959           62          864          610          573 
TCGA-69-7973 TCGA-69-7974 TCGA-69-A59K TCGA-73-4659 TCGA-73-4666 TCGA-73-4675 
         230          184          214          711          800           40 
TCGA-78-7150 TCGA-78-7155 TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 TCGA-78-7540 
        1963         1957         1937         1965         1949          881 
TCGA-78-8640 TCGA-78-8655 TCGA-83-5908 TCGA-86-6851 TCGA-86-7954 TCGA-86-8054 
        1949         1981          824         1959         1963          745 
TCGA-86-8055 TCGA-86-8074 TCGA-86-8075 TCGA-86-8278 TCGA-86-8280 TCGA-86-8359 
          10           24          479          476           16           26 
TCGA-86-8669 TCGA-91-6828 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6848 
          34          323          310           79          372          224 
TCGA-93-7348 TCGA-95-7043 TCGA-95-7947 TCGA-95-7948 TCGA-97-7546 TCGA-97-8547 
         127            2          477          476          964          148 
TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-A4AD TCGA-J2-A4AG TCGA-MP-A4T2 TCGA-MP-A4T9 
         271          154          287          238         1951         1980 
TCGA-MP-A4TK TCGA-MP-A5C7 
        1971         1490 

$`DEL PEAK 24(10P15.3) WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 
        1523          607          426         1369         1126         1947 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 
        1431          578          610         1958         1997          455 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 
         912          365          913          669          791          791 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 
         761          761          730          457          151          882 
TCGA-05-5428 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
         670           14          225          182          264         1952 
TCGA-38-4626 TCGA-38-4629 TCGA-38-4632 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 
        1962          864         1357         1971          133         1324 
TCGA-44-2656 TCGA-44-2659 TCGA-44-2661 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
        1429         1367          741         1301           97          246 
TCGA-44-3396 TCGA-44-3918 TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 
        1130         1036          722         1013          383          723 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6777 
         328          302          845          704          658         1942 
TCGA-44-6778 TCGA-44-7659 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7671 
        1864          444          366          218          557          535 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
         719          385          260          486          466          287 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4494 TCGA-49-4506 
         337          351          415         1932         1081          999 
TCGA-49-4507 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
         268         1700          369          890          522          354 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
        2174         2146          455          785          944         1499 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 
         246          282         1091         2370          653          567 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-7109 TCGA-50-8460 TCGA-53-7813 
         883          764          686          255          105          424 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 
         280          701         1178         1479         1375           87 
TCGA-55-6543 TCGA-55-6712 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6983 
           2           24         1239           25         1475         1826 
TCGA-55-6985 TCGA-55-6987 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        1233         1170          121            6            4           95 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
          40         1958           39           34           24           54 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 
          19           16          197           21            3            5 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8092 TCGA-55-8096 
          33           21          100            6           26           47 
TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 
          15           33           46           66          216           44 
TCGA-55-8302 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
          23           15          228            9            3          146 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48Y 
          15           48           49           66          106           42 
TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG 
          29         1952            1           28            5          162 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-A46U TCGA-62-A46V 
        1216         1289         1970         2696         2067         2199 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-1680 
        1246          910         1728          628         1189         1126 
TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3773 TCGA-67-3774 
        1305         1559          866           31          427          385 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
         174          141          422          202          186          690 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
         414          165           70           89          382          100 
TCGA-69-8254 TCGA-69-8255 TCGA-71-6725 TCGA-73-4658 TCGA-73-4662 TCGA-73-4668 
          77          129           61         1600          912          467 
TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-75-6214 
         131          164           38          621          519         1970 
TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
        1967         1956         1965         1973         1988         1950 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 
        1944         1093         1202          760         1948         1961 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        1963         1221          678          215         1940         1950 
TCGA-78-7166 TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 TCGA-78-7542 TCGA-78-7633 
        1934         1972         1944          327         1952          994 
TCGA-78-8648 TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 TCGA-86-7701 
        1971         1954         1964         1965         1972           11 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7955 TCGA-86-8056 
         630          422         1968          591          508         1963 
TCGA-86-8073 TCGA-86-8076 TCGA-86-8279 TCGA-86-8281 TCGA-86-8358 TCGA-86-8585 
          13          489          482         1955           19           35 
TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
          45           18           15          455          405           10 
TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6836 
          30           14           39         1940           60          417 
TCGA-91-6847 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
         842           35          492          197          174           36 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-8067 TCGA-95-7039 TCGA-95-7567 
          44          218          297          186           34          568 
TCGA-95-7944 TCGA-95-A4VK TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
         377          121         1965         1932         1332          775 
TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
         181           22          107          182         1965           87 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M2 TCGA-99-7458 TCGA-99-8025 
         147           15          115          197          392          427 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8194 TCGA-J2-A4AE TCGA-L4-A4E5 
         459           44          170          114          282          578 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
         435          116            6          285          622          353 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4TA 
        1946         1967         1954         1954         1957         1951 
TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        1944         1970         1970          142         1955 

  DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE 
                             2                              1 
  DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE 
                          2151                           2696 
  DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE 
                           476                            459 
[1] "2.0 - 2151.0 (476.0)" "1.0 - 2696.0 (459.0)"
[1] "hr=" "1.5"
D56V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 24(10P15.3) MUTATED         0       27       28        13        15
  DEL PEAK 24(10P15.3) WILD-TYPE       4       86      103        30        54
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 24(10P15.3) MUTATED           24          1        6
  DEL PEAK 24(10P15.3) WILD-TYPE         43         10       17
D56V3, multiclass
            clus
vv           DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE
  STAGE I                               0                              4
  STAGE IA                             27                             86
  STAGE IB                             28                            103
  STAGE IIA                            13                             30
  STAGE IIB                            15                             54
  STAGE IIIA                           24                             43
  STAGE IIIB                            1                             10
  STAGE IV                              6                             17
[1] 8 2
[1] TRUE
[1] "dimension of 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(10P15.3) MUTATED    40  61  10   2
  DEL PEAK 24(10P15.3) WILD-TYPE 103 198  30  16
D56V4, multiclass
    clus
vv   DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE
  T1                           40                            103
  T2                           61                            198
  T3                           10                             30
  T4                            2                             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 24(10P15.3) MUTATED    66  23    23
  DEL PEAK 24(10P15.3) WILD-TYPE 229  62    49
D56V5, multiclass
       clus
vv      DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE
  N0                              66                            229
  N1                              23                             62
  N2+N3                           23                             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"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 24(10P15.3) MUTATED    73   5   0   1  33
  DEL PEAK 24(10P15.3) WILD-TYPE 244  13   1   2  86
D56V6, multiclass
     clus
vv    DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE
  M0                            73                            244
  M1                             5                             13
  M1A                            0                              1
  M1B                            1                              2
  MX                            33                             86
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V7, binary
                                cls
clus                               0   1
  DEL PEAK 24(10P15.3) MUTATED    76  38
  DEL PEAK 24(10P15.3) WILD-TYPE 172 176
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(10P15.3) MUTATED     76   38
  DEL PEAK 24(10P15.3) WILD-TYPE  172  176
        clus
vv       DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE
  FEMALE                           76                            172
  MALE                             38                            176
[1] 2 2
[1] FALSE
D56V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 24(10P15.3) MUTATED                            3
  DEL PEAK 24(10P15.3) WILD-TYPE                         10
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 24(10P15.3) MUTATED                                  16
  DEL PEAK 24(10P15.3) WILD-TYPE                                77
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 24(10P15.3) MUTATED                                                   83
  DEL PEAK 24(10P15.3) WILD-TYPE                                                211
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 24(10P15.3) MUTATED                                            1
  DEL PEAK 24(10P15.3) WILD-TYPE                                          3
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 24(10P15.3) MUTATED                                               5
  DEL PEAK 24(10P15.3) WILD-TYPE                                            14
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 24(10P15.3) MUTATED                                0
  DEL PEAK 24(10P15.3) WILD-TYPE                              2
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 24(10P15.3) MUTATED                                    2
  DEL PEAK 24(10P15.3) WILD-TYPE                                  2
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 24(10P15.3) MUTATED                              0
  DEL PEAK 24(10P15.3) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 24(10P15.3) MUTATED                               2
  DEL PEAK 24(10P15.3) WILD-TYPE                            17
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 24(10P15.3) MUTATED                                 1
  DEL PEAK 24(10P15.3) WILD-TYPE                               0
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 24(10P15.3) MUTATED                                               0
  DEL PEAK 24(10P15.3) WILD-TYPE                                             4
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 24(10P15.3) MUTATED                              1
  DEL PEAK 24(10P15.3) WILD-TYPE                            6
D56V9, multiclass
                                                    clus
vv                                                   DEL PEAK 24(10P15.3) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            16
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           83
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 5
  LUNG CLEAR CELL ADENOCARCINOMA                                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            2
  LUNG MUCINOUS ADENOCARCINOMA                                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                                 2
  LUNG SIGNET RING ADENOCARCINOMA                                               1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 0
  MUCINOUS (COLLOID) CARCINOMA                                                  1
                                                    clus
vv                                                   DEL PEAK 24(10P15.3) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              77
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            211
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  14
  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                                   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"
D56V10, binary
                                cls
clus                               0   1
  DEL PEAK 24(10P15.3) MUTATED     5 109
  DEL PEAK 24(10P15.3) WILD-TYPE  16 332
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(10P15.3) MUTATED      5  109
  DEL PEAK 24(10P15.3) WILD-TYPE   16  332
     clus
vv    DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE
  NO                             5                             16
  YES                          109                            332
[1] 2 2
[1] FALSE
D56V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 24(10P15.3) MUTATED    83   3   1   4
  DEL PEAK 24(10P15.3) WILD-TYPE 235   8   3  15
D56V12, multiclass
    clus
vv   DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE
  R0                           83                            235
  R1                            3                              8
  R2                            1                              3
  RX                            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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 24(10P15.3) MUTATED                                  0     0
  DEL PEAK 24(10P15.3) WILD-TYPE                                1     6
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 24(10P15.3) MUTATED                           6    97
  DEL PEAK 24(10P15.3) WILD-TYPE                        20   265
D56V13, multiclass
                                  clus
vv                                 DEL PEAK 24(10P15.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   6
  WHITE                                                      97
                                  clus
vv                                 DEL PEAK 24(10P15.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         6
  BLACK OR AFRICAN AMERICAN                                    20
  WHITE                                                       265
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V14, binary
                                cls
clus                               0   1
  DEL PEAK 24(10P15.3) MUTATED     3  87
  DEL PEAK 24(10P15.3) WILD-TYPE   4 245
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(10P15.3) MUTATED      3   87
  DEL PEAK 24(10P15.3) WILD-TYPE    4  245
                        clus
vv                       DEL PEAK 24(10P15.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           87
                        clus
vv                       DEL PEAK 24(10P15.3) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            245
[1] 2 2
[1] FALSE

Clustering(57) Variable = DEL PEAK 25(10Q26.3) MUTATION ANALYSIS
D57V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 25(10Q26.3) MUTATED    92  25
  DEL PEAK 25(10Q26.3) WILD-TYPE 229  57
  DEL PEAK 25(10Q26.3) MUTATED DEL PEAK 25(10Q26.3) WILD-TYPE 
                           117                            286 
  DEL PEAK 25(10Q26.3) MUTATED DEL PEAK 25(10Q26.3) WILD-TYPE 
                            25                             57 
$`DEL PEAK 25(10Q26.3) MUTATED`
TCGA-05-4389 TCGA-05-4390 TCGA-05-4398 TCGA-05-4410 TCGA-05-4420 TCGA-05-4424 
        1369         1126         1431         1958          912          913 
TCGA-05-4430 TCGA-05-5429 TCGA-05-5715 TCGA-38-4628 TCGA-38-4631 TCGA-44-2657 
         761           30           62         1492          354          400 
TCGA-44-2662 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-6775 
        1280         1130         1163         1036          190          705 
TCGA-44-7660 TCGA-44-7662 TCGA-44-7669 TCGA-44-7670 TCGA-44-A4SU TCGA-49-4494 
         592          218         1970          882           76         1081 
TCGA-49-4505 TCGA-49-6742 TCGA-50-5049 TCGA-50-5931 TCGA-50-5941 TCGA-50-5944 
         428          445         2146          267          567          764 
TCGA-50-6597 TCGA-50-7109 TCGA-55-1592 TCGA-55-5899 TCGA-55-6971 TCGA-55-6980 
        1015          255          701           87           25           67 
TCGA-55-6986 TCGA-55-7281 TCGA-55-7994 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
        2151           18           31           43           26            4 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8505 TCGA-55-8508 TCGA-55-8514 TCGA-55-8614 
          46           66           29           15          202          536 
TCGA-55-A48X TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8402 TCGA-62-A46U TCGA-64-1676 
          33           47          162         1445         2067         1728 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 TCGA-67-3770 TCGA-67-3772 
        1686         1968         1959         1305           31          573 
TCGA-69-7978 TCGA-69-7979 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-73-4666 
          70           89          129          214           61          800 
TCGA-73-4668 TCGA-75-7031 TCGA-78-7147 TCGA-78-7154 TCGA-78-7155 TCGA-78-7220 
         467         1965         1950         1948         1957         1965 
TCGA-78-7535 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8655 TCGA-78-8660 
        1972          881         1952         1949         1981         1954 
TCGA-83-5908 TCGA-86-6851 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 TCGA-86-8074 
         824         1959         1963          508           10           24 
TCGA-86-8075 TCGA-86-8278 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8669 
         479          476           16           19           26           34 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6848 
         323         1940           79          417          372          224 
TCGA-91-8499 TCGA-93-7348 TCGA-95-7043 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
          36          127            2          377          477          476 
TCGA-97-7546 TCGA-97-7554 TCGA-97-8175 TCGA-97-8547 TCGA-97-A4M7 TCGA-J2-8192 
         964          775           87          148          271          154 
TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L9-A443 TCGA-MN-A4N5 TCGA-MP-A4T2 TCGA-MP-A4T4 
         287          238          116          353         1951         1954 
TCGA-MP-A4T9 TCGA-MP-A4TF TCGA-MP-A4TK 
        1980         1970         1971 

$`DEL PEAK 25(10Q26.3) WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4403 TCGA-05-4405 
        1523          607          426         1947          578          610 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 
        1997          455          365          669          791          791 
TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
         761          730          457          151          882          670 
TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
          14          225          182          264         1952         1962 
TCGA-38-4627 TCGA-38-4629 TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
        1147          864         1073         1357          448         1971 
TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2659 TCGA-44-2661 TCGA-44-2665 
         133         1324         1429         1367          741         1301 
TCGA-44-2666 TCGA-44-2668 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 
          97          246          722         1013          863          383 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
         723          328          302          845          704          658 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7661 
        1938         1942         1864         1978          444          366 
TCGA-44-7667 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
         557          535          719          385           99          260 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
         486          466          287          337          351          415 
TCGA-49-4486 TCGA-49-4501 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
        1932         1421          999          268          896          157 
TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-50-5045 
        1700          369          890          522          354         2174 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
         455          785          944         1499          246          282 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5942 TCGA-50-5946 TCGA-50-8460 
        1091         2370          653          883          686          105 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1595 
        1986         1971          424          280         1178         1479 
TCGA-55-1596 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6972 
        1375            2          993           24         1239         1475 
TCGA-55-6983 TCGA-55-6985 TCGA-55-6987 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
        1826         1233         1170           35          121            6 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
           4           95           40         1958           39           39 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
          34           24           54           19           16          197 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
          21            3            5           33           21          100 
TCGA-55-8090 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8299 TCGA-55-8301 
           6           47           15           33          216           44 
TCGA-55-8302 TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
          23           11            8          228            9            3 
TCGA-55-8513 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
         146           15           48           49           66          106 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
          42           29           48         1952            1           28 
TCGA-55-A494 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-A46V 
           5         1216         1289         1970         2696         2199 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1677 TCGA-64-1678 TCGA-64-1680 TCGA-64-5775 
        1246          910          628         1189         1126           62 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3773 TCGA-67-3774 
         864         1559          866          610          427          385 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
         174          141          422          202          186          690 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7980 TCGA-69-8253 
         414          165          230          184          382          100 
TCGA-69-8254 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4670 TCGA-73-4675 
          77         1600          711          912          131           40 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-75-6214 TCGA-75-7025 
         164           38          621          519         1970         1967 
TCGA-75-7027 TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
        1956         1973         1988         1944         1093         1963 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
        1202          760         1961         1963         1221          678 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7536 
         215         1940         1950         1934         1937         1949 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7633 TCGA-78-8648 TCGA-78-8662 TCGA-80-5607 
        1944          327          994         1971         1964         1965 
TCGA-80-5608 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        1972           11          630          422         1968          591 
TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 TCGA-86-8076 TCGA-86-8279 TCGA-86-8281 
         745         1963           13          489          482         1955 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
          35           45           18           15          455          405 
TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6830 TCGA-91-6831 
          10           30           14           39           60          310 
TCGA-91-6847 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC 
         842           35          492          197          174           44 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-8067 TCGA-95-7039 TCGA-95-7567 TCGA-95-A4VK 
         218          297          186           34          568          121 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 
        1965         1932         1332          181           22          107 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M2 
         182         1965          147           15          115          197 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8194 
         392          427          459           44          170          114 
TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
         282          578          435            6          285          622 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC 
        1946         1967         1954         1957         1951         1944 
TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A5C7 
        1970          142         1955         1490 

  DEL PEAK 25(10Q26.3) MUTATED DEL PEAK 25(10Q26.3) WILD-TYPE 
                             2                              1 
  DEL PEAK 25(10Q26.3) MUTATED DEL PEAK 25(10Q26.3) WILD-TYPE 
                          2151                           2696 
  DEL PEAK 25(10Q26.3) MUTATED DEL PEAK 25(10Q26.3) WILD-TYPE 
                           476                            456 
[1] "2.0 - 2151.0 (476.0)" "1.0 - 2696.0 (456.0)"
[1] "hr=" "1.1"
D57V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 25(10Q26.3) MUTATED         1       39       40        12        21
  DEL PEAK 25(10Q26.3) WILD-TYPE       3       74       91        31        48
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 25(10Q26.3) MUTATED           17          2        5
  DEL PEAK 25(10Q26.3) WILD-TYPE         50          9       18
D57V3, multiclass
            clus
vv           DEL PEAK 25(10Q26.3) MUTATED DEL PEAK 25(10Q26.3) WILD-TYPE
  STAGE I                               1                              3
  STAGE IA                             39                             74
  STAGE IB                             40                             91
  STAGE IIA                            12                             31
  STAGE IIB                            21                             48
  STAGE IIIA                           17                             50
  STAGE IIIB                            2                              9
  STAGE IV                              5                             18
[1] 8 2
[1] TRUE
[1] "dimension of 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(10Q26.3) MUTATED    48  77   9   2
  DEL PEAK 25(10Q26.3) WILD-TYPE  95 182  31  16
D57V4, multiclass
    clus
vv   DEL PEAK 25(10Q26.3) MUTATED DEL PEAK 25(10Q26.3) WILD-TYPE
  T1                           48                             95
  T2                           77                            182
  T3                            9                             31
  T4                            2                             16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1 N2+N3
  DEL PEAK 25(10Q26.3) MUTATED    88  27    20
  DEL PEAK 25(10Q26.3) WILD-TYPE 207  58    52
D57V5, multiclass
       clus
vv      DEL PEAK 25(10Q26.3) MUTATED DEL PEAK 25(10Q26.3) WILD-TYPE
  N0                              88                            207
  N1                              27                             58
  N2+N3                           20                             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"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 25(10Q26.3) MUTATED    98   4   0   1  34
  DEL PEAK 25(10Q26.3) WILD-TYPE 219  14   1   2  85
D57V6, multiclass
     clus
vv    DEL PEAK 25(10Q26.3) MUTATED DEL PEAK 25(10Q26.3) WILD-TYPE
  M0                            98                            219
  M1                             4                             14
  M1A                            0                              1
  M1B                            1                              2
  MX                            34                             85
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V7, binary
                                cls
clus                               0   1
  DEL PEAK 25(10Q26.3) MUTATED    80  57
  DEL PEAK 25(10Q26.3) WILD-TYPE 168 157
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(10Q26.3) MUTATED     80   57
  DEL PEAK 25(10Q26.3) WILD-TYPE  168  157
        clus
vv       DEL PEAK 25(10Q26.3) MUTATED DEL PEAK 25(10Q26.3) WILD-TYPE
  FEMALE                           80                            168
  MALE                             57                            157
[1] 2 2
[1] FALSE
D57V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 25(10Q26.3) MUTATED                            4
  DEL PEAK 25(10Q26.3) WILD-TYPE                          9
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 25(10Q26.3) MUTATED                                  24
  DEL PEAK 25(10Q26.3) WILD-TYPE                                69
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 25(10Q26.3) MUTATED                                                   92
  DEL PEAK 25(10Q26.3) WILD-TYPE                                                202
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 25(10Q26.3) MUTATED                                            1
  DEL PEAK 25(10Q26.3) WILD-TYPE                                          3
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 25(10Q26.3) MUTATED                                               6
  DEL PEAK 25(10Q26.3) WILD-TYPE                                            13
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 25(10Q26.3) MUTATED                                0
  DEL PEAK 25(10Q26.3) WILD-TYPE                              2
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 25(10Q26.3) MUTATED                                    3
  DEL PEAK 25(10Q26.3) WILD-TYPE                                  1
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 25(10Q26.3) MUTATED                              0
  DEL PEAK 25(10Q26.3) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 25(10Q26.3) MUTATED                               2
  DEL PEAK 25(10Q26.3) WILD-TYPE                            17
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 25(10Q26.3) MUTATED                                 1
  DEL PEAK 25(10Q26.3) WILD-TYPE                               0
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 25(10Q26.3) MUTATED                                               2
  DEL PEAK 25(10Q26.3) WILD-TYPE                                             2
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 25(10Q26.3) MUTATED                              2
  DEL PEAK 25(10Q26.3) WILD-TYPE                            5
D57V9, multiclass
                                                    clus
vv                                                   DEL PEAK 25(10Q26.3) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            24
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           92
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 6
  LUNG CLEAR CELL ADENOCARCINOMA                                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            3
  LUNG MUCINOUS ADENOCARCINOMA                                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                                 2
  LUNG SIGNET RING ADENOCARCINOMA                                               1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 2
  MUCINOUS (COLLOID) CARCINOMA                                                  2
                                                    clus
vv                                                   DEL PEAK 25(10Q26.3) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              69
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            202
  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                                                  17
  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"
D57V10, binary
                                cls
clus                               0   1
  DEL PEAK 25(10Q26.3) MUTATED     3 134
  DEL PEAK 25(10Q26.3) WILD-TYPE  18 307
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(10Q26.3) MUTATED      3  134
  DEL PEAK 25(10Q26.3) WILD-TYPE   18  307
     clus
vv    DEL PEAK 25(10Q26.3) MUTATED DEL PEAK 25(10Q26.3) WILD-TYPE
  NO                             3                             18
  YES                          134                            307
[1] 2 2
[1] FALSE
D57V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 25(10Q26.3) MUTATED   104   1   1   7
  DEL PEAK 25(10Q26.3) WILD-TYPE 214  10   3  12
D57V12, multiclass
    clus
vv   DEL PEAK 25(10Q26.3) MUTATED DEL PEAK 25(10Q26.3) WILD-TYPE
  R0                          104                            214
  R1                            1                             10
  R2                            1                              3
  RX                            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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 25(10Q26.3) MUTATED                                  1     1
  DEL PEAK 25(10Q26.3) WILD-TYPE                                0     5
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 25(10Q26.3) MUTATED                           4   108
  DEL PEAK 25(10Q26.3) WILD-TYPE                        22   254
D57V13, multiclass
                                  clus
vv                                 DEL PEAK 25(10Q26.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   4
  WHITE                                                     108
                                  clus
vv                                 DEL PEAK 25(10Q26.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         5
  BLACK OR AFRICAN AMERICAN                                    22
  WHITE                                                       254
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V14, binary
                                cls
clus                               0   1
  DEL PEAK 25(10Q26.3) MUTATED     3  94
  DEL PEAK 25(10Q26.3) WILD-TYPE   4 238
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(10Q26.3) MUTATED      3   94
  DEL PEAK 25(10Q26.3) WILD-TYPE    4  238
                        clus
vv                       DEL PEAK 25(10Q26.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           94
                        clus
vv                       DEL PEAK 25(10Q26.3) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            238
[1] 2 2
[1] FALSE

Clustering(58) Variable = DEL PEAK 26(11P15.5) MUTATION ANALYSIS
D58V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 26(11P15.5) MUTATED    87  27
  DEL PEAK 26(11P15.5) WILD-TYPE 234  55
  DEL PEAK 26(11P15.5) MUTATED DEL PEAK 26(11P15.5) WILD-TYPE 
                           114                            289 
  DEL PEAK 26(11P15.5) MUTATED DEL PEAK 26(11P15.5) WILD-TYPE 
                            27                             55 
$`DEL PEAK 26(11P15.5) MUTATED`
TCGA-05-4382 TCGA-05-4389 TCGA-05-4390 TCGA-05-4410 TCGA-05-4427 TCGA-05-5425 
         607         1369         1126         1958          791          882 
TCGA-05-5428 TCGA-35-5375 TCGA-38-4632 TCGA-44-2662 TCGA-44-5644 TCGA-44-7660 
         670          264         1357         1280          863          592 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7671 TCGA-44-8117 TCGA-44-A47F TCGA-44-A4SS 
         218          557          535          385          337          415 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-6743 
        1421          428          999          268          896          369 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5946 TCGA-50-8460 
         246          282          267         2370          686          105 
TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 
        1986         1971          280         1479         1375           87 
TCGA-55-6642 TCGA-55-6972 TCGA-55-7570 TCGA-55-7573 TCGA-55-7576 TCGA-55-7727 
         993         1475            6            4           40           34 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7994 TCGA-55-7995 TCGA-55-8089 TCGA-55-8092 
          54           19           31            5          100           26 
TCGA-55-8302 TCGA-55-8507 TCGA-55-8510 TCGA-55-8511 TCGA-55-8614 TCGA-55-A490 
          23            8          228            9          536           48 
TCGA-55-A4DG TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-A471 TCGA-62-A472 
         162         1289         1970         2696         1246          910 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-5774 TCGA-64-5778 TCGA-64-5781 
        1728          628         1686         1959         1305         1559 
TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-69-7763 TCGA-69-7974 TCGA-69-7979 
         866           31          610          690          184           89 
TCGA-69-A59K TCGA-73-4659 TCGA-73-4670 TCGA-73-4675 TCGA-73-7499 TCGA-75-7025 
         214          711          131           40          519         1967 
TCGA-78-7145 TCGA-78-7147 TCGA-78-7154 TCGA-78-7160 TCGA-78-7535 TCGA-78-8640 
        1973         1950         1948          678         1972         1949 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-7955 TCGA-86-8280 
          11          630          422          591          508           16 
TCGA-86-8358 TCGA-86-8669 TCGA-86-8673 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
          19           34          455          417          372          842 
TCGA-95-7039 TCGA-95-7043 TCGA-97-7553 TCGA-97-8174 TCGA-99-8025 TCGA-99-8028 
          34            2         1332         1965          427          459 
TCGA-99-8033 TCGA-J2-A4AD TCGA-L4-A4E5 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4T2 
         170          287          578          285          622         1951 
TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TK 
        1954         1957         1980         1970         1970         1971 

$`DEL PEAK 26(11P15.5) WILD-TYPE`
TCGA-05-4249 TCGA-05-4384 TCGA-05-4396 TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 
        1523          426         1947         1431          578          610 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
        1997          455          912          365          913          669 
TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 
         791          761          761          730          457          151 
TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 
          30           62           14          225          182         1952 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
        1962         1147         1492          864         1073          354 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 
         448         1971          133         1324         1429          400 
TCGA-44-2659 TCGA-44-2661 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 
        1367          741         1301           97          246         1130 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 
        1163         1036          190          722         1013          383 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
         723          328          302          845          704          658 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
         705         1938         1942         1864         1978          444 
TCGA-44-7661 TCGA-44-7669 TCGA-44-7670 TCGA-44-7672 TCGA-44-8119 TCGA-44-8120 
         366         1970          882          719           99          260 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SU TCGA-49-4486 
         486          466          287          351           76         1932 
TCGA-49-4494 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6744 TCGA-49-6745 
        1081          157         1700          445          890          522 
TCGA-49-6761 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
         354         2174         2146          455          785          944 
TCGA-50-5068 TCGA-50-5932 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
        1499         1091          653          567          883          764 
TCGA-50-6597 TCGA-50-7109 TCGA-53-7813 TCGA-55-1592 TCGA-55-1594 TCGA-55-6543 
        1015          255          424          701         1178            2 
TCGA-55-6712 TCGA-55-6969 TCGA-55-6971 TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 
          24         1239           25           67         1826         1233 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7574 
        2151         1170           18           35          121           95 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 TCGA-55-7907 TCGA-55-7910 
        1958           39           39           24           16          197 
TCGA-55-7911 TCGA-55-7914 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 
          21            3           33           21            6           43 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
           4           47           15           33           46           66 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 TCGA-55-8512 
         216           44           29           11           15            3 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
         146          202           15           48           49           66 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 
         106           33           42           29         1952            1 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-62-8395 TCGA-62-8402 TCGA-62-A46U 
          28            5           47         1216         1445         2067 
TCGA-62-A46V TCGA-64-1678 TCGA-64-1680 TCGA-64-1681 TCGA-64-5775 TCGA-64-5779 
        2199         1189         1126         1968           62          864 
TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
         573          427          385          174          141          422 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7978 
         202          186          414          165          230           70 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-71-6725 TCGA-73-4658 
         382          100           77          129           61         1600 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
         912          800          467          164           38          621 
TCGA-75-6214 TCGA-75-7027 TCGA-75-7031 TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 
        1970         1956         1965         1988         1944         1093 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
        1963         1202          760         1957         1961         1963 
TCGA-78-7159 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
        1221          215         1940         1950         1934         1937 
TCGA-78-7220 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
        1965         1949         1944          327          881         1952 
TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 
         994         1971         1981         1954         1964         1965 
TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 TCGA-86-7714 TCGA-86-7954 TCGA-86-8054 
        1972          824         1959         1968         1963          745 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
          10         1963           13           24          479          489 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8281 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
         476          482         1955           26           35           45 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 
          18           15          405           10           30           14 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
          39          323         1940           60          310           79 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
         224           35          492          197          174           36 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7567 
          44          218          297          127          186          568 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 
         377          477          476          121          964         1965 
TCGA-97-7552 TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
        1932          775          181           22          107          182 
TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 
          87          147           15          148          115          197 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8032 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE 
         271          392           44          154          114          282 
TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N5 TCGA-MP-A4SV 
         238          435          116            6          353         1946 
TCGA-MP-A4SW TCGA-MP-A4T7 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TH TCGA-MP-A4TI 
        1967         1954         1951         1944          142         1955 
TCGA-MP-A5C7 
        1490 

  DEL PEAK 26(11P15.5) MUTATED DEL PEAK 26(11P15.5) WILD-TYPE 
                             2                              1 
  DEL PEAK 26(11P15.5) MUTATED DEL PEAK 26(11P15.5) WILD-TYPE 
                          2696                           2199 
  DEL PEAK 26(11P15.5) MUTATED DEL PEAK 26(11P15.5) WILD-TYPE 
                         584.5                          444.0 
[1] "2.0 - 2696.0 (584.5)" "1.0 - 2199.0 (444.0)"
[1] "hr=" "1"  
D58V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 26(11P15.5) MUTATED         1       27       35        12        23
  DEL PEAK 26(11P15.5) WILD-TYPE       3       86       96        31        46
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 26(11P15.5) MUTATED           21          1        9
  DEL PEAK 26(11P15.5) WILD-TYPE         46         10       14
D58V3, multiclass
            clus
vv           DEL PEAK 26(11P15.5) MUTATED DEL PEAK 26(11P15.5) WILD-TYPE
  STAGE I                               1                              3
  STAGE IA                             27                             86
  STAGE IB                             35                             96
  STAGE IIA                            12                             31
  STAGE IIB                            23                             46
  STAGE IIIA                           21                             46
  STAGE IIIB                            1                             10
  STAGE IV                              9                             14
[1] 8 2
[1] TRUE
[1] "dimension of 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(11P15.5) MUTATED    35  73  15   4
  DEL PEAK 26(11P15.5) WILD-TYPE 108 186  25  14
D58V4, multiclass
    clus
vv   DEL PEAK 26(11P15.5) MUTATED DEL PEAK 26(11P15.5) WILD-TYPE
  T1                           35                            108
  T2                           73                            186
  T3                           15                             25
  T4                            4                             14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1 N2+N3
  DEL PEAK 26(11P15.5) MUTATED    81  26    21
  DEL PEAK 26(11P15.5) WILD-TYPE 214  59    51
D58V5, multiclass
       clus
vv      DEL PEAK 26(11P15.5) MUTATED DEL PEAK 26(11P15.5) WILD-TYPE
  N0                              81                            214
  N1                              26                             59
  N2+N3                           21                             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"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 26(11P15.5) MUTATED    86   9   0   0  33
  DEL PEAK 26(11P15.5) WILD-TYPE 231   9   1   3  86
D58V6, multiclass
     clus
vv    DEL PEAK 26(11P15.5) MUTATED DEL PEAK 26(11P15.5) WILD-TYPE
  M0                            86                            231
  M1                             9                              9
  M1A                            0                              1
  M1B                            0                              3
  MX                            33                             86
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V7, binary
                                cls
clus                               0   1
  DEL PEAK 26(11P15.5) MUTATED    57  72
  DEL PEAK 26(11P15.5) WILD-TYPE 191 142
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(11P15.5) MUTATED     57   72
  DEL PEAK 26(11P15.5) WILD-TYPE  191  142
        clus
vv       DEL PEAK 26(11P15.5) MUTATED DEL PEAK 26(11P15.5) WILD-TYPE
  FEMALE                           57                            191
  MALE                             72                            142
[1] 2 2
[1] FALSE
D58V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 26(11P15.5) MUTATED                            2
  DEL PEAK 26(11P15.5) WILD-TYPE                         11
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 26(11P15.5) MUTATED                                  25
  DEL PEAK 26(11P15.5) WILD-TYPE                                68
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 26(11P15.5) MUTATED                                                   90
  DEL PEAK 26(11P15.5) WILD-TYPE                                                204
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 26(11P15.5) MUTATED                                            0
  DEL PEAK 26(11P15.5) WILD-TYPE                                          4
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 26(11P15.5) MUTATED                                               4
  DEL PEAK 26(11P15.5) WILD-TYPE                                            15
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 26(11P15.5) MUTATED                                2
  DEL PEAK 26(11P15.5) WILD-TYPE                              0
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 26(11P15.5) MUTATED                                    0
  DEL PEAK 26(11P15.5) WILD-TYPE                                  4
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 26(11P15.5) MUTATED                              0
  DEL PEAK 26(11P15.5) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 26(11P15.5) MUTATED                               5
  DEL PEAK 26(11P15.5) WILD-TYPE                            14
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 26(11P15.5) MUTATED                                 0
  DEL PEAK 26(11P15.5) WILD-TYPE                               1
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 26(11P15.5) MUTATED                                               0
  DEL PEAK 26(11P15.5) WILD-TYPE                                             4
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 26(11P15.5) MUTATED                              1
  DEL PEAK 26(11P15.5) WILD-TYPE                            6
D58V9, multiclass
                                                    clus
vv                                                   DEL PEAK 26(11P15.5) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            25
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           90
  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 26(11P15.5) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              68
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            204
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  15
  LUNG CLEAR CELL ADENOCARCINOMA                                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              4
  LUNG MUCINOUS ADENOCARCINOMA                                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                                  14
  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"
D58V10, binary
                                cls
clus                               0   1
  DEL PEAK 26(11P15.5) MUTATED     5 124
  DEL PEAK 26(11P15.5) WILD-TYPE  16 317
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(11P15.5) MUTATED      5  124
  DEL PEAK 26(11P15.5) WILD-TYPE   16  317
     clus
vv    DEL PEAK 26(11P15.5) MUTATED DEL PEAK 26(11P15.5) WILD-TYPE
  NO                             5                             16
  YES                          124                            317
[1] 2 2
[1] FALSE
D58V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 26(11P15.5) MUTATED    86   2   1   8
  DEL PEAK 26(11P15.5) WILD-TYPE 232   9   3  11
D58V12, multiclass
    clus
vv   DEL PEAK 26(11P15.5) MUTATED DEL PEAK 26(11P15.5) WILD-TYPE
  R0                           86                            232
  R1                            2                              9
  R2                            1                              3
  RX                            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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 26(11P15.5) MUTATED                                  0     2
  DEL PEAK 26(11P15.5) WILD-TYPE                                1     4
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 26(11P15.5) MUTATED                          11   102
  DEL PEAK 26(11P15.5) WILD-TYPE                        15   260
D58V13, multiclass
                                  clus
vv                                 DEL PEAK 26(11P15.5) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  11
  WHITE                                                     102
                                  clus
vv                                 DEL PEAK 26(11P15.5) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    15
  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"
D58V14, binary
                                cls
clus                               0   1
  DEL PEAK 26(11P15.5) MUTATED     3 100
  DEL PEAK 26(11P15.5) WILD-TYPE   4 232
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(11P15.5) MUTATED      3  100
  DEL PEAK 26(11P15.5) WILD-TYPE    4  232
                        clus
vv                       DEL PEAK 26(11P15.5) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          100
                        clus
vv                       DEL PEAK 26(11P15.5) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            232
[1] 2 2
[1] FALSE

Clustering(59) Variable = DEL PEAK 27(11Q23.2) MUTATION ANALYSIS
D59V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 27(11Q23.2) MUTATED    78  19
  DEL PEAK 27(11Q23.2) WILD-TYPE 243  63
  DEL PEAK 27(11Q23.2) MUTATED DEL PEAK 27(11Q23.2) WILD-TYPE 
                            97                            306 
  DEL PEAK 27(11Q23.2) MUTATED DEL PEAK 27(11Q23.2) WILD-TYPE 
                            19                             63 
$`DEL PEAK 27(11Q23.2) MUTATED`
TCGA-05-4389 TCGA-05-4390 TCGA-05-4398 TCGA-05-4415 TCGA-05-4417 TCGA-05-4422 
        1369         1126         1431         1997          455          365 
TCGA-05-4427 TCGA-05-4433 TCGA-05-5420 TCGA-05-5425 TCGA-35-4122 TCGA-35-5375 
         791          730          457          882          225          264 
TCGA-38-4625 TCGA-38-4628 TCGA-38-4631 TCGA-38-4632 TCGA-44-3918 TCGA-44-4112 
        1952         1492          354         1357         1036          722 
TCGA-44-5643 TCGA-44-7667 TCGA-44-7671 TCGA-44-A47F TCGA-44-A4SS TCGA-49-4494 
        1013          557          535          337          415         1081 
TCGA-49-4506 TCGA-49-4510 TCGA-49-4514 TCGA-49-6744 TCGA-49-6761 TCGA-50-5066 
         999          896         1700          890          354          944 
TCGA-50-5072 TCGA-50-5931 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1595 TCGA-55-5899 
         246          267         1971          280         1479           87 
TCGA-55-6971 TCGA-55-6972 TCGA-55-7283 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
          25         1475           35           34           24           54 
TCGA-55-7903 TCGA-55-7995 TCGA-55-8085 TCGA-55-8094 TCGA-55-8302 TCGA-55-8615 
          19            5           33            4           23           15 
TCGA-55-A490 TCGA-55-A4DF TCGA-62-8395 TCGA-62-8397 TCGA-62-A46U TCGA-62-A472 
          48           47         1216         1289         2067          910 
TCGA-64-1678 TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 TCGA-64-5815 TCGA-69-7763 
        1189         1968         1959         1305          866          690 
TCGA-69-7764 TCGA-73-4662 TCGA-73-4675 TCGA-73-7499 TCGA-75-6214 TCGA-75-7025 
         414          912           40          519         1970         1967 
TCGA-78-7145 TCGA-78-7148 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7220 
        1973         1944         1221          678          215         1965 
TCGA-78-8640 TCGA-80-5608 TCGA-86-7701 TCGA-86-7713 TCGA-86-7953 TCGA-86-8054 
        1949         1972           11          422          591          745 
TCGA-86-8074 TCGA-86-8358 TCGA-86-8669 TCGA-86-8673 TCGA-86-A4D0 TCGA-91-6835 
          24           19           34          455           30           79 
TCGA-91-6836 TCGA-91-6849 TCGA-93-8067 TCGA-95-7043 TCGA-97-8174 TCGA-99-8033 
         417           35          186            2         1965          170 
TCGA-L4-A4E5 TCGA-L9-A443 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4T2 TCGA-MP-A4TE 
         578          116          285          353         1951         1970 
TCGA-MP-A4TF 
        1970 

$`DEL PEAK 27(11Q23.2) WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4403 TCGA-05-4405 
        1523          607          426         1947          578          610 
TCGA-05-4410 TCGA-05-4420 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 
        1958          912          913          669          791          761 
TCGA-05-4432 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
         761          151          670           30           62           14 
TCGA-35-4123 TCGA-38-4626 TCGA-38-4627 TCGA-38-4629 TCGA-38-4630 TCGA-38-6178 
         182         1962         1147          864         1073          448 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 
        1971          133         1324         1429          400         1367 
TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 
         741         1280         1301           97          246         1130 
TCGA-44-3398 TCGA-44-3919 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
        1163          190          863          383          723          328 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
         302          845          704          658          705         1938 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
        1942         1864         1978          444          592          366 
TCGA-44-7662 TCGA-44-7669 TCGA-44-7670 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
         218         1970          882          719          385           99 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SU 
         260          486          466          287          351           76 
TCGA-49-4486 TCGA-49-4501 TCGA-49-4505 TCGA-49-4507 TCGA-49-4512 TCGA-49-6742 
        1932         1421          428          268          157          445 
TCGA-49-6743 TCGA-49-6745 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
         369          522         2174         2146          455          785 
TCGA-50-5068 TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 
        1499          282         1091         2370          653          567 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 
         883          764          686         1015          255          105 
TCGA-53-7624 TCGA-53-7813 TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 TCGA-55-6543 
        1986          424          701         1178         1375            2 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 
         993           24         1239           67         1826         1233 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        2151         1170           18          121            6            4 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7907 
          95           40         1958           39           39           16 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-8087 TCGA-55-8089 
         197           21            3           31           21          100 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 
           6           43           26           47           15           33 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 
          46           66          216           44           29           11 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
           8           15          228            9            3          146 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
         202          536           48           49           66          106 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
          33           42           29         1952            1           28 
TCGA-55-A494 TCGA-55-A4DG TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46V 
           5          162         1970         2696         1445         2199 
TCGA-62-A471 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1680 TCGA-64-5775 
        1246         1728          628         1686         1126           62 
TCGA-64-5779 TCGA-64-5781 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
         864         1559           31          610          573          427 
TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
         385          174          141          422          202          186 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
         165          230          184           70           89          382 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 
         100           77          129          214           61         1600 
TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 
         711          800          467          131          164           38 
TCGA-73-7498 TCGA-75-7027 TCGA-75-7031 TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 
         621         1956         1965         1988         1950         1093 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
        1963         1202          760         1948         1957         1961 
TCGA-78-7158 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7535 
        1963         1940         1950         1934         1937         1972 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        1949         1944          327          881         1952          994 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 TCGA-83-5908 
        1971         1981         1954         1964         1965          824 
TCGA-86-6851 TCGA-86-7711 TCGA-86-7714 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 
        1959          630         1968         1963          508           10 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
        1963           13          479          489          476          482 
TCGA-86-8280 TCGA-86-8281 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 
          16         1955           26           35           45           18 
TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
          15          405           10           14           39          323 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
        1940           60          310          372          842          224 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
         492          197          174           36           44          218 
TCGA-93-7347 TCGA-93-7348 TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
         297          127           34          568          377          477 
TCGA-95-7948 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
         476          121          964         1965         1932         1332 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 
         775          181           22          107          182           87 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 
         147           15          148          115          197          271 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-J2-8192 TCGA-J2-8194 
         392          427          459           44          154          114 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A444 TCGA-MN-A4N4 
         287          282          238          435            6          622 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
        1946         1967         1954         1954         1957         1980 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
        1951         1944          142         1955         1971         1490 

  DEL PEAK 27(11Q23.2) MUTATED DEL PEAK 27(11Q23.2) WILD-TYPE 
                             2                              1 
  DEL PEAK 27(11Q23.2) MUTATED DEL PEAK 27(11Q23.2) WILD-TYPE 
                          2067                           2696 
  DEL PEAK 27(11Q23.2) MUTATED DEL PEAK 27(11Q23.2) WILD-TYPE 
                         578.0                          446.5 
[1] "2.0 - 2067.0 (578.0)" "1.0 - 2696.0 (446.5)"
[1] "hr=" "1.1"
D59V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 27(11Q23.2) MUTATED         1       26       26        13        18
  DEL PEAK 27(11Q23.2) WILD-TYPE       3       87      105        30        51
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 27(11Q23.2) MUTATED           14          3        7
  DEL PEAK 27(11Q23.2) WILD-TYPE         53          8       16
D59V3, multiclass
            clus
vv           DEL PEAK 27(11Q23.2) MUTATED DEL PEAK 27(11Q23.2) WILD-TYPE
  STAGE I                               1                              3
  STAGE IA                             26                             87
  STAGE IB                             26                            105
  STAGE IIA                            13                             30
  STAGE IIB                            18                             51
  STAGE IIIA                           14                             53
  STAGE IIIB                            3                              8
  STAGE IV                              7                             16
[1] 8 2
[1] TRUE
[1] "dimension of 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(11Q23.2) MUTATED    31  60  10   5
  DEL PEAK 27(11Q23.2) WILD-TYPE 112 199  30  13
D59V4, multiclass
    clus
vv   DEL PEAK 27(11Q23.2) MUTATED DEL PEAK 27(11Q23.2) WILD-TYPE
  T1                           31                            112
  T2                           60                            199
  T3                           10                             30
  T4                            5                             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 27(11Q23.2) MUTATED    66  23    17
  DEL PEAK 27(11Q23.2) WILD-TYPE 229  62    55
D59V5, multiclass
       clus
vv      DEL PEAK 27(11Q23.2) MUTATED DEL PEAK 27(11Q23.2) WILD-TYPE
  N0                              66                            229
  N1                              23                             62
  N2+N3                           17                             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"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 27(11Q23.2) MUTATED    80   6   0   1  21
  DEL PEAK 27(11Q23.2) WILD-TYPE 237  12   1   2  98
D59V6, multiclass
     clus
vv    DEL PEAK 27(11Q23.2) MUTATED DEL PEAK 27(11Q23.2) WILD-TYPE
  M0                            80                            237
  M1                             6                             12
  M1A                            0                              1
  M1B                            1                              2
  MX                            21                             98
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V7, binary
                                cls
clus                               0   1
  DEL PEAK 27(11Q23.2) MUTATED    49  59
  DEL PEAK 27(11Q23.2) WILD-TYPE 199 155
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(11Q23.2) MUTATED     49   59
  DEL PEAK 27(11Q23.2) WILD-TYPE  199  155
        clus
vv       DEL PEAK 27(11Q23.2) MUTATED DEL PEAK 27(11Q23.2) WILD-TYPE
  FEMALE                           49                            199
  MALE                             59                            155
[1] 2 2
[1] FALSE
D59V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 27(11Q23.2) MUTATED                            3
  DEL PEAK 27(11Q23.2) WILD-TYPE                         10
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 27(11Q23.2) MUTATED                                  27
  DEL PEAK 27(11Q23.2) WILD-TYPE                                66
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 27(11Q23.2) MUTATED                                                   67
  DEL PEAK 27(11Q23.2) WILD-TYPE                                                227
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 27(11Q23.2) MUTATED                                            0
  DEL PEAK 27(11Q23.2) WILD-TYPE                                          4
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 27(11Q23.2) MUTATED                                               3
  DEL PEAK 27(11Q23.2) WILD-TYPE                                            16
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 27(11Q23.2) MUTATED                                1
  DEL PEAK 27(11Q23.2) WILD-TYPE                              1
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 27(11Q23.2) MUTATED                                    0
  DEL PEAK 27(11Q23.2) WILD-TYPE                                  4
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 27(11Q23.2) MUTATED                              0
  DEL PEAK 27(11Q23.2) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 27(11Q23.2) MUTATED                               5
  DEL PEAK 27(11Q23.2) WILD-TYPE                            14
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 27(11Q23.2) MUTATED                                 0
  DEL PEAK 27(11Q23.2) WILD-TYPE                               1
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 27(11Q23.2) MUTATED                                               0
  DEL PEAK 27(11Q23.2) WILD-TYPE                                             4
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 27(11Q23.2) MUTATED                              2
  DEL PEAK 27(11Q23.2) WILD-TYPE                            5
D59V9, multiclass
                                                    clus
vv                                                   DEL PEAK 27(11Q23.2) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            27
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           67
  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                                 0
  MUCINOUS (COLLOID) CARCINOMA                                                  2
                                                    clus
vv                                                   DEL PEAK 27(11Q23.2) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              66
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            227
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  16
  LUNG CLEAR CELL ADENOCARCINOMA                                                  1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              4
  LUNG MUCINOUS ADENOCARCINOMA                                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                                  14
  LUNG SIGNET RING ADENOCARCINOMA                                                 1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                   4
  MUCINOUS (COLLOID) CARCINOMA                                                    5
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V10, binary
                                cls
clus                               0   1
  DEL PEAK 27(11Q23.2) MUTATED     3 105
  DEL PEAK 27(11Q23.2) WILD-TYPE  18 336
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(11Q23.2) MUTATED      3  105
  DEL PEAK 27(11Q23.2) WILD-TYPE   18  336
     clus
vv    DEL PEAK 27(11Q23.2) MUTATED DEL PEAK 27(11Q23.2) WILD-TYPE
  NO                             3                             18
  YES                          105                            336
[1] 2 2
[1] FALSE
D59V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 27(11Q23.2) MUTATED    82   3   0   6
  DEL PEAK 27(11Q23.2) WILD-TYPE 236   8   4  13
D59V12, multiclass
    clus
vv   DEL PEAK 27(11Q23.2) MUTATED DEL PEAK 27(11Q23.2) WILD-TYPE
  R0                           82                            236
  R1                            3                              8
  R2                            0                              4
  RX                            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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 27(11Q23.2) MUTATED                                  0     2
  DEL PEAK 27(11Q23.2) WILD-TYPE                                1     4
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 27(11Q23.2) MUTATED                           7    81
  DEL PEAK 27(11Q23.2) WILD-TYPE                        19   281
D59V13, multiclass
                                  clus
vv                                 DEL PEAK 27(11Q23.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   7
  WHITE                                                      81
                                  clus
vv                                 DEL PEAK 27(11Q23.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    19
  WHITE                                                       281
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V14, binary
                                cls
clus                               0   1
  DEL PEAK 27(11Q23.2) MUTATED     1  78
  DEL PEAK 27(11Q23.2) WILD-TYPE   6 254
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(11Q23.2) MUTATED      1   78
  DEL PEAK 27(11Q23.2) WILD-TYPE    6  254
                        clus
vv                       DEL PEAK 27(11Q23.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           78
                        clus
vv                       DEL PEAK 27(11Q23.2) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            254
[1] 2 2
[1] FALSE

Clustering(60) Variable = DEL PEAK 28(11Q25) MUTATION ANALYSIS
D60V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 28(11Q25) MUTATED    68  22
  DEL PEAK 28(11Q25) WILD-TYPE 253  60
  DEL PEAK 28(11Q25) MUTATED DEL PEAK 28(11Q25) WILD-TYPE 
                          90                          313 
  DEL PEAK 28(11Q25) MUTATED DEL PEAK 28(11Q25) WILD-TYPE 
                          22                           60 
$`DEL PEAK 28(11Q25) MUTATED`
TCGA-05-4390 TCGA-05-4415 TCGA-05-4422 TCGA-05-4427 TCGA-05-4433 TCGA-05-5420 
        1126         1997          365          791          730          457 
TCGA-05-5425 TCGA-35-4122 TCGA-35-5375 TCGA-38-4625 TCGA-38-4628 TCGA-38-4631 
         882          225          264         1952         1492          354 
TCGA-38-4632 TCGA-44-3918 TCGA-44-5643 TCGA-44-6779 TCGA-44-7667 TCGA-44-7671 
        1357         1036         1013         1978          557          535 
TCGA-44-7672 TCGA-44-A47F TCGA-49-4506 TCGA-49-4510 TCGA-49-4514 TCGA-49-6744 
         719          337          999          896         1700          890 
TCGA-49-6761 TCGA-50-5066 TCGA-50-5072 TCGA-50-5931 TCGA-53-7626 TCGA-53-A4EZ 
         354          944          246          267         1971          280 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6971 TCGA-55-6972 TCGA-55-7283 TCGA-55-7576 
        1479           87           25         1475           35           40 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-8085 TCGA-55-8094 
          34           24           54           19           33            4 
TCGA-55-8302 TCGA-55-8615 TCGA-55-A490 TCGA-62-8395 TCGA-62-8397 TCGA-62-A46U 
          23           15           48         1216         1289         2067 
TCGA-62-A472 TCGA-64-1678 TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 TCGA-64-5815 
         910         1189         1968         1959         1305          866 
TCGA-69-7763 TCGA-69-7764 TCGA-73-4662 TCGA-73-4675 TCGA-73-7499 TCGA-75-6214 
         690          414          912           40          519         1970 
TCGA-75-7025 TCGA-78-7145 TCGA-78-7148 TCGA-78-7154 TCGA-78-7159 TCGA-78-7160 
        1967         1973         1944         1948         1221          678 
TCGA-78-7220 TCGA-78-7539 TCGA-78-7542 TCGA-78-8640 TCGA-86-7701 TCGA-86-7713 
        1965          327         1952         1949           11          422 
TCGA-86-7953 TCGA-86-8054 TCGA-86-8074 TCGA-86-8358 TCGA-86-8669 TCGA-91-6849 
         591          745           24           19           34           35 
TCGA-93-8067 TCGA-95-7043 TCGA-97-8174 TCGA-L4-A4E5 TCGA-L9-A443 TCGA-MN-A4N1 
         186            2         1965          578          116          285 
TCGA-MN-A4N5 TCGA-MP-A4T2 TCGA-MP-A4T8 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TI 
         353         1951         1957         1970         1970         1955 

$`DEL PEAK 28(11Q25) WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4396 TCGA-05-4398 
        1523          607          426         1369         1947         1431 
TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 TCGA-05-4417 TCGA-05-4420 TCGA-05-4424 
         578          610         1958          455          912          913 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-5423 TCGA-05-5428 
         669          791          761          761          151          670 
TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4123 TCGA-38-4626 TCGA-38-4627 
          30           62           14          182         1962         1147 
TCGA-38-4629 TCGA-38-4630 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 
         864         1073          448         1971          133         1324 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 
        1429          400         1367          741         1280         1301 
TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 
          97          246         1130         1163          190          722 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
         863          383          723          328          302          845 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
         704          658          705         1938         1942         1864 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7669 TCGA-44-7670 
         444          592          366          218         1970          882 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
         385           99          260          486          466          287 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 
         351          415           76         1932         1081         1421 
TCGA-49-4505 TCGA-49-4507 TCGA-49-4512 TCGA-49-6742 TCGA-49-6743 TCGA-49-6745 
         428          268          157          445          369          522 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5068 TCGA-50-5930 
        2174         2146          455          785         1499          282 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
        1091         2370          653          567          883          764 
TCGA-50-5946 TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 TCGA-53-7624 TCGA-53-7813 
         686         1015          255          105         1986          424 
TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
         701         1178         1375            2          993           24 
TCGA-55-6969 TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
        1239           67         1826         1233         2151         1170 
TCGA-55-7281 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7724 
          18          121            6            4           95         1958 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
          39           39           16          197           21            3 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
          31            5           21          100            6           43 
TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
          26           47           15           33           46           66 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
         216           44           29           11            8           15 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
         228            9            3          146          202          536 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
          48           49           66          106           33           42 
TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
          29         1952            1           28            5           47 
TCGA-55-A4DG TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46V TCGA-62-A471 
         162         1970         2696         1445         2199         1246 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1680 TCGA-64-5775 TCGA-64-5779 
        1728          628         1686         1126           62          864 
TCGA-64-5781 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 
        1559           31          610          573          427          385 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7765 
         174          141          422          202          186          165 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
         230          184           70           89          382          100 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 
          77          129          214           61         1600          711 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
         800          467          131          164           38          621 
TCGA-75-7027 TCGA-75-7031 TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 
        1956         1965         1988         1950         1093         1963 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7161 
        1202          760         1957         1961         1963          215 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7535 TCGA-78-7536 
        1940         1950         1934         1937         1972         1949 
TCGA-78-7537 TCGA-78-7540 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
        1944          881          994         1971         1981         1954 
TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 TCGA-86-7711 
        1964         1965         1972          824         1959          630 
TCGA-86-7714 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
        1968         1963          508           10         1963           13 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8281 
         479          489          476          482           16         1955 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
          26           35           45           18           15          455 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
         405           10           30           14           39          323 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
        1940           60          310           79          417          372 
TCGA-91-6847 TCGA-91-6848 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
         842          224          492          197          174           36 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-95-7039 TCGA-95-7567 
          44          218          297          127           34          568 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 
         377          477          476          121          964         1965 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 
        1932         1332          775          181           22          107 
TCGA-97-8172 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
         182           87          147           15          148          115 
TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
         197          271          392          427          459           44 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
         170          154          114          287          282          238 
TCGA-L4-A4E6 TCGA-L9-A444 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T4 
         435            6          622         1946         1967         1954 
TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TH TCGA-MP-A4TK 
        1954         1980         1951         1944          142         1971 
TCGA-MP-A5C7 
        1490 

  DEL PEAK 28(11Q25) MUTATED DEL PEAK 28(11Q25) WILD-TYPE 
                           2                            1 
  DEL PEAK 28(11Q25) MUTATED DEL PEAK 28(11Q25) WILD-TYPE 
                        2067                         2696 
  DEL PEAK 28(11Q25) MUTATED DEL PEAK 28(11Q25) WILD-TYPE 
                       724.5                        435.0 
[1] "2.0 - 2067.0 (724.5)" "1.0 - 2696.0 (435.0)"
[1] "hr=" "1"  
D60V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 28(11Q25) MUTATED         1       21       25        14        18
  DEL PEAK 28(11Q25) WILD-TYPE       3       92      106        29        51
                              vv
clus                           STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 28(11Q25) MUTATED           16          2        6
  DEL PEAK 28(11Q25) WILD-TYPE         51          9       17
D60V3, multiclass
            clus
vv           DEL PEAK 28(11Q25) MUTATED DEL PEAK 28(11Q25) WILD-TYPE
  STAGE I                             1                            3
  STAGE IA                           21                           92
  STAGE IB                           25                          106
  STAGE IIA                          14                           29
  STAGE IIB                          18                           51
  STAGE IIIA                         16                           51
  STAGE IIIB                          2                            9
  STAGE IV                            6                           17
[1] 8 2
[1] TRUE
[1] "dimension of 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(11Q25) MUTATED    26  62  10   4
  DEL PEAK 28(11Q25) WILD-TYPE 117 197  30  14
D60V4, multiclass
    clus
vv   DEL PEAK 28(11Q25) MUTATED DEL PEAK 28(11Q25) WILD-TYPE
  T1                         26                          117
  T2                         62                          197
  T3                         10                           30
  T4                          4                           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 28(11Q25) MUTATED    59  25    18
  DEL PEAK 28(11Q25) WILD-TYPE 236  60    54
D60V5, multiclass
       clus
vv      DEL PEAK 28(11Q25) MUTATED DEL PEAK 28(11Q25) WILD-TYPE
  N0                            59                          236
  N1                            25                           60
  N2+N3                         18                           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"
                              vv
clus                            M0  M1 M1A M1B  MX
  DEL PEAK 28(11Q25) MUTATED    77   5   0   1  20
  DEL PEAK 28(11Q25) WILD-TYPE 240  13   1   2  99
D60V6, multiclass
     clus
vv    DEL PEAK 28(11Q25) MUTATED DEL PEAK 28(11Q25) WILD-TYPE
  M0                          77                          240
  M1                           5                           13
  M1A                          0                            1
  M1B                          1                            2
  MX                          20                           99
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V7, binary
                              cls
clus                             0   1
  DEL PEAK 28(11Q25) MUTATED    44  59
  DEL PEAK 28(11Q25) WILD-TYPE 204 155
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 28(11Q25) MUTATED     44   59
  DEL PEAK 28(11Q25) WILD-TYPE  204  155
        clus
vv       DEL PEAK 28(11Q25) MUTATED DEL PEAK 28(11Q25) WILD-TYPE
  FEMALE                         44                          204
  MALE                           59                          155
[1] 2 2
[1] FALSE
D60V8, continuous
                              vv
clus                           LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 28(11Q25) MUTATED                            3
  DEL PEAK 28(11Q25) WILD-TYPE                         10
                              vv
clus                           LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 28(11Q25) MUTATED                                  24
  DEL PEAK 28(11Q25) WILD-TYPE                                69
                              vv
clus                           LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 28(11Q25) MUTATED                                                   65
  DEL PEAK 28(11Q25) WILD-TYPE                                                229
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 28(11Q25) MUTATED                                            0
  DEL PEAK 28(11Q25) WILD-TYPE                                          4
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 28(11Q25) MUTATED                                               2
  DEL PEAK 28(11Q25) WILD-TYPE                                            17
                              vv
clus                           LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 28(11Q25) MUTATED                                1
  DEL PEAK 28(11Q25) WILD-TYPE                              1
                              vv
clus                           LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 28(11Q25) MUTATED                                    0
  DEL PEAK 28(11Q25) WILD-TYPE                                  4
                              vv
clus                           LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 28(11Q25) MUTATED                              0
  DEL PEAK 28(11Q25) WILD-TYPE                            2
                              vv
clus                           LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 28(11Q25) MUTATED                               5
  DEL PEAK 28(11Q25) WILD-TYPE                            14
                              vv
clus                           LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 28(11Q25) MUTATED                                 0
  DEL PEAK 28(11Q25) WILD-TYPE                               1
                              vv
clus                           LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 28(11Q25) MUTATED                                               1
  DEL PEAK 28(11Q25) WILD-TYPE                                             3
                              vv
clus                           MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 28(11Q25) MUTATED                              2
  DEL PEAK 28(11Q25) WILD-TYPE                            5
D60V9, multiclass
                                                    clus
vv                                                   DEL PEAK 28(11Q25) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                  3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                          24
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         65
  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                               1
  MUCINOUS (COLLOID) CARCINOMA                                                2
                                                    clus
vv                                                   DEL PEAK 28(11Q25) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                   10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            69
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          229
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                17
  LUNG CLEAR CELL ADENOCARCINOMA                                                1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            4
  LUNG MUCINOUS ADENOCARCINOMA                                                  2
  LUNG PAPILLARY ADENOCARCINOMA                                                14
  LUNG SIGNET RING ADENOCARCINOMA                                               1
  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"
D60V10, binary
                              cls
clus                             0   1
  DEL PEAK 28(11Q25) MUTATED     3 100
  DEL PEAK 28(11Q25) WILD-TYPE  18 341
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 28(11Q25) MUTATED      3  100
  DEL PEAK 28(11Q25) WILD-TYPE   18  341
     clus
vv    DEL PEAK 28(11Q25) MUTATED DEL PEAK 28(11Q25) WILD-TYPE
  NO                           3                           18
  YES                        100                          341
[1] 2 2
[1] FALSE
D60V11, continuous
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 28(11Q25) MUTATED    77   2   0   6
  DEL PEAK 28(11Q25) WILD-TYPE 241   9   4  13
D60V12, multiclass
    clus
vv   DEL PEAK 28(11Q25) MUTATED DEL PEAK 28(11Q25) WILD-TYPE
  R0                         77                          241
  R1                          2                            9
  R2                          0                            4
  RX                          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                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 28(11Q25) MUTATED                                  0     2
  DEL PEAK 28(11Q25) WILD-TYPE                                1     4
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 28(11Q25) MUTATED                           9    76
  DEL PEAK 28(11Q25) WILD-TYPE                        17   286
D60V13, multiclass
                                  clus
vv                                 DEL PEAK 28(11Q25) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     2
  BLACK OR AFRICAN AMERICAN                                 9
  WHITE                                                    76
                                  clus
vv                                 DEL PEAK 28(11Q25) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  17
  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"
D60V14, binary
                              cls
clus                             0   1
  DEL PEAK 28(11Q25) MUTATED     1  72
  DEL PEAK 28(11Q25) WILD-TYPE   6 260
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 28(11Q25) MUTATED      1   72
  DEL PEAK 28(11Q25) WILD-TYPE    6  260
                        clus
vv                       DEL PEAK 28(11Q25) MUTATED
  HISPANIC OR LATINO                              1
  NOT HISPANIC OR LATINO                         72
                        clus
vv                       DEL PEAK 28(11Q25) WILD-TYPE
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          260
[1] 2 2
[1] FALSE

Clustering(61) Variable = DEL PEAK 29(12P13.2) MUTATION ANALYSIS
D61V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 29(12P13.2) MUTATED    93  13
  DEL PEAK 29(12P13.2) WILD-TYPE 228  69
  DEL PEAK 29(12P13.2) MUTATED DEL PEAK 29(12P13.2) WILD-TYPE 
                           106                            297 
  DEL PEAK 29(12P13.2) MUTATED DEL PEAK 29(12P13.2) WILD-TYPE 
                            13                             69 
$`DEL PEAK 29(12P13.2) MUTATED`
TCGA-05-4249 TCGA-05-4390 TCGA-05-4405 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 
        1523         1126          610          669          791          791 
TCGA-05-4432 TCGA-38-6178 TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2666 
         761          448         1429          400          741           97 
TCGA-44-3396 TCGA-44-3918 TCGA-44-6775 TCGA-44-6778 TCGA-44-7662 TCGA-44-7671 
        1130         1036          705         1864          218          535 
TCGA-44-8117 TCGA-44-8120 TCGA-44-A47B TCGA-44-A47F TCGA-44-A4SU TCGA-49-4501 
         385          260          287          337           76         1421 
TCGA-49-6743 TCGA-49-6745 TCGA-49-6761 TCGA-50-5049 TCGA-50-5051 TCGA-50-5068 
         369          522          354         2146          455         1499 
TCGA-50-5935 TCGA-50-5942 TCGA-50-5946 TCGA-55-1592 TCGA-55-5899 TCGA-55-6986 
         653          883          686          701           87         2151 
TCGA-55-7283 TCGA-55-7573 TCGA-55-7727 TCGA-55-7728 TCGA-55-7910 TCGA-55-7914 
          35            4           34           24          197            3 
TCGA-55-8087 TCGA-55-8092 TCGA-55-8507 TCGA-55-8510 TCGA-55-8511 TCGA-55-8514 
          21           26            8          228            9          202 
TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 TCGA-55-A48X TCGA-55-A48Z TCGA-55-A491 
         536           48           49           33           29         1952 
TCGA-55-A4DG TCGA-62-A46V TCGA-64-1676 TCGA-64-1681 TCGA-64-5778 TCGA-67-3770 
         162         2199         1728         1968         1305           31 
TCGA-67-3771 TCGA-67-3774 TCGA-67-6217 TCGA-69-7763 TCGA-69-7765 TCGA-69-7974 
         610          385          422          690          165          184 
TCGA-69-7979 TCGA-69-8253 TCGA-71-6725 TCGA-73-4662 TCGA-73-4668 TCGA-73-4677 
          89          100           61          912          467           38 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7145 TCGA-78-7147 TCGA-78-7153 TCGA-78-7161 
         621          519         1973         1950          760          215 
TCGA-78-7535 TCGA-83-5908 TCGA-86-7701 TCGA-86-7955 TCGA-86-8073 TCGA-86-8074 
        1972          824           11          508           13           24 
TCGA-86-8279 TCGA-86-8358 TCGA-86-8672 TCGA-91-6828 TCGA-91-6835 TCGA-91-6836 
         482           19           15          323           79          417 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6849 TCGA-95-7567 TCGA-95-7947 TCGA-95-7948 
         372          842           35          568          477          476 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7554 TCGA-97-8177 TCGA-99-7458 TCGA-99-8025 
         964         1965          775          147          392          427 
TCGA-J2-A4AD TCGA-MN-A4N5 TCGA-MP-A4TC TCGA-MP-A4TH 
         287          353         1944          142 

$`DEL PEAK 29(12P13.2) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4396 TCGA-05-4398 TCGA-05-4403 
         607          426         1369         1947         1431          578 
TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        1958         1997          455          912          365          913 
TCGA-05-4430 TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
         761          730          457          151          882          670 
TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 
          30           62           14          225          182          264 
TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 
        1952         1962         1147         1492          864         1073 
TCGA-38-4631 TCGA-38-4632 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2659 
         354         1357         1971          133         1324         1367 
TCGA-44-2662 TCGA-44-2665 TCGA-44-2668 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 
        1280         1301          246         1163          190          722 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
        1013          863          383          723          328          302 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6776 TCGA-44-6777 TCGA-44-6779 
         845          704          658         1938         1942         1978 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
         444          592          366          557         1970          882 
TCGA-44-7672 TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47G TCGA-44-A4SS 
         719           99          486          466          351          415 
TCGA-49-4486 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
        1932         1081          428          999          268          896 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6744 TCGA-50-5045 TCGA-50-5055 
         157         1700          445          890         2174          785 
TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
         944          246          282          267         1091         2370 
TCGA-50-5941 TCGA-50-5944 TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 TCGA-53-7624 
         567          764         1015          255          105         1986 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 
        1971          424          280         1178         1479         1375 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 
           2          993           24         1239           25         1475 
TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 TCGA-55-6987 TCGA-55-7281 TCGA-55-7284 
          67         1826         1233         1170           18          121 
TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
           6           95           40         1958           39           39 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 TCGA-55-7994 TCGA-55-7995 
          54           19           16           21           31            5 
TCGA-55-8085 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8094 TCGA-55-8096 
          33          100            6           43            4           47 
TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 
          15           33           46           66          216           44 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 
          23           29           11           15            3          146 
TCGA-55-8615 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48Y TCGA-55-A490 TCGA-55-A492 
          15           66          106           42           48            1 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
          28            5           47         1216         1289         1970 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46U TCGA-62-A471 TCGA-62-A472 TCGA-64-1677 
        2696         1445         2067         1246          910          628 
TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-5774 TCGA-64-5775 TCGA-64-5779 
        1189         1686         1126         1959           62          864 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
        1559          866          573          427          174          141 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 TCGA-69-7973 TCGA-69-7978 TCGA-69-7980 
         202          186          414          230           70          382 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-73-4658 TCGA-73-4659 TCGA-73-4666 
          77          129          214         1600          711          800 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 
         131           40          164         1970         1967         1956 
TCGA-75-7031 TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        1965         1988         1944         1093         1963         1202 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
        1948         1957         1961         1963         1221          678 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 
        1940         1950         1934         1937         1965         1949 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
        1944          327          881         1952          994         1949 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 
        1971         1981         1954         1964         1965         1972 
TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
        1959          630          422         1968          591         1963 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
         745           10         1963          479          489          476 
TCGA-86-8280 TCGA-86-8281 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
          16         1955           26           35           45           34 
TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 
          18          455          405           10           30           14 
TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6848 TCGA-91-7771 
          39         1940           60          310          224          492 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
         197          174           36           44          218          297 
TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-95-7944 TCGA-95-A4VK 
         127          186           34            2          377          121 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
        1932         1332          181           22          107          182 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 
        1965           87           15          148          115          197 
TCGA-97-A4M7 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
         271          459           44          170          154          114 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
         282          238          578          435          116            6 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 
         285          622         1946         1967         1951         1954 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TE TCGA-MP-A4TF 
        1954         1957         1980         1951         1970         1970 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
        1955         1971         1490 

  DEL PEAK 29(12P13.2) MUTATED DEL PEAK 29(12P13.2) WILD-TYPE 
                             3                              1 
  DEL PEAK 29(12P13.2) MUTATED DEL PEAK 29(12P13.2) WILD-TYPE 
                          2199                           2696 
  DEL PEAK 29(12P13.2) MUTATED DEL PEAK 29(12P13.2) WILD-TYPE 
                         424.5                          486.0 
[1] "3.0 - 2199.0 (424.5)" "1.0 - 2696.0 (486.0)"
[1] "hr=" "1.3"
D61V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 29(12P13.2) MUTATED         0       33       44         6        15
  DEL PEAK 29(12P13.2) WILD-TYPE       4       80       87        37        54
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 29(12P13.2) MUTATED           19          1        7
  DEL PEAK 29(12P13.2) WILD-TYPE         48         10       16
D61V3, multiclass
            clus
vv           DEL PEAK 29(12P13.2) MUTATED DEL PEAK 29(12P13.2) WILD-TYPE
  STAGE I                               0                              4
  STAGE IA                             33                             80
  STAGE IB                             44                             87
  STAGE IIA                             6                             37
  STAGE IIB                            15                             54
  STAGE IIIA                           19                             48
  STAGE IIIB                            1                             10
  STAGE IV                              7                             16
[1] 8 2
[1] TRUE
[1] "dimension of 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(12P13.2) MUTATED    41  71   9   4
  DEL PEAK 29(12P13.2) WILD-TYPE 102 188  31  14
D61V4, multiclass
    clus
vv   DEL PEAK 29(12P13.2) MUTATED DEL PEAK 29(12P13.2) WILD-TYPE
  T1                           41                            102
  T2                           71                            188
  T3                            9                             31
  T4                            4                             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 29(12P13.2) MUTATED    86  20    18
  DEL PEAK 29(12P13.2) WILD-TYPE 209  65    54
D61V5, multiclass
       clus
vv      DEL PEAK 29(12P13.2) MUTATED DEL PEAK 29(12P13.2) WILD-TYPE
  N0                              86                            209
  N1                              20                             65
  N2+N3                           18                             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"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 29(12P13.2) MUTATED    82   6   0   0  36
  DEL PEAK 29(12P13.2) WILD-TYPE 235  12   1   3  83
D61V6, multiclass
     clus
vv    DEL PEAK 29(12P13.2) MUTATED DEL PEAK 29(12P13.2) WILD-TYPE
  M0                            82                            235
  M1                             6                             12
  M1A                            0                              1
  M1B                            0                              3
  MX                            36                             83
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V7, binary
                                cls
clus                               0   1
  DEL PEAK 29(12P13.2) MUTATED    81  44
  DEL PEAK 29(12P13.2) WILD-TYPE 167 170
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(12P13.2) MUTATED     81   44
  DEL PEAK 29(12P13.2) WILD-TYPE  167  170
        clus
vv       DEL PEAK 29(12P13.2) MUTATED DEL PEAK 29(12P13.2) WILD-TYPE
  FEMALE                           81                            167
  MALE                             44                            170
[1] 2 2
[1] FALSE
D61V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 29(12P13.2) MUTATED                            2
  DEL PEAK 29(12P13.2) WILD-TYPE                         11
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 29(12P13.2) MUTATED                                  28
  DEL PEAK 29(12P13.2) WILD-TYPE                                65
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 29(12P13.2) MUTATED                                                   79
  DEL PEAK 29(12P13.2) WILD-TYPE                                                215
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 29(12P13.2) MUTATED                                            0
  DEL PEAK 29(12P13.2) WILD-TYPE                                          4
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 29(12P13.2) MUTATED                                               7
  DEL PEAK 29(12P13.2) WILD-TYPE                                            12
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 29(12P13.2) MUTATED                                1
  DEL PEAK 29(12P13.2) WILD-TYPE                              1
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 29(12P13.2) MUTATED                                    1
  DEL PEAK 29(12P13.2) WILD-TYPE                                  3
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 29(12P13.2) MUTATED                              0
  DEL PEAK 29(12P13.2) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 29(12P13.2) MUTATED                               4
  DEL PEAK 29(12P13.2) WILD-TYPE                            15
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 29(12P13.2) MUTATED                                 0
  DEL PEAK 29(12P13.2) WILD-TYPE                               1
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 29(12P13.2) MUTATED                                               1
  DEL PEAK 29(12P13.2) WILD-TYPE                                             3
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 29(12P13.2) MUTATED                              2
  DEL PEAK 29(12P13.2) WILD-TYPE                            5
D61V9, multiclass
                                                    clus
vv                                                   DEL PEAK 29(12P13.2) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            28
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           79
  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                                                 4
  LUNG SIGNET RING ADENOCARCINOMA                                               0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 1
  MUCINOUS (COLLOID) CARCINOMA                                                  2
                                                    clus
vv                                                   DEL PEAK 29(12P13.2) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              65
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            215
  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                                                  15
  LUNG SIGNET RING ADENOCARCINOMA                                                 1
  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"
D61V10, binary
                                cls
clus                               0   1
  DEL PEAK 29(12P13.2) MUTATED     4 121
  DEL PEAK 29(12P13.2) WILD-TYPE  17 320
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(12P13.2) MUTATED      4  121
  DEL PEAK 29(12P13.2) WILD-TYPE   17  320
     clus
vv    DEL PEAK 29(12P13.2) MUTATED DEL PEAK 29(12P13.2) WILD-TYPE
  NO                             4                             17
  YES                          121                            320
[1] 2 2
[1] FALSE
D61V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 29(12P13.2) MUTATED    80   4   2   5
  DEL PEAK 29(12P13.2) WILD-TYPE 238   7   2  14
D61V12, multiclass
    clus
vv   DEL PEAK 29(12P13.2) MUTATED DEL PEAK 29(12P13.2) WILD-TYPE
  R0                           80                            238
  R1                            4                              7
  R2                            2                              2
  RX                            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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 29(12P13.2) MUTATED                                  1     1
  DEL PEAK 29(12P13.2) WILD-TYPE                                0     5
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 29(12P13.2) MUTATED                          11    99
  DEL PEAK 29(12P13.2) WILD-TYPE                        15   263
D61V13, multiclass
                                  clus
vv                                 DEL PEAK 29(12P13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                  11
  WHITE                                                      99
                                  clus
vv                                 DEL PEAK 29(12P13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         5
  BLACK OR AFRICAN AMERICAN                                    15
  WHITE                                                       263
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V14, binary
                                cls
clus                               0   1
  DEL PEAK 29(12P13.2) MUTATED     2  99
  DEL PEAK 29(12P13.2) WILD-TYPE   5 233
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(12P13.2) MUTATED      2   99
  DEL PEAK 29(12P13.2) WILD-TYPE    5  233
                        clus
vv                       DEL PEAK 29(12P13.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           99
                        clus
vv                       DEL PEAK 29(12P13.2) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            233
[1] 2 2
[1] FALSE

Clustering(62) Variable = DEL PEAK 30(12Q12) MUTATION ANALYSIS
D62V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 30(12Q12) MUTATED    64  11
  DEL PEAK 30(12Q12) WILD-TYPE 257  71
  DEL PEAK 30(12Q12) MUTATED DEL PEAK 30(12Q12) WILD-TYPE 
                          75                          328 
  DEL PEAK 30(12Q12) MUTATED DEL PEAK 30(12Q12) WILD-TYPE 
                          11                           71 
$`DEL PEAK 30(12Q12) MUTATED`
TCGA-05-4405 TCGA-05-4426 TCGA-35-3615 TCGA-38-4632 TCGA-38-6178 TCGA-44-2657 
         610          791           14         1357          448          400 
TCGA-44-2661 TCGA-44-2666 TCGA-44-6775 TCGA-44-6779 TCGA-44-7662 TCGA-44-7671 
         741           97          705         1978          218          535 
TCGA-44-8120 TCGA-44-A47F TCGA-44-A4SU TCGA-49-6745 TCGA-50-5049 TCGA-50-5051 
         260          337           76          522         2146          455 
TCGA-50-5068 TCGA-50-8460 TCGA-55-1592 TCGA-55-5899 TCGA-55-6712 TCGA-55-7283 
        1499          105          701           87           24           35 
TCGA-55-7727 TCGA-55-7907 TCGA-55-7914 TCGA-55-8089 TCGA-55-8092 TCGA-55-8207 
          34           16            3          100           26           66 
TCGA-55-8505 TCGA-55-8510 TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 
          29          228          202          536           48           49 
TCGA-55-A48X TCGA-55-A48Z TCGA-55-A491 TCGA-62-A46U TCGA-64-1676 TCGA-64-5778 
          33           29         1952         2067         1728         1305 
TCGA-67-6217 TCGA-69-7763 TCGA-69-7765 TCGA-71-6725 TCGA-73-4670 TCGA-73-4675 
         422          690          165           61          131           40 
TCGA-73-4677 TCGA-73-7498 TCGA-75-6214 TCGA-78-7153 TCGA-78-7535 TCGA-86-6851 
          38          621         1970          760         1972         1959 
TCGA-86-7955 TCGA-86-8074 TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 TCGA-86-8668 
         508           24          482           16           26           45 
TCGA-86-8672 TCGA-91-6847 TCGA-91-6849 TCGA-95-7039 TCGA-95-7043 TCGA-95-7948 
          15          842           35           34            2          476 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7554 TCGA-97-8177 TCGA-99-7458 TCGA-99-8025 
         964         1965          775          147          392          427 
TCGA-J2-A4AD TCGA-MP-A4TC TCGA-MP-A4TK 
         287         1944         1971 

$`DEL PEAK 30(12Q12) WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 
        1523          607          426         1369         1126         1947 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 
        1431          578         1958         1997          455          912 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
         365          913          669          791          761          761 
TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
         730          457          151          882          670           30 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
          62          225          182          264         1952         1962 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-7271 
        1147         1492          864         1073          354         1971 
TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2659 TCGA-44-2662 TCGA-44-2665 
         133         1324         1429         1367         1280         1301 
TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
         246         1130         1163         1036          190          722 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
        1013          863          383          723          328          302 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
         845          704          658         1938         1942         1864 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
         444          592          366          557         1970          882 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
         719          385           99          486          466          287 
TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
         351          415         1932         1081         1421          428 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 
         999          268          896          157         1700          445 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6761 TCGA-50-5045 TCGA-50-5055 TCGA-50-5066 
         369          890          354         2174          785          944 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
         246          282          267         1091         2370          653 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6597 TCGA-50-7109 
         567          883          764          686         1015          255 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1595 
        1986         1971          424          280         1178         1479 
TCGA-55-1596 TCGA-55-6543 TCGA-55-6642 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 
        1375            2          993         1239           25         1475 
TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 
          67         1826         1233         2151         1170           18 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
         121            6            4           95           40         1958 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7910 
          39           39           24           54           19          197 
TCGA-55-7911 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 
          21           31            5           33           21            6 
TCGA-55-8091 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 
          43            4           47           15           33           46 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
         216           44           23           11            8           15 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8615 TCGA-55-8620 TCGA-55-8621 
           9            3          146           15           66          106 
TCGA-55-A48Y TCGA-55-A490 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
          42           48            1           28            5           47 
TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
         162         1216         1289         1970         2696         1445 
TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 
        2199         1246          910          628         1189         1686 
TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5779 TCGA-64-5781 
        1126         1968         1959           62          864         1559 
TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 
         866           31          610          573          427          385 
TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 TCGA-69-7973 
         174          141          202          186          414          230 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
         184           70           89          382          100           77 
TCGA-69-8255 TCGA-69-A59K TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
         129          214         1600          711          912          800 
TCGA-73-4668 TCGA-73-4676 TCGA-73-7499 TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 
         467          164          519         1967         1956         1965 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
        1973         1988         1950         1944         1093         1963 
TCGA-78-7152 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
        1202         1948         1957         1961         1963         1221 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
         678          215         1940         1950         1934         1937 
TCGA-78-7220 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
        1965         1949         1944          327          881         1952 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
         994         1949         1971         1981         1954         1964 
TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
        1965         1972          824           11          630          422 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
        1968          591         1963          745           10         1963 
TCGA-86-8073 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8281 TCGA-86-8358 
          13          479          489          476         1955           19 
TCGA-86-8585 TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
          35           34           18          455          405           10 
TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
          30           14           39          323         1940           60 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6848 TCGA-91-7771 
         310           79          417          372          224          492 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
         197          174           36           44          218          297 
TCGA-93-7348 TCGA-93-8067 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-A4VK 
         127          186          568          377          477          121 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
        1932         1332          181           22          107          182 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 
        1965           87           15          148          115          197 
TCGA-97-A4M7 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
         271          459           44          170          154          114 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
         282          238          578          435          116            6 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 
         285          622          353         1946         1967         1951 
TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TE 
        1954         1954         1957         1980         1951         1970 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A5C7 
        1970          142         1955         1490 

  DEL PEAK 30(12Q12) MUTATED DEL PEAK 30(12Q12) WILD-TYPE 
                           2                            1 
  DEL PEAK 30(12Q12) MUTATED DEL PEAK 30(12Q12) WILD-TYPE 
                        2146                         2696 
  DEL PEAK 30(12Q12) MUTATED DEL PEAK 30(12Q12) WILD-TYPE 
                       337.0                        490.5 
[1] "2.0 - 2146.0 (337.0)" "1.0 - 2696.0 (490.5)"
[1] "hr=" "1.3"
D62V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 30(12Q12) MUTATED         0       17       27         9        11
  DEL PEAK 30(12Q12) WILD-TYPE       4       96      104        34        58
                              vv
clus                           STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 30(12Q12) MUTATED           20          1        4
  DEL PEAK 30(12Q12) WILD-TYPE         47         10       19
D62V3, multiclass
            clus
vv           DEL PEAK 30(12Q12) MUTATED DEL PEAK 30(12Q12) WILD-TYPE
  STAGE I                             0                            4
  STAGE IA                           17                           96
  STAGE IB                           27                          104
  STAGE IIA                           9                           34
  STAGE IIB                          11                           58
  STAGE IIIA                         20                           47
  STAGE IIIB                          1                           10
  STAGE IV                            4                           19
[1] 8 2
[1] TRUE
[1] "dimension of 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(12Q12) MUTATED    24  51  11   2
  DEL PEAK 30(12Q12) WILD-TYPE 119 208  29  16
D62V4, multiclass
    clus
vv   DEL PEAK 30(12Q12) MUTATED DEL PEAK 30(12Q12) WILD-TYPE
  T1                         24                          119
  T2                         51                          208
  T3                         11                           29
  T4                          2                           16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            N0  N1 N2+N3
  DEL PEAK 30(12Q12) MUTATED    52  18    18
  DEL PEAK 30(12Q12) WILD-TYPE 243  67    54
D62V5, multiclass
       clus
vv      DEL PEAK 30(12Q12) MUTATED DEL PEAK 30(12Q12) WILD-TYPE
  N0                            52                          243
  N1                            18                           67
  N2+N3                         18                           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"
                              vv
clus                            M0  M1 M1A M1B  MX
  DEL PEAK 30(12Q12) MUTATED    53   3   0   0  32
  DEL PEAK 30(12Q12) WILD-TYPE 264  15   1   3  87
D62V6, multiclass
     clus
vv    DEL PEAK 30(12Q12) MUTATED DEL PEAK 30(12Q12) WILD-TYPE
  M0                          53                          264
  M1                           3                           15
  M1A                          0                            1
  M1B                          0                            3
  MX                          32                           87
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V7, binary
                              cls
clus                             0   1
  DEL PEAK 30(12Q12) MUTATED    54  35
  DEL PEAK 30(12Q12) WILD-TYPE 194 179
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 30(12Q12) MUTATED     54   35
  DEL PEAK 30(12Q12) WILD-TYPE  194  179
        clus
vv       DEL PEAK 30(12Q12) MUTATED DEL PEAK 30(12Q12) WILD-TYPE
  FEMALE                         54                          194
  MALE                           35                          179
[1] 2 2
[1] FALSE
D62V8, continuous
                              vv
clus                           LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 30(12Q12) MUTATED                            2
  DEL PEAK 30(12Q12) WILD-TYPE                         11
                              vv
clus                           LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 30(12Q12) MUTATED                                  17
  DEL PEAK 30(12Q12) WILD-TYPE                                76
                              vv
clus                           LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 30(12Q12) MUTATED                                                   58
  DEL PEAK 30(12Q12) WILD-TYPE                                                236
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 30(12Q12) MUTATED                                            1
  DEL PEAK 30(12Q12) WILD-TYPE                                          3
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 30(12Q12) MUTATED                                               5
  DEL PEAK 30(12Q12) WILD-TYPE                                            14
                              vv
clus                           LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 30(12Q12) MUTATED                                0
  DEL PEAK 30(12Q12) WILD-TYPE                              2
                              vv
clus                           LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 30(12Q12) MUTATED                                    0
  DEL PEAK 30(12Q12) WILD-TYPE                                  4
                              vv
clus                           LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 30(12Q12) MUTATED                              0
  DEL PEAK 30(12Q12) WILD-TYPE                            2
                              vv
clus                           LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 30(12Q12) MUTATED                               5
  DEL PEAK 30(12Q12) WILD-TYPE                            14
                              vv
clus                           LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 30(12Q12) MUTATED                                 0
  DEL PEAK 30(12Q12) WILD-TYPE                               1
                              vv
clus                           LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 30(12Q12) MUTATED                                               0
  DEL PEAK 30(12Q12) WILD-TYPE                                             4
                              vv
clus                           MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 30(12Q12) MUTATED                              1
  DEL PEAK 30(12Q12) WILD-TYPE                            6
D62V9, multiclass
                                                    clus
vv                                                   DEL PEAK 30(12Q12) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                  2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                          17
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         58
  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                                                1
                                                    clus
vv                                                   DEL PEAK 30(12Q12) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                   11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            76
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          236
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                14
  LUNG CLEAR CELL ADENOCARCINOMA                                                2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            4
  LUNG MUCINOUS ADENOCARCINOMA                                                  2
  LUNG PAPILLARY ADENOCARCINOMA                                                14
  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"
D62V10, binary
                              cls
clus                             0   1
  DEL PEAK 30(12Q12) MUTATED     1  88
  DEL PEAK 30(12Q12) WILD-TYPE  20 353
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 30(12Q12) MUTATED      1   88
  DEL PEAK 30(12Q12) WILD-TYPE   20  353
     clus
vv    DEL PEAK 30(12Q12) MUTATED DEL PEAK 30(12Q12) WILD-TYPE
  NO                           1                           20
  YES                         88                          353
[1] 2 2
[1] FALSE
D62V11, continuous
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 30(12Q12) MUTATED    59   1   1   5
  DEL PEAK 30(12Q12) WILD-TYPE 259  10   3  14
D62V12, multiclass
    clus
vv   DEL PEAK 30(12Q12) MUTATED DEL PEAK 30(12Q12) WILD-TYPE
  R0                         59                          259
  R1                          1                           10
  R2                          1                            3
  RX                          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                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 30(12Q12) MUTATED                                  0     1
  DEL PEAK 30(12Q12) WILD-TYPE                                1     5
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 30(12Q12) MUTATED                           7    76
  DEL PEAK 30(12Q12) WILD-TYPE                        19   286
D62V13, multiclass
                                  clus
vv                                 DEL PEAK 30(12Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     1
  BLACK OR AFRICAN AMERICAN                                 7
  WHITE                                                    76
                                  clus
vv                                 DEL PEAK 30(12Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  19
  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"
D62V14, binary
                              cls
clus                             0   1
  DEL PEAK 30(12Q12) MUTATED     2  75
  DEL PEAK 30(12Q12) WILD-TYPE   5 257
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 30(12Q12) MUTATED      2   75
  DEL PEAK 30(12Q12) WILD-TYPE    5  257
                        clus
vv                       DEL PEAK 30(12Q12) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                         75
                        clus
vv                       DEL PEAK 30(12Q12) WILD-TYPE
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          257
[1] 2 2
[1] FALSE

Clustering(63) Variable = DEL PEAK 31(12Q24.33) MUTATION ANALYSIS
D63V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 31(12Q24.33) MUTATED    75  21
  DEL PEAK 31(12Q24.33) WILD-TYPE 246  61
  DEL PEAK 31(12Q24.33) MUTATED DEL PEAK 31(12Q24.33) WILD-TYPE 
                             96                             307 
  DEL PEAK 31(12Q24.33) MUTATED DEL PEAK 31(12Q24.33) WILD-TYPE 
                             21                              61 
$`DEL PEAK 31(12Q24.33) MUTATED`
TCGA-05-4424 TCGA-05-4426 TCGA-35-3615 TCGA-38-4628 TCGA-38-4632 TCGA-38-6178 
         913          791           14         1492         1357          448 
TCGA-44-2657 TCGA-44-2661 TCGA-44-6775 TCGA-44-6776 TCGA-44-6779 TCGA-44-7662 
         400          741          705         1938         1978          218 
TCGA-44-7671 TCGA-44-8120 TCGA-44-A47F TCGA-44-A4SU TCGA-49-4501 TCGA-49-4510 
         535          260          337           76         1421          896 
TCGA-49-6744 TCGA-49-6745 TCGA-50-5049 TCGA-50-5068 TCGA-50-5932 TCGA-50-5946 
         890          522         2146         1499         1091          686 
TCGA-50-6597 TCGA-50-8460 TCGA-55-1592 TCGA-55-6980 TCGA-55-6986 TCGA-55-7283 
        1015          105          701           67         2151           35 
TCGA-55-7727 TCGA-55-7911 TCGA-55-7914 TCGA-55-8087 TCGA-55-8506 TCGA-55-8508 
          34           21            3           21           11           15 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 
         228            9            3          202          536           48 
TCGA-55-8619 TCGA-55-A48X TCGA-55-A48Z TCGA-55-A4DF TCGA-55-A4DG TCGA-62-A46U 
          49           33           29           47          162         2067 
TCGA-64-5778 TCGA-67-3772 TCGA-67-3774 TCGA-67-6217 TCGA-69-7763 TCGA-69-7765 
        1305          573          385          422          690          165 
TCGA-69-7974 TCGA-69-7979 TCGA-69-8253 TCGA-71-6725 TCGA-73-4658 TCGA-73-4670 
         184           89          100           61         1600          131 
TCGA-73-4677 TCGA-75-7025 TCGA-78-7150 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
          38         1967         1963          760         1948         1957 
TCGA-78-7167 TCGA-78-7535 TCGA-78-8640 TCGA-86-8075 TCGA-86-8278 TCGA-86-8279 
        1937         1972         1949          479          476          482 
TCGA-86-8280 TCGA-86-A4D0 TCGA-91-6847 TCGA-91-6849 TCGA-91-7771 TCGA-93-7348 
          16           30          842           35          492          127 
TCGA-95-7039 TCGA-95-7947 TCGA-95-7948 TCGA-97-7546 TCGA-97-7547 TCGA-97-7554 
          34          477          476          964         1965          775 
TCGA-97-7937 TCGA-97-8174 TCGA-97-8552 TCGA-99-7458 TCGA-99-8025 TCGA-J2-A4AD 
         181         1965          115          392          427          287 
TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4T4 TCGA-MP-A4T9 TCGA-MP-A4TC TCGA-MP-A4TK 
         285          353         1954         1980         1944         1971 

$`DEL PEAK 31(12Q24.33) WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 
        1523          607          426         1369         1126         1947 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 
        1431          578          610         1958         1997          455 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4425 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
         912          365          669          791          761          761 
TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
         730          457          151          882          670           30 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
          62          225          182          264         1952         1962 
TCGA-38-4627 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-7271 TCGA-38-A44F 
        1147          864         1073          354         1971          133 
TCGA-44-2655 TCGA-44-2656 TCGA-44-2659 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 
        1324         1429         1367         1280         1301           97 
TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
         246         1130         1163         1036          190          722 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
        1013          863          383          723          328          302 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6777 TCGA-44-6778 TCGA-44-7659 
         845          704          658         1942         1864          444 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7672 
         592          366          557         1970          882          719 
TCGA-44-8117 TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G 
         385           99          486          466          287          351 
TCGA-44-A4SS TCGA-49-4486 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
         415         1932         1081          428          999          268 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6761 TCGA-50-5045 
         157         1700          445          369          354         2174 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
         455          785          944          246          282          267 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-7109 
        2370          653          567          883          764          255 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1595 
        1986         1971          424          280         1178         1479 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 
        1375           87            2          993           24         1239 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6983 TCGA-55-6985 TCGA-55-6987 TCGA-55-7281 
          25         1475         1826         1233         1170           18 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
         121            6            4           95           40         1958 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 
          39           39           24           54           19           16 
TCGA-55-7910 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8089 TCGA-55-8090 
         197           31            5           33          100            6 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 
          43           26            4           47           15           33 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
          46           66          216           44           23           29 
TCGA-55-8507 TCGA-55-8513 TCGA-55-8615 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48Y 
           8          146           15           66          106           42 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-62-8395 
          48         1952            1           28            5         1216 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46V TCGA-62-A471 
        1289         1970         2696         1445         2199         1246 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 
         910         1728          628         1189         1686         1126 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
        1968         1959           62          864         1559          866 
TCGA-67-3770 TCGA-67-3771 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 
          31          610          427          174          141          202 
TCGA-69-7761 TCGA-69-7764 TCGA-69-7973 TCGA-69-7978 TCGA-69-7980 TCGA-69-8254 
         186          414          230           70          382           77 
TCGA-69-8255 TCGA-69-A59K TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
         129          214          711          912          800          467 
TCGA-73-4675 TCGA-73-4676 TCGA-73-7498 TCGA-73-7499 TCGA-75-6214 TCGA-75-7027 
          40          164          621          519         1970         1956 
TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
        1965         1973         1988         1950         1944         1093 
TCGA-78-7152 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
        1202         1961         1963         1221          678          215 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7220 TCGA-78-7536 TCGA-78-7537 
        1940         1950         1934         1965         1949         1944 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 
         327          881         1952          994         1971         1981 
TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 
        1954         1964         1965         1972          824         1959 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
          11          630          422         1968          591         1963 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
         508          745           10         1963           13           24 
TCGA-86-8076 TCGA-86-8281 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
         489         1955           19           26           35           45 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
          34           18           15          455          405           10 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
          14           39          323         1940           60          310 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6848 TCGA-91-8496 TCGA-91-8497 
          79          417          372          224          197          174 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-8067 TCGA-95-7043 
          36           44          218          297          186            2 
TCGA-95-7567 TCGA-95-7944 TCGA-95-A4VK TCGA-97-7552 TCGA-97-7553 TCGA-97-7941 
         568          377          121         1932         1332           22 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
         107          182           87          147           15          148 
TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
         197          271          459           44          170          154 
TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
         114          282          238          578          435          116 
TCGA-L9-A444 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T7 
           6          622         1946         1967         1951         1954 
TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        1957         1951         1970         1970          142         1955 
TCGA-MP-A5C7 
        1490 

  DEL PEAK 31(12Q24.33) MUTATED DEL PEAK 31(12Q24.33) WILD-TYPE 
                              3                               1 
  DEL PEAK 31(12Q24.33) MUTATED DEL PEAK 31(12Q24.33) WILD-TYPE 
                           2151                            2696 
  DEL PEAK 31(12Q24.33) MUTATED DEL PEAK 31(12Q24.33) WILD-TYPE 
                            476                             459 
[1] "3.0 - 2151.0 (476.0)" "1.0 - 2696.0 (459.0)"
[1] "hr=" "1"  
D63V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 31(12Q24.33) MUTATED         1       19       38        12        20
  DEL PEAK 31(12Q24.33) WILD-TYPE       3       94       93        31        49
                                 vv
clus                              STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 31(12Q24.33) MUTATED           18          1        7
  DEL PEAK 31(12Q24.33) WILD-TYPE         49         10       16
D63V3, multiclass
            clus
vv           DEL PEAK 31(12Q24.33) MUTATED DEL PEAK 31(12Q24.33) WILD-TYPE
  STAGE I                                1                               3
  STAGE IA                              19                              94
  STAGE IB                              38                              93
  STAGE IIA                             12                              31
  STAGE IIB                             20                              49
  STAGE IIIA                            18                              49
  STAGE IIIB                             1                              10
  STAGE IV                               7                              16
[1] 8 2
[1] TRUE
[1] "dimension of 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(12Q24.33) MUTATED    28  76   9   3
  DEL PEAK 31(12Q24.33) WILD-TYPE 115 183  31  15
D63V4, multiclass
    clus
vv   DEL PEAK 31(12Q24.33) MUTATED DEL PEAK 31(12Q24.33) WILD-TYPE
  T1                            28                             115
  T2                            76                             183
  T3                             9                              31
  T4                             3                              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 31(12Q24.33) MUTATED    70  27    18
  DEL PEAK 31(12Q24.33) WILD-TYPE 225  58    54
D63V5, multiclass
       clus
vv      DEL PEAK 31(12Q24.33) MUTATED DEL PEAK 31(12Q24.33) WILD-TYPE
  N0                               70                             225
  N1                               27                              58
  N2+N3                            18                              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"
                                 vv
clus                               M0  M1 M1A M1B  MX
  DEL PEAK 31(12Q24.33) MUTATED    67   5   0   1  42
  DEL PEAK 31(12Q24.33) WILD-TYPE 250  13   1   2  77
D63V6, multiclass
     clus
vv    DEL PEAK 31(12Q24.33) MUTATED DEL PEAK 31(12Q24.33) WILD-TYPE
  M0                             67                             250
  M1                              5                              13
  M1A                             0                               1
  M1B                             1                               2
  MX                             42                              77
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V7, binary
                                 cls
clus                                0   1
  DEL PEAK 31(12Q24.33) MUTATED    71  45
  DEL PEAK 31(12Q24.33) WILD-TYPE 177 169
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 31(12Q24.33) MUTATED     71   45
  DEL PEAK 31(12Q24.33) WILD-TYPE  177  169
        clus
vv       DEL PEAK 31(12Q24.33) MUTATED DEL PEAK 31(12Q24.33) WILD-TYPE
  FEMALE                            71                             177
  MALE                              45                             169
[1] 2 2
[1] FALSE
D63V8, continuous
                                 vv
clus                              LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 31(12Q24.33) MUTATED                            2
  DEL PEAK 31(12Q24.33) WILD-TYPE                         11
                                 vv
clus                              LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 31(12Q24.33) MUTATED                                  20
  DEL PEAK 31(12Q24.33) WILD-TYPE                                73
                                 vv
clus                              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 31(12Q24.33) MUTATED                                                   74
  DEL PEAK 31(12Q24.33) WILD-TYPE                                                220
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 31(12Q24.33) MUTATED                                            0
  DEL PEAK 31(12Q24.33) WILD-TYPE                                          4
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 31(12Q24.33) MUTATED                                               9
  DEL PEAK 31(12Q24.33) WILD-TYPE                                            10
                                 vv
clus                              LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 31(12Q24.33) MUTATED                                0
  DEL PEAK 31(12Q24.33) WILD-TYPE                              2
                                 vv
clus                              LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 31(12Q24.33) MUTATED                                    1
  DEL PEAK 31(12Q24.33) WILD-TYPE                                  3
                                 vv
clus                              LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 31(12Q24.33) MUTATED                              0
  DEL PEAK 31(12Q24.33) WILD-TYPE                            2
                                 vv
clus                              LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 31(12Q24.33) MUTATED                               7
  DEL PEAK 31(12Q24.33) WILD-TYPE                            12
                                 vv
clus                              LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 31(12Q24.33) MUTATED                                 0
  DEL PEAK 31(12Q24.33) WILD-TYPE                               1
                                 vv
clus                              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 31(12Q24.33) MUTATED                                               1
  DEL PEAK 31(12Q24.33) WILD-TYPE                                             3
                                 vv
clus                              MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 31(12Q24.33) MUTATED                              2
  DEL PEAK 31(12Q24.33) WILD-TYPE                            5
D63V9, multiclass
                                                    clus
vv                                                   DEL PEAK 31(12Q24.33) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                     2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             20
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            74
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  9
  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                                                   2
                                                    clus
vv                                                   DEL PEAK 31(12Q24.33) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                               73
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             220
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                   10
  LUNG CLEAR CELL ADENOCARCINOMA                                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                               3
  LUNG MUCINOUS ADENOCARCINOMA                                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                                   12
  LUNG SIGNET RING ADENOCARCINOMA                                                  1
  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"
D63V10, binary
                                 cls
clus                                0   1
  DEL PEAK 31(12Q24.33) MUTATED     2 114
  DEL PEAK 31(12Q24.33) WILD-TYPE  19 327
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 31(12Q24.33) MUTATED      2  114
  DEL PEAK 31(12Q24.33) WILD-TYPE   19  327
     clus
vv    DEL PEAK 31(12Q24.33) MUTATED DEL PEAK 31(12Q24.33) WILD-TYPE
  NO                              2                              19
  YES                           114                             327
[1] 2 2
[1] FALSE
D63V11, continuous
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 31(12Q24.33) MUTATED    75   2   1   5
  DEL PEAK 31(12Q24.33) WILD-TYPE 243   9   3  14
D63V12, multiclass
    clus
vv   DEL PEAK 31(12Q24.33) MUTATED DEL PEAK 31(12Q24.33) WILD-TYPE
  R0                            75                             243
  R1                             2                               9
  R2                             1                               3
  RX                             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                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 31(12Q24.33) MUTATED                                  0     1
  DEL PEAK 31(12Q24.33) WILD-TYPE                                1     5
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 31(12Q24.33) MUTATED                          11    95
  DEL PEAK 31(12Q24.33) WILD-TYPE                        15   267
D63V13, multiclass
                                  clus
vv                                 DEL PEAK 31(12Q24.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                   11
  WHITE                                                       95
                                  clus
vv                                 DEL PEAK 31(12Q24.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          5
  BLACK OR AFRICAN AMERICAN                                     15
  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"
D63V14, binary
                                 cls
clus                                0   1
  DEL PEAK 31(12Q24.33) MUTATED     1  89
  DEL PEAK 31(12Q24.33) WILD-TYPE   6 243
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 31(12Q24.33) MUTATED      1   89
  DEL PEAK 31(12Q24.33) WILD-TYPE    6  243
                        clus
vv                       DEL PEAK 31(12Q24.33) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            89
                        clus
vv                       DEL PEAK 31(12Q24.33) WILD-TYPE
  HISPANIC OR LATINO                                   6
  NOT HISPANIC OR LATINO                             243
[1] 2 2
[1] FALSE

Clustering(64) Variable = DEL PEAK 32(13Q12.11) MUTATION ANALYSIS
D64V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 32(13Q12.11) MUTATED   181  46
  DEL PEAK 32(13Q12.11) WILD-TYPE 140  36
  DEL PEAK 32(13Q12.11) MUTATED DEL PEAK 32(13Q12.11) WILD-TYPE 
                            227                             176 
  DEL PEAK 32(13Q12.11) MUTATED DEL PEAK 32(13Q12.11) WILD-TYPE 
                             46                              36 
$`DEL PEAK 32(13Q12.11) MUTATED`
TCGA-05-4382 TCGA-05-4389 TCGA-05-4390 TCGA-05-4398 TCGA-05-4405 TCGA-05-4410 
         607         1369         1126         1431          610         1958 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
        1997          455          912          913          669          791 
TCGA-05-4430 TCGA-05-4432 TCGA-05-5423 TCGA-05-5425 TCGA-35-4122 TCGA-35-4123 
         761          761          151          882          225          182 
TCGA-35-5375 TCGA-38-4625 TCGA-38-4628 TCGA-38-4632 TCGA-38-6178 TCGA-44-2656 
         264         1952         1492         1357          448         1429 
TCGA-44-2662 TCGA-44-2665 TCGA-44-3919 TCGA-44-5643 TCGA-44-5644 TCGA-44-6147 
        1280         1301          190         1013          863          845 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 
        1942         1864         1978          592          218          557 
TCGA-44-7669 TCGA-44-7670 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 
        1970          882          385           99          260          486 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A4SU TCGA-49-4501 TCGA-49-4506 TCGA-49-4507 
         287          337           76         1421          999          268 
TCGA-49-4510 TCGA-49-4512 TCGA-49-6743 TCGA-49-6761 TCGA-50-5045 TCGA-50-5051 
         896          157          369          354         2174          455 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5935 
         944         1499          282          267         2370          653 
TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 
         567          764          686         1015          255          105 
TCGA-53-7813 TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 
         424          701         1178         1479         1375           87 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 TCGA-55-6985 
         993           24           25         1475           67         1233 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7570 TCGA-55-7573 TCGA-55-7576 TCGA-55-7724 
        2151         1170            6            4           40         1958 
TCGA-55-7727 TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 TCGA-55-7994 TCGA-55-7995 
          34           54           19           21           31            5 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8206 
         100            6           43           26            4           46 
TCGA-55-8207 TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
          66           44           23           11            8           15 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 
         228            9          536           15           48           66 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A493 TCGA-55-A4DG TCGA-62-8395 
          29           48         1952           28          162         1216 
TCGA-62-8397 TCGA-62-8399 TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 
        1289         2696         2067         2199         1246          910 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 
        1728          628         1686         1968         1959         1305 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-6217 TCGA-69-7760 
         864         1559          866           31          422          202 
TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 TCGA-69-7978 TCGA-69-7980 TCGA-69-8255 
         186          414          165           70          382          129 
TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4675 
         214           61         1600          711          912           40 
TCGA-73-7499 TCGA-75-6214 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7154 
         519         1970         1973         1988         1950         1948 
TCGA-78-7155 TCGA-78-7160 TCGA-78-7161 TCGA-78-7167 TCGA-78-7535 TCGA-78-7537 
        1957          678          215         1937         1972         1944 
TCGA-78-7539 TCGA-78-8640 TCGA-78-8660 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 
         327         1949         1954          824         1959           11 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
         630          422          591         1963          508          745 
TCGA-86-8055 TCGA-86-8073 TCGA-86-8075 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
          10           13          479          482           16           19 
TCGA-86-8359 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 TCGA-86-A456 
          26           45           34           18          455           10 
TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
          30          323         1940          310           79          417 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-7771 TCGA-91-8499 TCGA-93-8067 
         372          842          224          492           36          186 
TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-97-7546 
          34          568          377          477          476          964 
TCGA-97-7554 TCGA-97-8174 TCGA-97-8177 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 
         775         1965          147          148          115          197 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
         271          392          427          459           44          170 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
         154          114          287          282          238          578 
TCGA-L9-A443 TCGA-MP-A4SV TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4T9 
         116         1946         1951         1954         1957         1980 
TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TK 
        1944         1970         1970         1955         1971 

$`DEL PEAK 32(13Q12.11) WILD-TYPE`
TCGA-05-4249 TCGA-05-4384 TCGA-05-4396 TCGA-05-4403 TCGA-05-4422 TCGA-05-4427 
        1523          426         1947          578          365          791 
TCGA-05-4433 TCGA-05-5420 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
         730          457          670           30           62           14 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-7271 
        1962         1147          864         1073          354         1971 
TCGA-38-A44F TCGA-44-2655 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2666 
         133         1324          400         1367          741           97 
TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-4112 TCGA-44-5645 
         246         1130         1163         1036          722          383 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
         723          328          302          704          658          705 
TCGA-44-6776 TCGA-44-7659 TCGA-44-7661 TCGA-44-7671 TCGA-44-7672 TCGA-44-A47A 
        1938          444          366          535          719          466 
TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4494 TCGA-49-4505 TCGA-49-4514 
         351          415         1932         1081          428         1700 
TCGA-49-6742 TCGA-49-6744 TCGA-49-6745 TCGA-50-5049 TCGA-50-5055 TCGA-50-5072 
         445          890          522         2146          785          246 
TCGA-50-5932 TCGA-50-5942 TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-6543 
        1091          883         1986         1971          280            2 
TCGA-55-6969 TCGA-55-6983 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7574 
        1239         1826           18           35          121           95 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 TCGA-55-7907 TCGA-55-7910 TCGA-55-7914 
          39           39           24           16          197            3 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8299 
          33           21           47           15           33          216 
TCGA-55-8505 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8619 TCGA-55-8621 
          29            3          146          202           49          106 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A492 TCGA-55-A494 TCGA-55-A4DF TCGA-62-8398 
          33           42            1            5           47         1970 
TCGA-62-8402 TCGA-64-1678 TCGA-64-1680 TCGA-64-5775 TCGA-67-3771 TCGA-67-3772 
        1445         1189         1126           62          610          573 
TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-69-7763 TCGA-69-7973 
         427          385          174          141          690          230 
TCGA-69-7974 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-73-4666 TCGA-73-4668 
         184           89          100           77          800          467 
TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-75-7025 TCGA-75-7027 
         131          164           38          621         1967         1956 
TCGA-75-7031 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
        1965         1944         1093         1963         1202          760 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
        1961         1963         1221         1940         1950         1934 
TCGA-78-7220 TCGA-78-7536 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 
        1965         1949          881         1952          994         1971 
TCGA-78-8655 TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 TCGA-86-7714 TCGA-86-8056 
        1981         1964         1965         1972         1968         1963 
TCGA-86-8074 TCGA-86-8076 TCGA-86-8278 TCGA-86-8281 TCGA-86-8585 TCGA-86-8672 
          24          489          476         1955           35           15 
TCGA-86-8674 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6830 TCGA-91-6849 TCGA-91-8496 
         405           14           39           60           35          197 
TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-95-7043 
         174           44          218          297          127            2 
TCGA-95-A4VK TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 TCGA-97-7941 
         121         1965         1932         1332          181           22 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 TCGA-97-8179 TCGA-L4-A4E6 TCGA-L9-A444 
         107          182           87           15          435            6 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T7 TCGA-MP-A4TA 
         285          622          353         1967         1954         1951 
TCGA-MP-A4TH TCGA-MP-A5C7 
         142         1490 

  DEL PEAK 32(13Q12.11) MUTATED DEL PEAK 32(13Q12.11) WILD-TYPE 
                              4                               1 
  DEL PEAK 32(13Q12.11) MUTATED DEL PEAK 32(13Q12.11) WILD-TYPE 
                           2696                            2146 
  DEL PEAK 32(13Q12.11) MUTATED DEL PEAK 32(13Q12.11) WILD-TYPE 
                          479.0                           444.5 
[1] "4.0 - 2696.0 (479.0)" "1.0 - 2146.0 (444.5)"
[1] "hr=" "1.2"
D64V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 32(13Q12.11) MUTATED         4       58       77        22        42
  DEL PEAK 32(13Q12.11) WILD-TYPE       0       55       54        21        27
                                 vv
clus                              STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 32(13Q12.11) MUTATED           38          7       14
  DEL PEAK 32(13Q12.11) WILD-TYPE         29          4        9
D64V3, multiclass
            clus
vv           DEL PEAK 32(13Q12.11) MUTATED DEL PEAK 32(13Q12.11) WILD-TYPE
  STAGE I                                4                               0
  STAGE IA                              58                              55
  STAGE IB                              77                              54
  STAGE IIA                             22                              21
  STAGE IIB                             42                              27
  STAGE IIIA                            38                              29
  STAGE IIIB                             7                               4
  STAGE IV                              14                               9
[1] 8 2
[1] TRUE
[1] "dimension of 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(13Q12.11) MUTATED    74 154  23  10
  DEL PEAK 32(13Q12.11) WILD-TYPE  69 105  17   8
D64V4, multiclass
    clus
vv   DEL PEAK 32(13Q12.11) MUTATED DEL PEAK 32(13Q12.11) WILD-TYPE
  T1                            74                              69
  T2                           154                             105
  T3                            23                              17
  T4                            10                               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 32(13Q12.11) MUTATED   169  47    42
  DEL PEAK 32(13Q12.11) WILD-TYPE 126  38    30
D64V5, multiclass
       clus
vv      DEL PEAK 32(13Q12.11) MUTATED DEL PEAK 32(13Q12.11) WILD-TYPE
  N0                              169                             126
  N1                               47                              38
  N2+N3                            42                              30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               M0  M1 M1A M1B  MX
  DEL PEAK 32(13Q12.11) MUTATED   176  11   0   2  71
  DEL PEAK 32(13Q12.11) WILD-TYPE 141   7   1   1  48
D64V6, multiclass
     clus
vv    DEL PEAK 32(13Q12.11) MUTATED DEL PEAK 32(13Q12.11) WILD-TYPE
  M0                            176                             141
  M1                             11                               7
  M1A                             0                               1
  M1B                             2                               1
  MX                             71                              48
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V7, binary
                                 cls
clus                                0   1
  DEL PEAK 32(13Q12.11) MUTATED   127 135
  DEL PEAK 32(13Q12.11) WILD-TYPE 121  79
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(13Q12.11) MUTATED    127  135
  DEL PEAK 32(13Q12.11) WILD-TYPE  121   79
        clus
vv       DEL PEAK 32(13Q12.11) MUTATED DEL PEAK 32(13Q12.11) WILD-TYPE
  FEMALE                           127                             121
  MALE                             135                              79
[1] 2 2
[1] FALSE
D64V8, continuous
                                 vv
clus                              LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 32(13Q12.11) MUTATED                            7
  DEL PEAK 32(13Q12.11) WILD-TYPE                          6
                                 vv
clus                              LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 32(13Q12.11) MUTATED                                  53
  DEL PEAK 32(13Q12.11) WILD-TYPE                                40
                                 vv
clus                              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 32(13Q12.11) MUTATED                                                  170
  DEL PEAK 32(13Q12.11) WILD-TYPE                                                124
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 32(13Q12.11) MUTATED                                            1
  DEL PEAK 32(13Q12.11) WILD-TYPE                                          3
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 32(13Q12.11) MUTATED                                              13
  DEL PEAK 32(13Q12.11) WILD-TYPE                                             6
                                 vv
clus                              LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 32(13Q12.11) MUTATED                                2
  DEL PEAK 32(13Q12.11) WILD-TYPE                              0
                                 vv
clus                              LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 32(13Q12.11) MUTATED                                    1
  DEL PEAK 32(13Q12.11) WILD-TYPE                                  3
                                 vv
clus                              LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 32(13Q12.11) MUTATED                              0
  DEL PEAK 32(13Q12.11) WILD-TYPE                            2
                                 vv
clus                              LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 32(13Q12.11) MUTATED                              10
  DEL PEAK 32(13Q12.11) WILD-TYPE                             9
                                 vv
clus                              LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 32(13Q12.11) MUTATED                                 1
  DEL PEAK 32(13Q12.11) WILD-TYPE                               0
                                 vv
clus                              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 32(13Q12.11) MUTATED                                               2
  DEL PEAK 32(13Q12.11) WILD-TYPE                                             2
                                 vv
clus                              MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 32(13Q12.11) MUTATED                              2
  DEL PEAK 32(13Q12.11) WILD-TYPE                            5
D64V9, multiclass
                                                    clus
vv                                                   DEL PEAK 32(13Q12.11) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                     7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             53
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           170
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 13
  LUNG CLEAR CELL ADENOCARCINOMA                                                 2
  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                                                   2
                                                    clus
vv                                                   DEL PEAK 32(13Q12.11) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                       6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                               40
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             124
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                       3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                    6
  LUNG CLEAR CELL ADENOCARCINOMA                                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                               3
  LUNG MUCINOUS ADENOCARCINOMA                                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                                    9
  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"
D64V10, binary
                                 cls
clus                                0   1
  DEL PEAK 32(13Q12.11) MUTATED     8 254
  DEL PEAK 32(13Q12.11) WILD-TYPE  13 187
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(13Q12.11) MUTATED      8  254
  DEL PEAK 32(13Q12.11) WILD-TYPE   13  187
     clus
vv    DEL PEAK 32(13Q12.11) MUTATED DEL PEAK 32(13Q12.11) WILD-TYPE
  NO                              8                              13
  YES                           254                             187
[1] 2 2
[1] FALSE
D64V11, continuous
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 32(13Q12.11) MUTATED   181   7   2  11
  DEL PEAK 32(13Q12.11) WILD-TYPE 137   4   2   8
D64V12, multiclass
    clus
vv   DEL PEAK 32(13Q12.11) MUTATED DEL PEAK 32(13Q12.11) WILD-TYPE
  R0                           181                             137
  R1                             7                               4
  R2                             2                               2
  RX                            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                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 32(13Q12.11) MUTATED                                  0     5
  DEL PEAK 32(13Q12.11) WILD-TYPE                                1     1
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 32(13Q12.11) MUTATED                          16   202
  DEL PEAK 32(13Q12.11) WILD-TYPE                        10   160
D64V13, multiclass
                                  clus
vv                                 DEL PEAK 32(13Q12.11) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                   16
  WHITE                                                      202
                                  clus
vv                                 DEL PEAK 32(13Q12.11) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          1
  BLACK OR AFRICAN AMERICAN                                     10
  WHITE                                                        160
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V14, binary
                                 cls
clus                                0   1
  DEL PEAK 32(13Q12.11) MUTATED     3 192
  DEL PEAK 32(13Q12.11) WILD-TYPE   4 140
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(13Q12.11) MUTATED      3  192
  DEL PEAK 32(13Q12.11) WILD-TYPE    4  140
                        clus
vv                       DEL PEAK 32(13Q12.11) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           192
                        clus
vv                       DEL PEAK 32(13Q12.11) WILD-TYPE
  HISPANIC OR LATINO                                   4
  NOT HISPANIC OR LATINO                             140
[1] 2 2
[1] FALSE

Clustering(65) Variable = DEL PEAK 33(13Q12.13) MUTATION ANALYSIS
D65V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 33(13Q12.13) MUTATED   179  46
  DEL PEAK 33(13Q12.13) WILD-TYPE 142  36
  DEL PEAK 33(13Q12.13) MUTATED DEL PEAK 33(13Q12.13) WILD-TYPE 
                            225                             178 
  DEL PEAK 33(13Q12.13) MUTATED DEL PEAK 33(13Q12.13) WILD-TYPE 
                             46                              36 
$`DEL PEAK 33(13Q12.13) MUTATED`
TCGA-05-4389 TCGA-05-4390 TCGA-05-4398 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 
        1369         1126         1431          610         1958         1997 
TCGA-05-4417 TCGA-05-4420 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 
         455          912          913          669          791          761 
TCGA-05-4432 TCGA-05-5423 TCGA-05-5425 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 
         761          151          882          225          182          264 
TCGA-38-4625 TCGA-38-4628 TCGA-38-4629 TCGA-38-4632 TCGA-38-6178 TCGA-44-2656 
        1952         1492          864         1357          448         1429 
TCGA-44-2662 TCGA-44-3919 TCGA-44-5643 TCGA-44-5644 TCGA-44-6147 TCGA-44-6777 
        1280          190         1013          863          845         1942 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
        1864         1978          218          557         1970          882 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B TCGA-44-A47F 
         385           99          260          486          287          337 
TCGA-44-A4SU TCGA-49-4501 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
          76         1421          999          268          896          157 
TCGA-49-6743 TCGA-49-6761 TCGA-50-5045 TCGA-50-5051 TCGA-50-5066 TCGA-50-5068 
         369          354         2174          455          944         1499 
TCGA-50-5931 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 
         267         2370          653          567          764          686 
TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 TCGA-53-7813 TCGA-55-1592 TCGA-55-1594 
        1015          255          105          424          701         1178 
TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6642 TCGA-55-6712 TCGA-55-6971 
        1479         1375           87          993           24           25 
TCGA-55-6972 TCGA-55-6980 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7283 
        1475           67         1233         2151         1170           35 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7576 TCGA-55-7724 TCGA-55-7727 TCGA-55-7815 
           6            4           40         1958           34           54 
TCGA-55-7903 TCGA-55-7911 TCGA-55-7994 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
          19           21           31          100            6           43 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8206 TCGA-55-8207 TCGA-55-8301 TCGA-55-8506 
          26            4           46           66           44           11 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8614 TCGA-55-8615 
           8           15          228            9          536           15 
TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A493 
          48           66           29           48         1952           28 
TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 TCGA-62-A46U TCGA-62-A46V 
         162         1216         1289         2696         2067         2199 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
        1246          910         1728          628         1686         1968 
TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 
        1959         1305          864         1559          866           31 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 TCGA-69-7978 
         422          202          186          414          165           70 
TCGA-69-7980 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 
         382          129          214           61         1600          711 
TCGA-73-4662 TCGA-73-4675 TCGA-73-7499 TCGA-75-6214 TCGA-75-7031 TCGA-78-7145 
         912           40          519         1970         1965         1973 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7154 TCGA-78-7155 TCGA-78-7160 TCGA-78-7161 
        1988         1950         1948         1957          678          215 
TCGA-78-7167 TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 TCGA-78-8640 TCGA-78-8660 
        1937         1972         1944          327         1949         1954 
TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 
         824         1959           11          630          422          591 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8073 TCGA-86-8075 
        1963          508          745           10           13          479 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8668 TCGA-86-8669 
         482           16           19           26           45           34 
TCGA-86-8671 TCGA-86-8673 TCGA-86-A456 TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6829 
          18          455           10           30          323         1940 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
         310           79          417          372          842          224 
TCGA-91-7771 TCGA-91-8499 TCGA-93-8067 TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 
         492           36          186           34          568          377 
TCGA-95-7947 TCGA-95-7948 TCGA-97-7546 TCGA-97-7554 TCGA-97-8174 TCGA-97-8177 
         477          476          964          775         1965          147 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
         148          115          197          271          392          427 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
         459           44          170          154          114          287 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L9-A443 TCGA-L9-A444 TCGA-MP-A4SV 
         282          238          578          116            6         1946 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TC TCGA-MP-A4TE 
        1951         1954         1957         1980         1944         1970 
TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TK 
        1970         1955         1971 

$`DEL PEAK 33(13Q12.13) WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4403 TCGA-05-4422 
        1523          607          426         1947          578          365 
TCGA-05-4427 TCGA-05-4433 TCGA-05-5420 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
         791          730          457          670           30           62 
TCGA-35-3615 TCGA-38-4626 TCGA-38-4627 TCGA-38-4630 TCGA-38-4631 TCGA-38-7271 
          14         1962         1147         1073          354         1971 
TCGA-38-A44F TCGA-44-2655 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2665 
         133         1324          400         1367          741         1301 
TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-4112 
          97          246         1130         1163         1036          722 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6148 TCGA-44-6774 
         383          723          328          302          704          658 
TCGA-44-6775 TCGA-44-6776 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7671 
         705         1938          444          592          366          535 
TCGA-44-7672 TCGA-44-A47A TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4494 
         719          466          351          415         1932         1081 
TCGA-49-4505 TCGA-49-4514 TCGA-49-6742 TCGA-49-6744 TCGA-49-6745 TCGA-50-5049 
         428         1700          445          890          522         2146 
TCGA-50-5055 TCGA-50-5072 TCGA-50-5930 TCGA-50-5932 TCGA-50-5942 TCGA-53-7624 
         785          246          282         1091          883         1986 
TCGA-53-7626 TCGA-53-A4EZ TCGA-55-6543 TCGA-55-6969 TCGA-55-6983 TCGA-55-7281 
        1971          280            2         1239         1826           18 
TCGA-55-7284 TCGA-55-7574 TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 TCGA-55-7907 
         121           95           39           39           24           16 
TCGA-55-7910 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8096 
         197            3            5           33           21           47 
TCGA-55-8097 TCGA-55-8205 TCGA-55-8299 TCGA-55-8302 TCGA-55-8505 TCGA-55-8512 
          15           33          216           23           29            3 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
         146          202           49          106           33           42 
TCGA-55-A492 TCGA-55-A494 TCGA-55-A4DF TCGA-62-8398 TCGA-62-8402 TCGA-64-1678 
           1            5           47         1970         1445         1189 
TCGA-64-1680 TCGA-64-5775 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 
        1126           62          610          573          427          385 
TCGA-67-6215 TCGA-67-6216 TCGA-69-7763 TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 
         174          141          690          230          184           89 
TCGA-69-8253 TCGA-69-8254 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 
         100           77          800          467          131          164 
TCGA-73-4677 TCGA-73-7498 TCGA-75-7025 TCGA-75-7027 TCGA-78-7148 TCGA-78-7149 
          38          621         1967         1956         1944         1093 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
        1963         1202          760         1961         1963         1221 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7220 TCGA-78-7536 TCGA-78-7540 
        1940         1950         1934         1965         1949          881 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5607 
        1952          994         1971         1981         1964         1965 
TCGA-80-5608 TCGA-86-7714 TCGA-86-8056 TCGA-86-8074 TCGA-86-8076 TCGA-86-8278 
        1972         1968         1963           24          489          476 
TCGA-86-8281 TCGA-86-8585 TCGA-86-8672 TCGA-86-8674 TCGA-86-A4P7 TCGA-86-A4P8 
        1955           35           15          405           14           39 
TCGA-91-6830 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD 
          60           35          197          174           44          218 
TCGA-93-7347 TCGA-93-7348 TCGA-95-7043 TCGA-95-A4VK TCGA-97-7547 TCGA-97-7552 
         297          127            2          121         1965         1932 
TCGA-97-7553 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 
        1332          181           22          107          182           87 
TCGA-97-8179 TCGA-L4-A4E6 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SW 
          15          435          285          622          353         1967 
TCGA-MP-A4T7 TCGA-MP-A4TA TCGA-MP-A4TH TCGA-MP-A5C7 
        1954         1951          142         1490 

  DEL PEAK 33(13Q12.13) MUTATED DEL PEAK 33(13Q12.13) WILD-TYPE 
                              4                               1 
  DEL PEAK 33(13Q12.13) MUTATED DEL PEAK 33(13Q12.13) WILD-TYPE 
                           2696                            2146 
  DEL PEAK 33(13Q12.13) MUTATED DEL PEAK 33(13Q12.13) WILD-TYPE 
                          479.0                           444.5 
[1] "4.0 - 2696.0 (479.0)" "1.0 - 2146.0 (444.5)"
[1] "hr=" "1.2"
D65V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 33(13Q12.13) MUTATED         4       58       76        22        42
  DEL PEAK 33(13Q12.13) WILD-TYPE       0       55       55        21        27
                                 vv
clus                              STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 33(13Q12.13) MUTATED           38          7       14
  DEL PEAK 33(13Q12.13) WILD-TYPE         29          4        9
D65V3, multiclass
            clus
vv           DEL PEAK 33(13Q12.13) MUTATED DEL PEAK 33(13Q12.13) WILD-TYPE
  STAGE I                                4                               0
  STAGE IA                              58                              55
  STAGE IB                              76                              55
  STAGE IIA                             22                              21
  STAGE IIB                             42                              27
  STAGE IIIA                            38                              29
  STAGE IIIB                             7                               4
  STAGE IV                              14                               9
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  DEL PEAK 33(13Q12.13) MUTATED    74 151  25  10
  DEL PEAK 33(13Q12.13) WILD-TYPE  69 108  15   8
D65V4, multiclass
    clus
vv   DEL PEAK 33(13Q12.13) MUTATED DEL PEAK 33(13Q12.13) WILD-TYPE
  T1                            74                              69
  T2                           151                             108
  T3                            25                              15
  T4                            10                               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 33(13Q12.13) MUTATED   169  46    42
  DEL PEAK 33(13Q12.13) WILD-TYPE 126  39    30
D65V5, multiclass
       clus
vv      DEL PEAK 33(13Q12.13) MUTATED DEL PEAK 33(13Q12.13) WILD-TYPE
  N0                              169                             126
  N1                               46                              39
  N2+N3                            42                              30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               M0  M1 M1A M1B  MX
  DEL PEAK 33(13Q12.13) MUTATED   175  11   0   2  71
  DEL PEAK 33(13Q12.13) WILD-TYPE 142   7   1   1  48
D65V6, multiclass
     clus
vv    DEL PEAK 33(13Q12.13) MUTATED DEL PEAK 33(13Q12.13) WILD-TYPE
  M0                            175                             142
  M1                             11                               7
  M1A                             0                               1
  M1B                             2                               1
  MX                             71                              48
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V7, binary
                                 cls
clus                                0   1
  DEL PEAK 33(13Q12.13) MUTATED   129 132
  DEL PEAK 33(13Q12.13) WILD-TYPE 119  82
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(13Q12.13) MUTATED    129  132
  DEL PEAK 33(13Q12.13) WILD-TYPE  119   82
        clus
vv       DEL PEAK 33(13Q12.13) MUTATED DEL PEAK 33(13Q12.13) WILD-TYPE
  FEMALE                           129                             119
  MALE                             132                              82
[1] 2 2
[1] FALSE
D65V8, continuous
                                 vv
clus                              LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 33(13Q12.13) MUTATED                            7
  DEL PEAK 33(13Q12.13) WILD-TYPE                          6
                                 vv
clus                              LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 33(13Q12.13) MUTATED                                  51
  DEL PEAK 33(13Q12.13) WILD-TYPE                                42
                                 vv
clus                              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 33(13Q12.13) MUTATED                                                  170
  DEL PEAK 33(13Q12.13) WILD-TYPE                                                124
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 33(13Q12.13) MUTATED                                            1
  DEL PEAK 33(13Q12.13) WILD-TYPE                                          3
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 33(13Q12.13) MUTATED                                              14
  DEL PEAK 33(13Q12.13) WILD-TYPE                                             5
                                 vv
clus                              LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 33(13Q12.13) MUTATED                                2
  DEL PEAK 33(13Q12.13) WILD-TYPE                              0
                                 vv
clus                              LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 33(13Q12.13) MUTATED                                    1
  DEL PEAK 33(13Q12.13) WILD-TYPE                                  3
                                 vv
clus                              LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 33(13Q12.13) MUTATED                              0
  DEL PEAK 33(13Q12.13) WILD-TYPE                            2
                                 vv
clus                              LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 33(13Q12.13) MUTATED                              10
  DEL PEAK 33(13Q12.13) WILD-TYPE                             9
                                 vv
clus                              LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 33(13Q12.13) MUTATED                                 1
  DEL PEAK 33(13Q12.13) WILD-TYPE                               0
                                 vv
clus                              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 33(13Q12.13) MUTATED                                               2
  DEL PEAK 33(13Q12.13) WILD-TYPE                                             2
                                 vv
clus                              MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 33(13Q12.13) MUTATED                              2
  DEL PEAK 33(13Q12.13) WILD-TYPE                            5
D65V9, multiclass
                                                    clus
vv                                                   DEL PEAK 33(13Q12.13) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                     7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             51
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           170
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 14
  LUNG CLEAR CELL ADENOCARCINOMA                                                 2
  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                                                   2
                                                    clus
vv                                                   DEL PEAK 33(13Q12.13) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                       6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                               42
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             124
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                       3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                    5
  LUNG CLEAR CELL ADENOCARCINOMA                                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                               3
  LUNG MUCINOUS ADENOCARCINOMA                                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                                    9
  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"
D65V10, binary
                                 cls
clus                                0   1
  DEL PEAK 33(13Q12.13) MUTATED     7 254
  DEL PEAK 33(13Q12.13) WILD-TYPE  14 187
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(13Q12.13) MUTATED      7  254
  DEL PEAK 33(13Q12.13) WILD-TYPE   14  187
     clus
vv    DEL PEAK 33(13Q12.13) MUTATED DEL PEAK 33(13Q12.13) WILD-TYPE
  NO                              7                              14
  YES                           254                             187
[1] 2 2
[1] FALSE
D65V11, continuous
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 33(13Q12.13) MUTATED   181   7   2  11
  DEL PEAK 33(13Q12.13) WILD-TYPE 137   4   2   8
D65V12, multiclass
    clus
vv   DEL PEAK 33(13Q12.13) MUTATED DEL PEAK 33(13Q12.13) WILD-TYPE
  R0                           181                             137
  R1                             7                               4
  R2                             2                               2
  RX                            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                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 33(13Q12.13) MUTATED                                  0     5
  DEL PEAK 33(13Q12.13) WILD-TYPE                                1     1
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 33(13Q12.13) MUTATED                          16   200
  DEL PEAK 33(13Q12.13) WILD-TYPE                        10   162
D65V13, multiclass
                                  clus
vv                                 DEL PEAK 33(13Q12.13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                   16
  WHITE                                                      200
                                  clus
vv                                 DEL PEAK 33(13Q12.13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          1
  BLACK OR AFRICAN AMERICAN                                     10
  WHITE                                                        162
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V14, binary
                                 cls
clus                                0   1
  DEL PEAK 33(13Q12.13) MUTATED     3 191
  DEL PEAK 33(13Q12.13) WILD-TYPE   4 141
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(13Q12.13) MUTATED      3  191
  DEL PEAK 33(13Q12.13) WILD-TYPE    4  141
                        clus
vv                       DEL PEAK 33(13Q12.13) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           191
                        clus
vv                       DEL PEAK 33(13Q12.13) WILD-TYPE
  HISPANIC OR LATINO                                   4
  NOT HISPANIC OR LATINO                             141
[1] 2 2
[1] FALSE

Clustering(66) Variable = DEL PEAK 34(13Q14.2) MUTATION ANALYSIS
D66V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 34(13Q14.2) MUTATED   173  44
  DEL PEAK 34(13Q14.2) WILD-TYPE 148  38
  DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE 
                           217                            186 
  DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE 
                            44                             38 
$`DEL PEAK 34(13Q14.2) MUTATED`
TCGA-05-4389 TCGA-05-4390 TCGA-05-4398 TCGA-05-4405 TCGA-05-4417 TCGA-05-4420 
        1369         1126         1431          610          455          912 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-5423 
         913          669          791          761          761          151 
TCGA-05-5425 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4628 
         882          225          182          264         1952         1492 
TCGA-38-4629 TCGA-38-4632 TCGA-38-6178 TCGA-44-2656 TCGA-44-2662 TCGA-44-3919 
         864         1357          448         1429         1280          190 
TCGA-44-5643 TCGA-44-5644 TCGA-44-6147 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
        1013          863          845         1942         1864         1978 
TCGA-44-7662 TCGA-44-7669 TCGA-44-7670 TCGA-44-8117 TCGA-44-8119 TCGA-44-A479 
         218         1970          882          385           99          486 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A4SU TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
         287          337           76         1421          428          999 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-6743 TCGA-49-6744 TCGA-49-6761 
         268          896          157          369          890          354 
TCGA-50-5045 TCGA-50-5051 TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 
        2174          455          944         1499          282          267 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 TCGA-50-6597 
        2370          653          567          764          686         1015 
TCGA-50-7109 TCGA-50-8460 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 
         255          105          424          280          701         1479 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6642 TCGA-55-6712 TCGA-55-6971 TCGA-55-6972 
        1375           87          993           24           25         1475 
TCGA-55-6980 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7570 TCGA-55-7573 
          67         1233         2151         1170            6            4 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7727 TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 
          40         1958           34           54           19           21 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8094 
          31            5          100            6           43            4 
TCGA-55-8207 TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
          66           44           23           11            8           15 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-A48Z 
         228            9          202          536           15           29 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8395 
          48         1952           28            5          162         1216 
TCGA-62-8397 TCGA-62-8399 TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 
        1289         2696         2067         2199         1246          910 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
        1728          628         1189         1686         1968         1959 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-67-3770 TCGA-67-6217 TCGA-69-7760 
        1305          864         1559           31          422          202 
TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 TCGA-69-7978 TCGA-69-7979 TCGA-69-8255 
         186          414          165           70           89          129 
TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
         214           61         1600          711          912          800 
TCGA-73-4668 TCGA-73-4675 TCGA-73-7499 TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 
         467           40          519         1965         1973         1988 
TCGA-78-7147 TCGA-78-7154 TCGA-78-7155 TCGA-78-7160 TCGA-78-7161 TCGA-78-7536 
        1950         1948         1957          678          215         1949 
TCGA-78-7539 TCGA-78-8640 TCGA-78-8660 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 
         327         1949         1954          824         1959           11 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
         630          422          591         1963          508          745 
TCGA-86-8055 TCGA-86-8075 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
          10          479          482           16           19           26 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 TCGA-86-A456 
          35           45           34           18          455           10 
TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
          30          323         1940          310           79          417 
TCGA-91-6840 TCGA-91-8499 TCGA-93-8067 TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 
         372           36          186           34          568          377 
TCGA-95-7947 TCGA-95-7948 TCGA-97-7546 TCGA-97-7554 TCGA-97-8174 TCGA-97-8177 
         477          476          964          775         1965          147 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
         148          115          197          392          427          459 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
          44          170          154          114          287          282 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L9-A443 TCGA-L9-A444 TCGA-MP-A4SV TCGA-MP-A4T2 
         238          578          116            6         1946         1951 
TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TC TCGA-MP-A4TF TCGA-MP-A4TI 
        1954         1957         1980         1944         1970         1955 
TCGA-MP-A4TK 
        1971 

$`DEL PEAK 34(13Q14.2) WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4403 TCGA-05-4410 
        1523          607          426         1947          578         1958 
TCGA-05-4415 TCGA-05-4422 TCGA-05-4427 TCGA-05-4433 TCGA-05-5420 TCGA-05-5428 
        1997          365          791          730          457          670 
TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-38-4626 TCGA-38-4627 TCGA-38-4630 
          30           62           14         1962         1147         1073 
TCGA-38-4631 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2657 TCGA-44-2659 
         354         1971          133         1324          400         1367 
TCGA-44-2661 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 
         741         1301           97          246         1130         1163 
TCGA-44-3918 TCGA-44-4112 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
        1036          722          383          723          328          302 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-7659 TCGA-44-7660 
         704          658          705         1938          444          592 
TCGA-44-7661 TCGA-44-7667 TCGA-44-7671 TCGA-44-7672 TCGA-44-8120 TCGA-44-A47A 
         366          557          535          719          260          466 
TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4494 TCGA-49-4514 TCGA-49-6742 
         351          415         1932         1081         1700          445 
TCGA-49-6745 TCGA-50-5049 TCGA-50-5055 TCGA-50-5072 TCGA-50-5932 TCGA-50-5942 
         522         2146          785          246         1091          883 
TCGA-53-7624 TCGA-53-7626 TCGA-55-1594 TCGA-55-6543 TCGA-55-6969 TCGA-55-6983 
        1986         1971         1178            2         1239         1826 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7574 TCGA-55-7725 TCGA-55-7726 
          18           35          121           95           39           39 
TCGA-55-7728 TCGA-55-7907 TCGA-55-7910 TCGA-55-7914 TCGA-55-8085 TCGA-55-8087 
          24           16          197            3           33           21 
TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8299 
          26           47           15           33           46          216 
TCGA-55-8505 TCGA-55-8512 TCGA-55-8513 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
          29            3          146           48           49           66 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A492 TCGA-55-A4DF TCGA-62-8398 
         106           33           42            1           47         1970 
TCGA-62-8402 TCGA-64-1680 TCGA-64-5775 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
        1445         1126           62          866          610          573 
TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-69-7763 TCGA-69-7973 
         427          385          174          141          690          230 
TCGA-69-7974 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-73-4670 TCGA-73-4676 
         184          382          100           77          131          164 
TCGA-73-4677 TCGA-73-7498 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7148 
          38          621         1970         1967         1956         1944 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7156 TCGA-78-7158 
        1093         1963         1202          760         1961         1963 
TCGA-78-7159 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        1221         1940         1950         1934         1937         1965 
TCGA-78-7535 TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 
        1972         1944          881         1952          994         1971 
TCGA-78-8655 TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 TCGA-86-7714 TCGA-86-8056 
        1981         1964         1965         1972         1968         1963 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8076 TCGA-86-8278 TCGA-86-8281 TCGA-86-8672 
          13           24          489          476         1955           15 
TCGA-86-8674 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6830 TCGA-91-6847 TCGA-91-6848 
         405           14           39           60          842          224 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD 
          35          492          197          174           44          218 
TCGA-93-7347 TCGA-93-7348 TCGA-95-7043 TCGA-95-A4VK TCGA-97-7547 TCGA-97-7552 
         297          127            2          121         1965         1932 
TCGA-97-7553 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 
        1332          181           22          107          182           87 
TCGA-97-8179 TCGA-97-A4M7 TCGA-L4-A4E6 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
          15          271          435          285          622          353 
TCGA-MP-A4SW TCGA-MP-A4T7 TCGA-MP-A4TA TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A5C7 
        1967         1954         1951         1970          142         1490 

  DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE 
                             4                              1 
  DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE 
                          2696                           2146 
  DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE 
                           459                            471 
[1] "4.0 - 2696.0 (459.0)" "1.0 - 2146.0 (471.0)"
[1] "hr=" "1"  
D66V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 34(13Q14.2) MUTATED         3       56       72        24        40
  DEL PEAK 34(13Q14.2) WILD-TYPE       1       57       59        19        29
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 34(13Q14.2) MUTATED           37          6       13
  DEL PEAK 34(13Q14.2) WILD-TYPE         30          5       10
D66V3, multiclass
            clus
vv           DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE
  STAGE I                               3                              1
  STAGE IA                             56                             57
  STAGE IB                             72                             59
  STAGE IIA                            24                             19
  STAGE IIB                            40                             29
  STAGE IIIA                           37                             30
  STAGE IIIB                            6                              5
  STAGE IV                             13                             10
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 34(13Q14.2) MUTATED    72 148  21   9
  DEL PEAK 34(13Q14.2) WILD-TYPE  71 111  19   9
D66V4, multiclass
    clus
vv   DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE
  T1                           72                             71
  T2                          148                            111
  T3                           21                             19
  T4                            9                              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1 N2+N3
  DEL PEAK 34(13Q14.2) MUTATED   159  48    40
  DEL PEAK 34(13Q14.2) WILD-TYPE 136  37    32
D66V5, multiclass
       clus
vv      DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE
  N0                             159                            136
  N1                              48                             37
  N2+N3                           40                             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"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 34(13Q14.2) MUTATED   168  11   0   1  69
  DEL PEAK 34(13Q14.2) WILD-TYPE 149   7   1   2  50
D66V6, multiclass
     clus
vv    DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE
  M0                           168                            149
  M1                            11                              7
  M1A                            0                              1
  M1B                            1                              2
  MX                            69                             50
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V7, binary
                                cls
clus                               0   1
  DEL PEAK 34(13Q14.2) MUTATED   132 119
  DEL PEAK 34(13Q14.2) WILD-TYPE 116  95
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(13Q14.2) MUTATED    132  119
  DEL PEAK 34(13Q14.2) WILD-TYPE  116   95
        clus
vv       DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE
  FEMALE                          132                            116
  MALE                            119                             95
[1] 2 2
[1] FALSE
D66V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 34(13Q14.2) MUTATED                            9
  DEL PEAK 34(13Q14.2) WILD-TYPE                          4
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 34(13Q14.2) MUTATED                                  49
  DEL PEAK 34(13Q14.2) WILD-TYPE                                44
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 34(13Q14.2) MUTATED                                                  163
  DEL PEAK 34(13Q14.2) WILD-TYPE                                                131
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 34(13Q14.2) MUTATED                                            1
  DEL PEAK 34(13Q14.2) WILD-TYPE                                          3
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 34(13Q14.2) MUTATED                                              11
  DEL PEAK 34(13Q14.2) WILD-TYPE                                             8
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 34(13Q14.2) MUTATED                                2
  DEL PEAK 34(13Q14.2) WILD-TYPE                              0
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 34(13Q14.2) MUTATED                                    2
  DEL PEAK 34(13Q14.2) WILD-TYPE                                  2
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 34(13Q14.2) MUTATED                              0
  DEL PEAK 34(13Q14.2) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 34(13Q14.2) MUTATED                               9
  DEL PEAK 34(13Q14.2) WILD-TYPE                            10
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 34(13Q14.2) MUTATED                                 1
  DEL PEAK 34(13Q14.2) WILD-TYPE                               0
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 34(13Q14.2) MUTATED                                               2
  DEL PEAK 34(13Q14.2) WILD-TYPE                                             2
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 34(13Q14.2) MUTATED                              2
  DEL PEAK 34(13Q14.2) WILD-TYPE                            5
D66V9, multiclass
                                                    clus
vv                                                   DEL PEAK 34(13Q14.2) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            49
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          163
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                11
  LUNG CLEAR CELL ADENOCARCINOMA                                                2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            2
  LUNG MUCINOUS ADENOCARCINOMA                                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                                 9
  LUNG SIGNET RING ADENOCARCINOMA                                               1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 2
  MUCINOUS (COLLOID) CARCINOMA                                                  2
                                                    clus
vv                                                   DEL PEAK 34(13Q14.2) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              44
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            131
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                   8
  LUNG CLEAR CELL ADENOCARCINOMA                                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              2
  LUNG MUCINOUS ADENOCARCINOMA                                                    2
  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"
D66V10, binary
                                cls
clus                               0   1
  DEL PEAK 34(13Q14.2) MUTATED    10 241
  DEL PEAK 34(13Q14.2) WILD-TYPE  11 200
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(13Q14.2) MUTATED     10  241
  DEL PEAK 34(13Q14.2) WILD-TYPE   11  200
     clus
vv    DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE
  NO                            10                             11
  YES                          241                            200
[1] 2 2
[1] FALSE
D66V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 34(13Q14.2) MUTATED   177   7   2  10
  DEL PEAK 34(13Q14.2) WILD-TYPE 141   4   2   9
D66V12, multiclass
    clus
vv   DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE
  R0                          177                            141
  R1                            7                              4
  R2                            2                              2
  RX                           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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 34(13Q14.2) MUTATED                                  1     5
  DEL PEAK 34(13Q14.2) WILD-TYPE                                0     1
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 34(13Q14.2) MUTATED                          16   195
  DEL PEAK 34(13Q14.2) WILD-TYPE                        10   167
D66V13, multiclass
                                  clus
vv                                 DEL PEAK 34(13Q14.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  16
  WHITE                                                     195
                                  clus
vv                                 DEL PEAK 34(13Q14.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         1
  BLACK OR AFRICAN AMERICAN                                    10
  WHITE                                                       167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V14, binary
                                cls
clus                               0   1
  DEL PEAK 34(13Q14.2) MUTATED     4 185
  DEL PEAK 34(13Q14.2) WILD-TYPE   3 147
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(13Q14.2) MUTATED      4  185
  DEL PEAK 34(13Q14.2) WILD-TYPE    3  147
                        clus
vv                       DEL PEAK 34(13Q14.2) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          185
                        clus
vv                       DEL PEAK 34(13Q14.2) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            147
[1] 2 2
[1] FALSE

Clustering(67) Variable = DEL PEAK 35(13Q34) MUTATION ANALYSIS
D67V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 35(13Q34) MUTATED   146  39
  DEL PEAK 35(13Q34) WILD-TYPE 175  43
  DEL PEAK 35(13Q34) MUTATED DEL PEAK 35(13Q34) WILD-TYPE 
                         185                          218 
  DEL PEAK 35(13Q34) MUTATED DEL PEAK 35(13Q34) WILD-TYPE 
                          39                           43 
$`DEL PEAK 35(13Q34) MUTATED`
TCGA-05-4389 TCGA-05-4390 TCGA-05-4398 TCGA-05-4405 TCGA-05-4417 TCGA-05-4420 
        1369         1126         1431          610          455          912 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4430 TCGA-05-4432 TCGA-05-5423 TCGA-05-5425 
         913          669          761          761          151          882 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4628 TCGA-38-4632 
         225          182          264         1952         1492         1357 
TCGA-38-6178 TCGA-44-2656 TCGA-44-5643 TCGA-44-5644 TCGA-44-6147 TCGA-44-6777 
         448         1429         1013          863          845         1942 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-8117 
        1864         1978          218          557         1970          385 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B TCGA-44-A47F TCGA-49-4505 
          99          260          486          287          337          428 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-6744 TCGA-49-6761 
         999          268          896          157          890          354 
TCGA-50-5051 TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5935 
         455         1499          282          267         2370          653 
TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 
         567          764          686         1015          255          105 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 
         424          280          701         1479         1375           87 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 TCGA-55-6985 
         993           24           25         1475           67         1233 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7570 TCGA-55-7573 TCGA-55-7576 TCGA-55-7724 
        2151         1170            6            4           40         1958 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 TCGA-55-8090 TCGA-55-8091 TCGA-55-8207 
          54           19           21            6           43           66 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8510 TCGA-55-8514 TCGA-55-8614 
          44           23           11          228          202          536 
TCGA-55-8615 TCGA-55-8616 TCGA-55-A491 TCGA-55-A493 TCGA-55-A4DG TCGA-62-8395 
          15           48         1952           28          162         1216 
TCGA-62-8397 TCGA-62-8399 TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
        1289         2696         2199         1246          910         1728 
TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 TCGA-64-5775 TCGA-64-5779 
         628         1189         1686         1968           62          864 
TCGA-64-5781 TCGA-67-3770 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 
        1559           31          422          202          186          414 
TCGA-69-7765 TCGA-69-7978 TCGA-69-7979 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
         165           70           89          129          214           61 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4675 
        1600          711          912          800          467           40 
TCGA-73-7499 TCGA-78-7145 TCGA-78-7146 TCGA-78-7154 TCGA-78-7160 TCGA-78-7161 
         519         1973         1988         1948          678          215 
TCGA-78-7162 TCGA-78-8640 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-7701 
        1940         1949         1954         1964          824           11 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
         630          422          591         1963          508          745 
TCGA-86-8055 TCGA-86-8279 TCGA-86-8280 TCGA-86-8281 TCGA-86-8359 TCGA-86-8585 
          10          482           16         1955           26           35 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8672 TCGA-86-A456 TCGA-86-A4D0 TCGA-91-6828 
          45           34           15           10           30          323 
TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-8499 
        1940          310           79          417          372           36 
TCGA-93-8067 TCGA-95-7039 TCGA-95-7948 TCGA-97-7554 TCGA-97-8171 TCGA-97-8174 
         186           34          476          775          107         1965 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
         148          115          197          392          427          459 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AG 
          44          170          154          114          287          238 
TCGA-L4-A4E5 TCGA-L9-A443 TCGA-L9-A444 TCGA-MP-A4SV TCGA-MP-A4T2 TCGA-MP-A4T4 
         578          116            6         1946         1951         1954 
TCGA-MP-A4T9 TCGA-MP-A4TC TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TK 
        1980         1944         1970         1955         1971 

$`DEL PEAK 35(13Q34) WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4403 TCGA-05-4410 
        1523          607          426         1947          578         1958 
TCGA-05-4415 TCGA-05-4422 TCGA-05-4426 TCGA-05-4427 TCGA-05-4433 TCGA-05-5420 
        1997          365          791          791          730          457 
TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-38-4626 TCGA-38-4627 
         670           30           62           14         1962         1147 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 
         864         1073          354         1971          133         1324 
TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 
         400         1367          741         1280         1301           97 
TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
         246         1130         1163         1036          190          722 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6148 TCGA-44-6774 
         383          723          328          302          704          658 
TCGA-44-6775 TCGA-44-6776 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7670 
         705         1938          444          592          366          882 
TCGA-44-7671 TCGA-44-7672 TCGA-44-A47A TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
         535          719          466          351          415           76 
TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        1932         1081         1421         1700          445          369 
TCGA-49-6745 TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 
         522         2174         2146          785          944          246 
TCGA-50-5932 TCGA-50-5942 TCGA-53-7624 TCGA-53-7626 TCGA-55-1594 TCGA-55-6543 
        1091          883         1986         1971         1178            2 
TCGA-55-6969 TCGA-55-6983 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7574 
        1239         1826           18           35          121           95 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7907 TCGA-55-7910 
          39           39           34           24           16          197 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
           3           31            5           33           21          100 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 
          26            4           47           15           33           46 
TCGA-55-8299 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8511 TCGA-55-8512 
         216           29            8           15            9            3 
TCGA-55-8513 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
         146           49           66          106           33           42 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A492 TCGA-55-A494 TCGA-55-A4DF TCGA-62-8398 
          29           48            1            5           47         1970 
TCGA-62-8402 TCGA-62-A46U TCGA-64-1680 TCGA-64-5774 TCGA-64-5778 TCGA-64-5815 
        1445         2067         1126         1959         1305          866 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 
         610          573          427          385          174          141 
TCGA-69-7763 TCGA-69-7973 TCGA-69-7974 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
         690          230          184          382          100           77 
TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-75-6214 TCGA-75-7025 
         131          164           38          621         1970         1967 
TCGA-75-7027 TCGA-75-7031 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
        1956         1965         1950         1944         1093         1963 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
        1202          760         1957         1961         1963         1221 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
        1950         1934         1937         1965         1972         1949 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 
        1944          327          881         1952          994         1971 
TCGA-78-8655 TCGA-80-5607 TCGA-80-5608 TCGA-86-6851 TCGA-86-7714 TCGA-86-8056 
        1981         1965         1972         1959         1968         1963 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8358 
          13           24          479          489          476           19 
TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6830 
          18          455          405           14           39           60 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
         842          224           35          492          197          174 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-95-7043 TCGA-95-7567 
          44          218          297          127            2          568 
TCGA-95-7944 TCGA-95-7947 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
         377          477          121          964         1965         1932 
TCGA-97-7553 TCGA-97-7937 TCGA-97-7941 TCGA-97-8172 TCGA-97-8175 TCGA-97-8177 
        1332          181           22          182           87          147 
TCGA-97-8179 TCGA-97-A4M7 TCGA-J2-A4AE TCGA-L4-A4E6 TCGA-MN-A4N1 TCGA-MN-A4N4 
          15          271          282          435          285          622 
TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TE 
         353         1967         1954         1957         1951         1970 
TCGA-MP-A4TH TCGA-MP-A5C7 
         142         1490 

  DEL PEAK 35(13Q34) MUTATED DEL PEAK 35(13Q34) WILD-TYPE 
                           4                            1 
  DEL PEAK 35(13Q34) MUTATED DEL PEAK 35(13Q34) WILD-TYPE 
                        2696                         2174 
  DEL PEAK 35(13Q34) MUTATED DEL PEAK 35(13Q34) WILD-TYPE 
                         459                          471 
[1] "4.0 - 2696.0 (459.0)" "1.0 - 2174.0 (471.0)"
[1] "hr=" "1.1"
D67V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 35(13Q34) MUTATED         3       48       60        18        35
  DEL PEAK 35(13Q34) WILD-TYPE       1       65       71        25        34
                              vv
clus                           STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 35(13Q34) MUTATED           33          4       12
  DEL PEAK 35(13Q34) WILD-TYPE         34          7       11
D67V3, multiclass
            clus
vv           DEL PEAK 35(13Q34) MUTATED DEL PEAK 35(13Q34) WILD-TYPE
  STAGE I                             3                            1
  STAGE IA                           48                           65
  STAGE IB                           60                           71
  STAGE IIA                          18                           25
  STAGE IIB                          35                           34
  STAGE IIIA                         33                           34
  STAGE IIIB                          4                            7
  STAGE IV                           12                           11
[1] 8 2
[1] TRUE
[1] "dimension of 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(13Q34) MUTATED    59 123  21   9
  DEL PEAK 35(13Q34) WILD-TYPE  84 136  19   9
D67V4, multiclass
    clus
vv   DEL PEAK 35(13Q34) MUTATED DEL PEAK 35(13Q34) WILD-TYPE
  T1                         59                           84
  T2                        123                          136
  T3                         21                           19
  T4                          9                            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 35(13Q34) MUTATED   136  38    34
  DEL PEAK 35(13Q34) WILD-TYPE 159  47    38
D67V5, multiclass
       clus
vv      DEL PEAK 35(13Q34) MUTATED DEL PEAK 35(13Q34) WILD-TYPE
  N0                           136                          159
  N1                            38                           47
  N2+N3                         34                           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"
                              vv
clus                            M0  M1 M1A M1B  MX
  DEL PEAK 35(13Q34) MUTATED   141  10   1   0  59
  DEL PEAK 35(13Q34) WILD-TYPE 176   8   0   3  60
D67V6, multiclass
     clus
vv    DEL PEAK 35(13Q34) MUTATED DEL PEAK 35(13Q34) WILD-TYPE
  M0                         141                          176
  M1                          10                            8
  M1A                          1                            0
  M1B                          0                            3
  MX                          59                           60
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V7, binary
                              cls
clus                             0   1
  DEL PEAK 35(13Q34) MUTATED   112 101
  DEL PEAK 35(13Q34) WILD-TYPE 136 113
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 35(13Q34) MUTATED    112  101
  DEL PEAK 35(13Q34) WILD-TYPE  136  113
        clus
vv       DEL PEAK 35(13Q34) MUTATED DEL PEAK 35(13Q34) WILD-TYPE
  FEMALE                        112                          136
  MALE                          101                          113
[1] 2 2
[1] FALSE
D67V8, continuous
                              vv
clus                           LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 35(13Q34) MUTATED                            8
  DEL PEAK 35(13Q34) WILD-TYPE                          5
                              vv
clus                           LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 35(13Q34) MUTATED                                  38
  DEL PEAK 35(13Q34) WILD-TYPE                                55
                              vv
clus                           LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 35(13Q34) MUTATED                                                  142
  DEL PEAK 35(13Q34) WILD-TYPE                                                152
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 35(13Q34) MUTATED                                            1
  DEL PEAK 35(13Q34) WILD-TYPE                                          3
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 35(13Q34) MUTATED                                               8
  DEL PEAK 35(13Q34) WILD-TYPE                                            11
                              vv
clus                           LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 35(13Q34) MUTATED                                1
  DEL PEAK 35(13Q34) WILD-TYPE                              1
                              vv
clus                           LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 35(13Q34) MUTATED                                    2
  DEL PEAK 35(13Q34) WILD-TYPE                                  2
                              vv
clus                           LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 35(13Q34) MUTATED                              0
  DEL PEAK 35(13Q34) WILD-TYPE                            2
                              vv
clus                           LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 35(13Q34) MUTATED                               9
  DEL PEAK 35(13Q34) WILD-TYPE                            10
                              vv
clus                           LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 35(13Q34) MUTATED                                 0
  DEL PEAK 35(13Q34) WILD-TYPE                               1
                              vv
clus                           LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 35(13Q34) MUTATED                                               3
  DEL PEAK 35(13Q34) WILD-TYPE                                             1
                              vv
clus                           MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 35(13Q34) MUTATED                              1
  DEL PEAK 35(13Q34) WILD-TYPE                            6
D67V9, multiclass
                                                    clus
vv                                                   DEL PEAK 35(13Q34) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                  8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                          38
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                        142
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                  1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                               8
  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                               3
  MUCINOUS (COLLOID) CARCINOMA                                                1
                                                    clus
vv                                                   DEL PEAK 35(13Q34) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                    5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            55
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          152
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                11
  LUNG CLEAR CELL ADENOCARCINOMA                                                1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            2
  LUNG MUCINOUS ADENOCARCINOMA                                                  2
  LUNG PAPILLARY ADENOCARCINOMA                                                10
  LUNG SIGNET RING ADENOCARCINOMA                                               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"
D67V10, binary
                              cls
clus                             0   1
  DEL PEAK 35(13Q34) MUTATED     8 205
  DEL PEAK 35(13Q34) WILD-TYPE  13 236
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 35(13Q34) MUTATED      8  205
  DEL PEAK 35(13Q34) WILD-TYPE   13  236
     clus
vv    DEL PEAK 35(13Q34) MUTATED DEL PEAK 35(13Q34) WILD-TYPE
  NO                           8                           13
  YES                        205                          236
[1] 2 2
[1] FALSE
D67V11, continuous
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 35(13Q34) MUTATED   143   7   2  10
  DEL PEAK 35(13Q34) WILD-TYPE 175   4   2   9
D67V12, multiclass
    clus
vv   DEL PEAK 35(13Q34) MUTATED DEL PEAK 35(13Q34) WILD-TYPE
  R0                        143                          175
  R1                          7                            4
  R2                          2                            2
  RX                         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                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 35(13Q34) MUTATED                                  1     6
  DEL PEAK 35(13Q34) WILD-TYPE                                0     0
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 35(13Q34) MUTATED                          14   162
  DEL PEAK 35(13Q34) WILD-TYPE                        12   200
D67V13, multiclass
                                  clus
vv                                 DEL PEAK 35(13Q34) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          1
  ASIAN                                                     6
  BLACK OR AFRICAN AMERICAN                                14
  WHITE                                                   162
                                  clus
vv                                 DEL PEAK 35(13Q34) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                  12
  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"
D67V14, binary
                              cls
clus                             0   1
  DEL PEAK 35(13Q34) MUTATED     3 157
  DEL PEAK 35(13Q34) WILD-TYPE   4 175
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 35(13Q34) MUTATED      3  157
  DEL PEAK 35(13Q34) WILD-TYPE    4  175
                        clus
vv                       DEL PEAK 35(13Q34) MUTATED
  HISPANIC OR LATINO                              3
  NOT HISPANIC OR LATINO                        157
                        clus
vv                       DEL PEAK 35(13Q34) WILD-TYPE
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          175
[1] 2 2
[1] FALSE

Clustering(68) Variable = DEL PEAK 36(14Q32.33) MUTATION ANALYSIS
D68V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 36(14Q32.33) MUTATED    96  27
  DEL PEAK 36(14Q32.33) WILD-TYPE 225  55
  DEL PEAK 36(14Q32.33) MUTATED DEL PEAK 36(14Q32.33) WILD-TYPE 
                            123                             280 
  DEL PEAK 36(14Q32.33) MUTATED DEL PEAK 36(14Q32.33) WILD-TYPE 
                             27                              55 
$`DEL PEAK 36(14Q32.33) MUTATED`
TCGA-05-4382 TCGA-05-4396 TCGA-05-4405 TCGA-05-4420 TCGA-05-4427 TCGA-05-5425 
         607         1947          610          912          791          882 
TCGA-35-4122 TCGA-38-4628 TCGA-38-4631 TCGA-38-4632 TCGA-44-2659 TCGA-44-2662 
         225         1492          354         1357         1367         1280 
TCGA-44-3398 TCGA-44-5643 TCGA-44-5644 TCGA-44-6145 TCGA-44-6146 TCGA-44-6775 
        1163         1013          863          328          302          705 
TCGA-44-7659 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-8120 
         444          557         1970          882          535          260 
TCGA-44-A47F TCGA-44-A4SS TCGA-49-4507 TCGA-49-4510 TCGA-49-4514 TCGA-49-6742 
         337          415          268          896         1700          445 
TCGA-49-6743 TCGA-49-6744 TCGA-50-5068 TCGA-50-5931 TCGA-50-5933 TCGA-50-5935 
         369          890         1499          267         2370          653 
TCGA-50-6597 TCGA-53-7626 TCGA-55-1592 TCGA-55-1595 TCGA-55-1596 TCGA-55-6712 
        1015         1971          701         1479         1375           24 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7727 TCGA-55-7910 TCGA-55-8092 TCGA-55-8094 
          18           35           34          197           26            4 
TCGA-55-8097 TCGA-55-8505 TCGA-55-8508 TCGA-55-8514 TCGA-55-8619 TCGA-55-A491 
          15           29           15          202           49         1952 
TCGA-55-A492 TCGA-62-8398 TCGA-62-A46U TCGA-62-A471 TCGA-64-1680 TCGA-64-5778 
           1         1970         2067         1246         1126         1305 
TCGA-64-5779 TCGA-64-5781 TCGA-67-3771 TCGA-67-3774 TCGA-67-6217 TCGA-69-7760 
         864         1559          610          385          422          202 
TCGA-69-7761 TCGA-69-7765 TCGA-69-7974 TCGA-69-7980 TCGA-69-A59K TCGA-73-4662 
         186          165          184          382          214          912 
TCGA-73-4675 TCGA-75-6214 TCGA-75-7027 TCGA-78-7146 TCGA-78-7147 TCGA-78-7155 
          40         1970         1956         1988         1950         1957 
TCGA-78-7220 TCGA-78-7535 TCGA-78-8640 TCGA-78-8660 TCGA-86-7711 TCGA-86-7713 
        1965         1972         1949         1954          630          422 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8056 TCGA-86-8279 
         591         1963          508          745         1963          482 
TCGA-86-8359 TCGA-86-8668 TCGA-86-8669 TCGA-86-8672 TCGA-86-A4D0 TCGA-91-6829 
          26           45           34           15           30         1940 
TCGA-91-6830 TCGA-91-6848 TCGA-91-7771 TCGA-91-8497 TCGA-93-7347 TCGA-95-7039 
          60          224          492          174          297           34 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7948 TCGA-97-7546 TCGA-97-7547 TCGA-97-8174 
         568          377          476          964         1965         1965 
TCGA-97-8177 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD 
         147          427          459           44          170          287 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L9-A443 TCGA-MN-A4N1 TCGA-MP-A4SW TCGA-MP-A4T7 
         238          578          116          285         1967         1954 
TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-MP-A4TK 
        1957         1944         1971 

$`DEL PEAK 36(14Q32.33) WILD-TYPE`
TCGA-05-4249 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4398 TCGA-05-4403 
        1523          426         1369         1126         1431          578 
TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
        1958         1997          455          365          913          669 
TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 
         791          761          761          730          457          151 
TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4123 TCGA-35-5375 
         670           30           62           14          182          264 
TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4629 TCGA-38-4630 TCGA-38-6178 
        1952         1962         1147          864         1073          448 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
        1971          133         1324         1429          400          741 
TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3918 TCGA-44-3919 
        1301           97          246         1130         1036          190 
TCGA-44-4112 TCGA-44-5645 TCGA-44-6144 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
         722          383          723          845          704          658 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 TCGA-44-7661 
        1938         1942         1864         1978          592          366 
TCGA-44-7662 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A 
         218          719          385           99          486          466 
TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 
         287          351           76         1932         1081         1421 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4512 TCGA-49-6745 TCGA-49-6761 TCGA-50-5045 
         428          999          157          522          354         2174 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 
        2146          455          785          944          246          282 
TCGA-50-5932 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-7109 
        1091          567          883          764          686          255 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-5899 
         105         1986          424          280         1178           87 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 
           2          993         1239           25         1475           67 
TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7284 TCGA-55-7570 
        1826         1233         2151         1170          121            6 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
           4           95           40         1958           39           39 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 TCGA-55-7914 
          24           54           19           16           21            3 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
          31            5           33           21          100            6 
TCGA-55-8091 TCGA-55-8096 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 
          43           47           33           46           66          216 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 TCGA-55-8511 
          44           23           11            8          228            9 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 
           3          146          536           15           48           66 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 
         106           33           42           29           48           28 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 
           5           47          162         1216         1289         2696 
TCGA-62-8402 TCGA-62-A46V TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 
        1445         2199          910         1728          628         1189 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5815 TCGA-67-3770 
        1686         1968         1959           62          866           31 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-69-7763 TCGA-69-7764 
         573          427          174          141          690          414 
TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
         230           70           89          100           77          129 
TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
          61         1600          711          800          467          131 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-75-7025 TCGA-75-7031 
         164           38          621          519         1967         1965 
TCGA-78-7145 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
        1973         1944         1093         1963         1202          760 
TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
        1948         1961         1963         1221          678          215 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7536 TCGA-78-7537 
        1940         1950         1934         1937         1949         1944 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 
         327          881         1952          994         1971         1981 
TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 
        1964         1965         1972          824         1959           11 
TCGA-86-7714 TCGA-86-8055 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        1968           10           13           24          479          489 
TCGA-86-8278 TCGA-86-8280 TCGA-86-8281 TCGA-86-8358 TCGA-86-8585 TCGA-86-8671 
         476           16         1955           19           35           18 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
         455          405           10           14           39          323 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6849 
         310           79          417          372          842           35 
TCGA-91-8496 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7348 TCGA-93-8067 
         197           36           44          218          127          186 
TCGA-95-7043 TCGA-95-7947 TCGA-95-A4VK TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
           2          477          121         1932         1332          775 
TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 TCGA-97-8179 
         181           22          107          182           87           15 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 TCGA-J2-8192 
         148          115          197          271          392          154 
TCGA-J2-8194 TCGA-J2-A4AE TCGA-L4-A4E6 TCGA-L9-A444 TCGA-MN-A4N4 TCGA-MN-A4N5 
         114          282          435            6          622          353 
TCGA-MP-A4SV TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TE 
        1946         1951         1954         1980         1951         1970 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A5C7 
        1970          142         1955         1490 

  DEL PEAK 36(14Q32.33) MUTATED DEL PEAK 36(14Q32.33) WILD-TYPE 
                              1                               2 
  DEL PEAK 36(14Q32.33) MUTATED DEL PEAK 36(14Q32.33) WILD-TYPE 
                           2370                            2696 
  DEL PEAK 36(14Q32.33) MUTATED DEL PEAK 36(14Q32.33) WILD-TYPE 
                          568.0                           431.5 
[1] "1.0 - 2370.0 (568.0)" "2.0 - 2696.0 (431.5)"
[1] "hr=" "1"  
D68V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 36(14Q32.33) MUTATED         2       27       32        16        28
  DEL PEAK 36(14Q32.33) WILD-TYPE       2       86       99        27        41
                                 vv
clus                              STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 36(14Q32.33) MUTATED           23          3        6
  DEL PEAK 36(14Q32.33) WILD-TYPE         44          8       17
D68V3, multiclass
            clus
vv           DEL PEAK 36(14Q32.33) MUTATED DEL PEAK 36(14Q32.33) WILD-TYPE
  STAGE I                                2                               2
  STAGE IA                              27                              86
  STAGE IB                              32                              99
  STAGE IIA                             16                              27
  STAGE IIB                             28                              41
  STAGE IIIA                            23                              44
  STAGE IIIB                             3                               8
  STAGE IV                               6                              17
[1] 8 2
[1] TRUE
[1] "dimension of 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(14Q32.33) MUTATED    39  75  17   5
  DEL PEAK 36(14Q32.33) WILD-TYPE 104 184  23  13
D68V4, multiclass
    clus
vv   DEL PEAK 36(14Q32.33) MUTATED DEL PEAK 36(14Q32.33) WILD-TYPE
  T1                            39                             104
  T2                            75                             184
  T3                            17                              23
  T4                             5                              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 36(14Q32.33) MUTATED    78  35    23
  DEL PEAK 36(14Q32.33) WILD-TYPE 217  50    49
D68V5, multiclass
       clus
vv      DEL PEAK 36(14Q32.33) MUTATED DEL PEAK 36(14Q32.33) WILD-TYPE
  N0                               78                             217
  N1                               35                              50
  N2+N3                            23                              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"
                                 vv
clus                               M0  M1 M1A M1B  MX
  DEL PEAK 36(14Q32.33) MUTATED    97   4   0   1  34
  DEL PEAK 36(14Q32.33) WILD-TYPE 220  14   1   2  85
D68V6, multiclass
     clus
vv    DEL PEAK 36(14Q32.33) MUTATED DEL PEAK 36(14Q32.33) WILD-TYPE
  M0                             97                             220
  M1                              4                              14
  M1A                             0                               1
  M1B                             1                               2
  MX                             34                              85
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V7, binary
                                 cls
clus                                0   1
  DEL PEAK 36(14Q32.33) MUTATED    71  66
  DEL PEAK 36(14Q32.33) WILD-TYPE 177 148
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 36(14Q32.33) MUTATED     71   66
  DEL PEAK 36(14Q32.33) WILD-TYPE  177  148
        clus
vv       DEL PEAK 36(14Q32.33) MUTATED DEL PEAK 36(14Q32.33) WILD-TYPE
  FEMALE                            71                             177
  MALE                              66                             148
[1] 2 2
[1] FALSE
D68V8, continuous
                                 vv
clus                              LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 36(14Q32.33) MUTATED                            5
  DEL PEAK 36(14Q32.33) WILD-TYPE                          8
                                 vv
clus                              LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 36(14Q32.33) MUTATED                                  26
  DEL PEAK 36(14Q32.33) WILD-TYPE                                67
                                 vv
clus                              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 36(14Q32.33) MUTATED                                                   90
  DEL PEAK 36(14Q32.33) WILD-TYPE                                                204
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 36(14Q32.33) MUTATED                                            1
  DEL PEAK 36(14Q32.33) WILD-TYPE                                          3
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 36(14Q32.33) MUTATED                                               4
  DEL PEAK 36(14Q32.33) WILD-TYPE                                            15
                                 vv
clus                              LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 36(14Q32.33) MUTATED                                2
  DEL PEAK 36(14Q32.33) WILD-TYPE                              0
                                 vv
clus                              LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 36(14Q32.33) MUTATED                                    0
  DEL PEAK 36(14Q32.33) WILD-TYPE                                  4
                                 vv
clus                              LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 36(14Q32.33) MUTATED                              1
  DEL PEAK 36(14Q32.33) WILD-TYPE                            1
                                 vv
clus                              LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 36(14Q32.33) MUTATED                               4
  DEL PEAK 36(14Q32.33) WILD-TYPE                            15
                                 vv
clus                              LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 36(14Q32.33) MUTATED                                 0
  DEL PEAK 36(14Q32.33) WILD-TYPE                               1
                                 vv
clus                              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 36(14Q32.33) MUTATED                                               0
  DEL PEAK 36(14Q32.33) WILD-TYPE                                             4
                                 vv
clus                              MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 36(14Q32.33) MUTATED                              4
  DEL PEAK 36(14Q32.33) WILD-TYPE                            3
D68V9, multiclass
                                                    clus
vv                                                   DEL PEAK 36(14Q32.33) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                     5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             26
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            90
  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                                  0
  MUCINOUS (COLLOID) CARCINOMA                                                   4
                                                    clus
vv                                                   DEL PEAK 36(14Q32.33) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                       8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                               67
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             204
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                       3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                   15
  LUNG CLEAR CELL ADENOCARCINOMA                                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                               4
  LUNG MUCINOUS ADENOCARCINOMA                                                     1
  LUNG PAPILLARY ADENOCARCINOMA                                                   15
  LUNG SIGNET RING ADENOCARCINOMA                                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                    4
  MUCINOUS (COLLOID) CARCINOMA                                                     3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V10, binary
                                 cls
clus                                0   1
  DEL PEAK 36(14Q32.33) MUTATED     8 129
  DEL PEAK 36(14Q32.33) WILD-TYPE  13 312
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 36(14Q32.33) MUTATED      8  129
  DEL PEAK 36(14Q32.33) WILD-TYPE   13  312
     clus
vv    DEL PEAK 36(14Q32.33) MUTATED DEL PEAK 36(14Q32.33) WILD-TYPE
  NO                              8                              13
  YES                           129                             312
[1] 2 2
[1] FALSE
D68V11, continuous
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 36(14Q32.33) MUTATED    93   0   0   6
  DEL PEAK 36(14Q32.33) WILD-TYPE 225  11   4  13
D68V12, multiclass
    clus
vv   DEL PEAK 36(14Q32.33) MUTATED DEL PEAK 36(14Q32.33) WILD-TYPE
  R0                            93                             225
  R1                             0                              11
  R2                             0                               4
  RX                             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                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 36(14Q32.33) MUTATED                                  0     2
  DEL PEAK 36(14Q32.33) WILD-TYPE                                1     4
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 36(14Q32.33) MUTATED                          16    99
  DEL PEAK 36(14Q32.33) WILD-TYPE                        10   263
D68V13, multiclass
                                  clus
vv                                 DEL PEAK 36(14Q32.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   16
  WHITE                                                       99
                                  clus
vv                                 DEL PEAK 36(14Q32.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          4
  BLACK OR AFRICAN AMERICAN                                     10
  WHITE                                                        263
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V14, binary
                                 cls
clus                                0   1
  DEL PEAK 36(14Q32.33) MUTATED     3 102
  DEL PEAK 36(14Q32.33) WILD-TYPE   4 230
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 36(14Q32.33) MUTATED      3  102
  DEL PEAK 36(14Q32.33) WILD-TYPE    4  230
                        clus
vv                       DEL PEAK 36(14Q32.33) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           102
                        clus
vv                       DEL PEAK 36(14Q32.33) WILD-TYPE
  HISPANIC OR LATINO                                   4
  NOT HISPANIC OR LATINO                             230
[1] 2 2
[1] FALSE

Clustering(69) Variable = DEL PEAK 37(15Q11.2) MUTATION ANALYSIS
D69V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 37(15Q11.2) MUTATED   166  38
  DEL PEAK 37(15Q11.2) WILD-TYPE 155  44
  DEL PEAK 37(15Q11.2) MUTATED DEL PEAK 37(15Q11.2) WILD-TYPE 
                           204                            199 
  DEL PEAK 37(15Q11.2) MUTATED DEL PEAK 37(15Q11.2) WILD-TYPE 
                            38                             44 
$`DEL PEAK 37(15Q11.2) MUTATED`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4389 TCGA-05-4390 TCGA-05-4398 TCGA-05-4405 
        1523          607         1369         1126         1431          610 
TCGA-05-4410 TCGA-05-4417 TCGA-05-4420 TCGA-05-4424 TCGA-05-4432 TCGA-05-5425 
        1958          455          912          913          761          882 
TCGA-05-5428 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4627 
         670          225          182          264         1952         1147 
TCGA-38-4628 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-44-2656 
        1492         1073          354         1357          448         1429 
TCGA-44-2657 TCGA-44-2659 TCGA-44-2662 TCGA-44-2668 TCGA-44-3918 TCGA-44-3919 
         400         1367         1280          246         1036          190 
TCGA-44-6144 TCGA-44-6147 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-7660 
         723          845          658          705         1942          592 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7670 TCGA-44-7672 TCGA-44-8117 
         366          218          557          882          719          385 
TCGA-44-8120 TCGA-44-A47F TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4505 TCGA-49-4510 
         260          337          415           76          428          896 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-50-5045 
         157         1700          890          522          354         2174 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5066 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 
        2146          455          944         2370          653          567 
TCGA-50-5946 TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 TCGA-53-7626 TCGA-53-A4EZ 
         686         1015          255          105         1971          280 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 
         701         1479           87          993           24         1239 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 TCGA-55-7281 
          25         1475           67         1826         1233           18 
TCGA-55-7283 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7815 TCGA-55-7903 
          35           95           40           34           54           19 
TCGA-55-7910 TCGA-55-7914 TCGA-55-8089 TCGA-55-8091 TCGA-55-8094 TCGA-55-8205 
         197            3          100           43            4           33 
TCGA-55-8207 TCGA-55-8301 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
          66           44           11            8           15          228 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48X TCGA-55-A48Z 
         536           15           48           66           33           29 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A493 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8397 
          48         1952           28           47          162         1289 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 
         910         1728          628         1189         1686         1968 
TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 
        1959         1305          864           31          610          573 
TCGA-67-6217 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
         422          165          230          184           70           89 
TCGA-69-7980 TCGA-69-8253 TCGA-69-A59K TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
         382          100          214          711          912          800 
TCGA-73-4668 TCGA-73-4675 TCGA-73-7499 TCGA-75-6214 TCGA-75-7025 TCGA-75-7031 
         467           40          519         1970         1967         1965 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7153 TCGA-78-7158 TCGA-78-7159 
        1973         1988         1950          760         1963         1221 
TCGA-78-7167 TCGA-78-7535 TCGA-78-7539 TCGA-78-7542 TCGA-78-8640 TCGA-80-5608 
        1937         1972          327         1952         1949         1972 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8073 
        1959           11          591         1963          508           13 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
          24          479          482           19           26           35 
TCGA-86-8669 TCGA-86-8671 TCGA-86-A456 TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6835 
          34           18           10           30          323           79 
TCGA-91-6840 TCGA-91-6847 TCGA-91-7771 TCGA-91-8499 TCGA-91-A4BC TCGA-93-7347 
         372          842          492           36           44          297 
TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7567 TCGA-97-7546 TCGA-97-7554 
         127          186           34          568          964          775 
TCGA-97-7937 TCGA-97-8172 TCGA-97-8174 TCGA-97-8177 TCGA-97-A4M7 TCGA-99-7458 
         181          182         1965          147          271          392 
TCGA-99-8028 TCGA-J2-8192 TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L9-A443 TCGA-L9-A444 
         459          154          238          578          116            6 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 
         285          622         1946         1967         1951         1954 
TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TK 
        1957         1944         1970         1970         1955         1971 

$`DEL PEAK 37(15Q11.2) WILD-TYPE`
TCGA-05-4384 TCGA-05-4396 TCGA-05-4403 TCGA-05-4415 TCGA-05-4422 TCGA-05-4425 
         426         1947          578         1997          365          669 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 
         791          791          761          730          457          151 
TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-38-4626 TCGA-38-4629 TCGA-38-7271 
          30           62           14         1962          864         1971 
TCGA-38-A44F TCGA-44-2655 TCGA-44-2661 TCGA-44-2665 TCGA-44-2666 TCGA-44-3396 
         133         1324          741         1301           97         1130 
TCGA-44-3398 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6145 
        1163          722         1013          863          383          328 
TCGA-44-6146 TCGA-44-6148 TCGA-44-6776 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
         302          704         1938         1864         1978          444 
TCGA-44-7669 TCGA-44-7671 TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
        1970          535           99          486          466          287 
TCGA-44-A47G TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 TCGA-49-4506 TCGA-49-4507 
         351         1932         1081         1421          999          268 
TCGA-49-6742 TCGA-49-6743 TCGA-50-5055 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
         445          369          785         1499          246          282 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5942 TCGA-50-5944 TCGA-53-7624 TCGA-53-7813 
         267         1091          883          764         1986          424 
TCGA-55-1594 TCGA-55-1596 TCGA-55-6543 TCGA-55-6986 TCGA-55-6987 TCGA-55-7284 
        1178         1375            2         2151         1170          121 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 
           6            4         1958           39           39           24 
TCGA-55-7907 TCGA-55-7911 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
          16           21           31            5           33           21 
TCGA-55-8090 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8299 
           6           26           47           15           46          216 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
          23           29            9            3          146          202 
TCGA-55-8619 TCGA-55-8621 TCGA-55-A48Y TCGA-55-A492 TCGA-55-A494 TCGA-62-8395 
          49          106           42            1            5         1216 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 
        1970         2696         1445         2067         2199         1246 
TCGA-64-1680 TCGA-64-5775 TCGA-64-5781 TCGA-64-5815 TCGA-67-3773 TCGA-67-3774 
        1126           62         1559          866          427          385 
TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
         174          141          202          186          690          414 
TCGA-69-8254 TCGA-69-8255 TCGA-71-6725 TCGA-73-4658 TCGA-73-4670 TCGA-73-4676 
          77          129           61         1600          131          164 
TCGA-73-4677 TCGA-73-7498 TCGA-75-7027 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
          38          621         1956         1944         1093         1963 
TCGA-78-7152 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7160 TCGA-78-7161 
        1202         1948         1957         1961          678          215 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7220 TCGA-78-7536 TCGA-78-7537 
        1940         1950         1934         1965         1949         1944 
TCGA-78-7540 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
         881          994         1971         1981         1954         1964 
TCGA-80-5607 TCGA-83-5908 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-8054 
        1965          824          630          422         1968          745 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8281 
          10         1963          489          476           16         1955 
TCGA-86-8668 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4P7 TCGA-86-A4P8 
          45           15          455          405           14           39 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6836 TCGA-91-6848 TCGA-91-6849 
        1940           60          310          417          224           35 
TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD TCGA-95-7043 TCGA-95-7944 TCGA-95-7947 
         197          174          218            2          377          477 
TCGA-95-7948 TCGA-95-A4VK TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7941 
         476          121         1965         1932         1332           22 
TCGA-97-8171 TCGA-97-8175 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 
         107           87           15          148          115          197 
TCGA-99-8025 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
         427           44          170          114          287          282 
TCGA-L4-A4E6 TCGA-MN-A4N5 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TH 
         435          353         1954         1980         1951          142 
TCGA-MP-A5C7 
        1490 

  DEL PEAK 37(15Q11.2) MUTATED DEL PEAK 37(15Q11.2) WILD-TYPE 
                             3                              1 
  DEL PEAK 37(15Q11.2) MUTATED DEL PEAK 37(15Q11.2) WILD-TYPE 
                          2370                           2696 
  DEL PEAK 37(15Q11.2) MUTATED DEL PEAK 37(15Q11.2) WILD-TYPE 
                         513.5                          435.0 
[1] "3.0 - 2370.0 (513.5)" "1.0 - 2696.0 (435.0)"
[1] "hr=" "1.1"
D69V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 37(15Q11.2) MUTATED         3       55       68        29        32
  DEL PEAK 37(15Q11.2) WILD-TYPE       1       58       63        14        37
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 37(15Q11.2) MUTATED           32          6       12
  DEL PEAK 37(15Q11.2) WILD-TYPE         35          5       11
D69V3, multiclass
            clus
vv           DEL PEAK 37(15Q11.2) MUTATED DEL PEAK 37(15Q11.2) WILD-TYPE
  STAGE I                               3                              1
  STAGE IA                             55                             58
  STAGE IB                             68                             63
  STAGE IIA                            29                             14
  STAGE IIB                            32                             37
  STAGE IIIA                           32                             35
  STAGE IIIB                            6                              5
  STAGE IV                             12                             11
[1] 8 2
[1] TRUE
[1] "dimension of 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(15Q11.2) MUTATED    77 135  17   8
  DEL PEAK 37(15Q11.2) WILD-TYPE  66 124  23  10
D69V4, multiclass
    clus
vv   DEL PEAK 37(15Q11.2) MUTATED DEL PEAK 37(15Q11.2) WILD-TYPE
  T1                           77                             66
  T2                          135                            124
  T3                           17                             23
  T4                            8                             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(15Q11.2) MUTATED   148  47    37
  DEL PEAK 37(15Q11.2) WILD-TYPE 147  38    35
D69V5, multiclass
       clus
vv      DEL PEAK 37(15Q11.2) MUTATED DEL PEAK 37(15Q11.2) WILD-TYPE
  N0                             148                            147
  N1                              47                             38
  N2+N3                           37                             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"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 37(15Q11.2) MUTATED   167   9   0   2  58
  DEL PEAK 37(15Q11.2) WILD-TYPE 150   9   1   1  61
D69V6, multiclass
     clus
vv    DEL PEAK 37(15Q11.2) MUTATED DEL PEAK 37(15Q11.2) WILD-TYPE
  M0                           167                            150
  M1                             9                              9
  M1A                            0                              1
  M1B                            2                              1
  MX                            58                             61
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V7, binary
                                cls
clus                               0   1
  DEL PEAK 37(15Q11.2) MUTATED   130 107
  DEL PEAK 37(15Q11.2) WILD-TYPE 118 107
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(15Q11.2) MUTATED    130  107
  DEL PEAK 37(15Q11.2) WILD-TYPE  118  107
        clus
vv       DEL PEAK 37(15Q11.2) MUTATED DEL PEAK 37(15Q11.2) WILD-TYPE
  FEMALE                          130                            118
  MALE                            107                            107
[1] 2 2
[1] FALSE
D69V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 37(15Q11.2) MUTATED                            6
  DEL PEAK 37(15Q11.2) WILD-TYPE                          7
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 37(15Q11.2) MUTATED                                  42
  DEL PEAK 37(15Q11.2) WILD-TYPE                                51
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 37(15Q11.2) MUTATED                                                  162
  DEL PEAK 37(15Q11.2) WILD-TYPE                                                132
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 37(15Q11.2) MUTATED                                            0
  DEL PEAK 37(15Q11.2) WILD-TYPE                                          4
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 37(15Q11.2) MUTATED                                               7
  DEL PEAK 37(15Q11.2) WILD-TYPE                                            12
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 37(15Q11.2) MUTATED                                1
  DEL PEAK 37(15Q11.2) WILD-TYPE                              1
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 37(15Q11.2) MUTATED                                    3
  DEL PEAK 37(15Q11.2) WILD-TYPE                                  1
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 37(15Q11.2) MUTATED                              0
  DEL PEAK 37(15Q11.2) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 37(15Q11.2) MUTATED                              11
  DEL PEAK 37(15Q11.2) WILD-TYPE                             8
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 37(15Q11.2) MUTATED                                 1
  DEL PEAK 37(15Q11.2) WILD-TYPE                               0
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 37(15Q11.2) MUTATED                                               2
  DEL PEAK 37(15Q11.2) WILD-TYPE                                             2
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 37(15Q11.2) MUTATED                              2
  DEL PEAK 37(15Q11.2) WILD-TYPE                            5
D69V9, multiclass
                                                    clus
vv                                                   DEL PEAK 37(15Q11.2) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            42
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          162
  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                                                11
  LUNG SIGNET RING ADENOCARCINOMA                                               1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 2
  MUCINOUS (COLLOID) CARCINOMA                                                  2
                                                    clus
vv                                                   DEL PEAK 37(15Q11.2) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              51
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            132
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  12
  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                                   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"
D69V10, binary
                                cls
clus                               0   1
  DEL PEAK 37(15Q11.2) MUTATED    10 227
  DEL PEAK 37(15Q11.2) WILD-TYPE  11 214
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(15Q11.2) MUTATED     10  227
  DEL PEAK 37(15Q11.2) WILD-TYPE   11  214
     clus
vv    DEL PEAK 37(15Q11.2) MUTATED DEL PEAK 37(15Q11.2) WILD-TYPE
  NO                            10                             11
  YES                          227                            214
[1] 2 2
[1] FALSE
D69V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 37(15Q11.2) MUTATED   164   7   2  11
  DEL PEAK 37(15Q11.2) WILD-TYPE 154   4   2   8
D69V12, multiclass
    clus
vv   DEL PEAK 37(15Q11.2) MUTATED DEL PEAK 37(15Q11.2) WILD-TYPE
  R0                          164                            154
  R1                            7                              4
  R2                            2                              2
  RX                           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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 37(15Q11.2) MUTATED                                  1     3
  DEL PEAK 37(15Q11.2) WILD-TYPE                                0     3
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 37(15Q11.2) MUTATED                          15   183
  DEL PEAK 37(15Q11.2) WILD-TYPE                        11   179
D69V13, multiclass
                                  clus
vv                                 DEL PEAK 37(15Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  15
  WHITE                                                     183
                                  clus
vv                                 DEL PEAK 37(15Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         3
  BLACK OR AFRICAN AMERICAN                                    11
  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"
D69V14, binary
                                cls
clus                               0   1
  DEL PEAK 37(15Q11.2) MUTATED     3 168
  DEL PEAK 37(15Q11.2) WILD-TYPE   4 164
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(15Q11.2) MUTATED      3  168
  DEL PEAK 37(15Q11.2) WILD-TYPE    4  164
                        clus
vv                       DEL PEAK 37(15Q11.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          168
                        clus
vv                       DEL PEAK 37(15Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            164
[1] 2 2
[1] FALSE

Clustering(70) Variable = DEL PEAK 38(16Q23.1) MUTATION ANALYSIS
D70V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 38(16Q23.1) MUTATED   110  25
  DEL PEAK 38(16Q23.1) WILD-TYPE 211  57
  DEL PEAK 38(16Q23.1) MUTATED DEL PEAK 38(16Q23.1) WILD-TYPE 
                           135                            268 
  DEL PEAK 38(16Q23.1) MUTATED DEL PEAK 38(16Q23.1) WILD-TYPE 
                            25                             57 
$`DEL PEAK 38(16Q23.1) MUTATED`
TCGA-05-4382 TCGA-05-4389 TCGA-05-4390 TCGA-05-4398 TCGA-05-4405 TCGA-05-4415 
         607         1369         1126         1431          610         1997 
TCGA-05-4420 TCGA-05-4424 TCGA-05-4427 TCGA-05-4432 TCGA-05-5428 TCGA-35-4122 
         912          913          791          761          670          225 
TCGA-35-4123 TCGA-38-4625 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
         182         1952         1492          864         1073          354 
TCGA-44-2661 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
         741         1036          190          722         1013          863 
TCGA-44-6775 TCGA-44-6777 TCGA-44-7660 TCGA-44-7661 TCGA-44-7669 TCGA-44-8117 
         705         1942          592          366         1970          385 
TCGA-44-8119 TCGA-44-A47B TCGA-49-4494 TCGA-49-4507 TCGA-49-4510 TCGA-49-6742 
          99          287         1081          268          896          445 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-50-5049 TCGA-50-5066 
         369          890          522          354         2146          944 
TCGA-50-5068 TCGA-50-5933 TCGA-50-5946 TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ 
        1499         2370          686         1986          424          280 
TCGA-55-1595 TCGA-55-6712 TCGA-55-6971 TCGA-55-6986 TCGA-55-7281 TCGA-55-7576 
        1479           24           25         2151           18           40 
TCGA-55-7724 TCGA-55-7726 TCGA-55-7727 TCGA-55-7903 TCGA-55-8091 TCGA-55-8205 
        1958           39           34           19           43           33 
TCGA-55-8207 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8514 TCGA-55-8616 
          66           29           11            8          202           48 
TCGA-55-8620 TCGA-55-A48X TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A493 
          66           33           29           48         1952           28 
TCGA-62-8397 TCGA-62-A46U TCGA-62-A471 TCGA-62-A472 TCGA-64-1677 TCGA-64-1679 
        1289         2067         1246          910          628         1686 
TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 TCGA-69-7763 TCGA-69-7974 TCGA-69-7978 
        1959         1305          864          690          184           70 
TCGA-69-7979 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4662 
          89          129          214           61         1600          912 
TCGA-73-4675 TCGA-75-6214 TCGA-75-7031 TCGA-78-7146 TCGA-78-7150 TCGA-78-7152 
          40         1970         1965         1988         1963         1202 
TCGA-78-7155 TCGA-78-7159 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
        1957         1221         1937         1965         1972         1949 
TCGA-83-5908 TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 
         824         1959          630          422          591         1963 
TCGA-86-8054 TCGA-86-8073 TCGA-86-8075 TCGA-86-8278 TCGA-86-8359 TCGA-86-8668 
         745           13          479          476           26           45 
TCGA-86-8672 TCGA-91-6836 TCGA-91-6847 TCGA-91-7771 TCGA-91-8499 TCGA-93-7348 
          15          417          842          492           36          127 
TCGA-93-8067 TCGA-95-7567 TCGA-97-7546 TCGA-97-7554 TCGA-97-7937 TCGA-97-8171 
         186          568          964          775          181          107 
TCGA-97-8175 TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
          87          238          578          116            6          285 
TCGA-MN-A4N5 TCGA-MP-A4TC TCGA-MP-A4TF 
         353         1944         1970 

$`DEL PEAK 38(16Q23.1) WILD-TYPE`
TCGA-05-4249 TCGA-05-4384 TCGA-05-4396 TCGA-05-4403 TCGA-05-4410 TCGA-05-4417 
        1523          426         1947          578         1958          455 
TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4433 TCGA-05-5420 
         365          669          791          761          730          457 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-5375 
         151          882           30           62           14          264 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F 
        1962         1147         1357          448         1971          133 
TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2662 TCGA-44-2665 
        1324         1429          400         1367         1280         1301 
TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-5645 TCGA-44-6144 
          97          246         1130         1163          383          723 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6776 
         328          302          845          704          658         1938 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7662 TCGA-44-7667 TCGA-44-7670 
        1864         1978          444          218          557          882 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47F 
         535          719          260          486          466          337 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4501 TCGA-49-4505 
         351          415           76         1932         1421          428 
TCGA-49-4506 TCGA-49-4512 TCGA-49-4514 TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 
         999          157         1700         2174          455          785 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5935 TCGA-50-5941 
         246          282          267         1091          653          567 
TCGA-50-5942 TCGA-50-5944 TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 TCGA-53-7626 
         883          764         1015          255          105         1971 
TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
         701         1178         1375           87            2          993 
TCGA-55-6969 TCGA-55-6972 TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 TCGA-55-6987 
        1239         1475           67         1826         1233         1170 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7725 
          35          121            6            4           95           39 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
          24           54           16          197           21            3 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
          31            5           33           21          100            6 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8299 
          26            4           47           15           46          216 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
          44           23           15          228            9            3 
TCGA-55-8513 TCGA-55-8614 TCGA-55-8615 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48Y 
         146          536           15           49          106           42 
TCGA-55-A492 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 TCGA-62-8398 
           1            5           47          162         1216         1970 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46V TCGA-64-1676 TCGA-64-1678 TCGA-64-1680 
        2696         1445         2199         1728         1189         1126 
TCGA-64-1681 TCGA-64-5775 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 
        1968           62         1559          866           31          610 
TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
         573          427          385          174          141          422 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7980 
         202          186          414          165          230          382 
TCGA-69-8253 TCGA-69-8254 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
         100           77          711          800          467          131 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-75-7025 TCGA-75-7027 
         164           38          621          519         1967         1956 
TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7153 TCGA-78-7154 
        1973         1950         1944         1093          760         1948 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        1961         1963          678          215         1940         1950 
TCGA-78-7166 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        1934         1944          327          881         1952          994 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 
        1949         1971         1981         1954         1964         1965 
TCGA-80-5608 TCGA-86-7701 TCGA-86-7714 TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 
        1972           11         1968          508           10         1963 
TCGA-86-8074 TCGA-86-8076 TCGA-86-8279 TCGA-86-8280 TCGA-86-8281 TCGA-86-8358 
          24          489          482           16         1955           19 
TCGA-86-8585 TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
          35           34           18          455          405           10 
TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
          30           14           39          323         1940           60 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 
         310           79          372          224           35          197 
TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-95-7039 TCGA-95-7043 
         174           44          218          297           34            2 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-97-7547 TCGA-97-7552 
         377          477          476          121         1965         1932 
TCGA-97-7553 TCGA-97-7941 TCGA-97-8172 TCGA-97-8174 TCGA-97-8177 TCGA-97-8179 
        1332           22          182         1965          147           15 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
         148          115          197          271          392          427 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
         459           44          170          154          114          287 
TCGA-J2-A4AE TCGA-L4-A4E6 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 
         282          435          622         1946         1967         1951 
TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TE 
        1954         1954         1957         1980         1951         1970 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
         142         1955         1971         1490 

  DEL PEAK 38(16Q23.1) MUTATED DEL PEAK 38(16Q23.1) WILD-TYPE 
                             6                              1 
  DEL PEAK 38(16Q23.1) MUTATED DEL PEAK 38(16Q23.1) WILD-TYPE 
                          2370                           2696 
  DEL PEAK 38(16Q23.1) MUTATED DEL PEAK 38(16Q23.1) WILD-TYPE 
                         610.0                          427.5 
[1] "6.0 - 2370.0 (610.0)" "1.0 - 2696.0 (427.5)"
[1] "hr=" "1.4"
D70V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 38(16Q23.1) MUTATED         1       29       48        13        26
  DEL PEAK 38(16Q23.1) WILD-TYPE       3       84       83        30        43
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 38(16Q23.1) MUTATED           24          6        8
  DEL PEAK 38(16Q23.1) WILD-TYPE         43          5       15
D70V3, multiclass
            clus
vv           DEL PEAK 38(16Q23.1) MUTATED DEL PEAK 38(16Q23.1) WILD-TYPE
  STAGE I                               1                              3
  STAGE IA                             29                             84
  STAGE IB                             48                             83
  STAGE IIA                            13                             30
  STAGE IIB                            26                             43
  STAGE IIIA                           24                             43
  STAGE IIIB                            6                              5
  STAGE IV                              8                             15
[1] 8 2
[1] TRUE
[1] "dimension of 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(16Q23.1) MUTATED    43  92  15   5
  DEL PEAK 38(16Q23.1) WILD-TYPE 100 167  25  13
D70V4, multiclass
    clus
vv   DEL PEAK 38(16Q23.1) MUTATED DEL PEAK 38(16Q23.1) WILD-TYPE
  T1                           43                            100
  T2                           92                            167
  T3                           15                             25
  T4                            5                             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 38(16Q23.1) MUTATED    96  27    29
  DEL PEAK 38(16Q23.1) WILD-TYPE 199  58    43
D70V5, multiclass
       clus
vv      DEL PEAK 38(16Q23.1) MUTATED DEL PEAK 38(16Q23.1) WILD-TYPE
  N0                              96                            199
  N1                              27                             58
  N2+N3                           29                             43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 38(16Q23.1) MUTATED   106   6   1   1  40
  DEL PEAK 38(16Q23.1) WILD-TYPE 211  12   0   2  79
D70V6, multiclass
     clus
vv    DEL PEAK 38(16Q23.1) MUTATED DEL PEAK 38(16Q23.1) WILD-TYPE
  M0                           106                            211
  M1                             6                             12
  M1A                            1                              0
  M1B                            1                              2
  MX                            40                             79
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V7, binary
                                cls
clus                               0   1
  DEL PEAK 38(16Q23.1) MUTATED    82  73
  DEL PEAK 38(16Q23.1) WILD-TYPE 166 141
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(16Q23.1) MUTATED     82   73
  DEL PEAK 38(16Q23.1) WILD-TYPE  166  141
        clus
vv       DEL PEAK 38(16Q23.1) MUTATED DEL PEAK 38(16Q23.1) WILD-TYPE
  FEMALE                           82                            166
  MALE                             73                            141
[1] 2 2
[1] FALSE
D70V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 38(16Q23.1) MUTATED                            7
  DEL PEAK 38(16Q23.1) WILD-TYPE                          6
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 38(16Q23.1) MUTATED                                  32
  DEL PEAK 38(16Q23.1) WILD-TYPE                                61
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 38(16Q23.1) MUTATED                                                   97
  DEL PEAK 38(16Q23.1) WILD-TYPE                                                197
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 38(16Q23.1) MUTATED                                            1
  DEL PEAK 38(16Q23.1) WILD-TYPE                                          3
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 38(16Q23.1) MUTATED                                               6
  DEL PEAK 38(16Q23.1) WILD-TYPE                                            13
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 38(16Q23.1) MUTATED                                2
  DEL PEAK 38(16Q23.1) WILD-TYPE                              0
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 38(16Q23.1) MUTATED                                    1
  DEL PEAK 38(16Q23.1) WILD-TYPE                                  3
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 38(16Q23.1) MUTATED                              0
  DEL PEAK 38(16Q23.1) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 38(16Q23.1) MUTATED                               5
  DEL PEAK 38(16Q23.1) WILD-TYPE                            14
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 38(16Q23.1) MUTATED                                 0
  DEL PEAK 38(16Q23.1) WILD-TYPE                               1
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 38(16Q23.1) MUTATED                                               2
  DEL PEAK 38(16Q23.1) WILD-TYPE                                             2
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 38(16Q23.1) MUTATED                              2
  DEL PEAK 38(16Q23.1) WILD-TYPE                            5
D70V9, multiclass
                                                    clus
vv                                                   DEL PEAK 38(16Q23.1) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            32
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           97
  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                                                 5
  LUNG SIGNET RING ADENOCARCINOMA                                               0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 2
  MUCINOUS (COLLOID) CARCINOMA                                                  2
                                                    clus
vv                                                   DEL PEAK 38(16Q23.1) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              61
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            197
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  13
  LUNG CLEAR CELL ADENOCARCINOMA                                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              3
  LUNG MUCINOUS ADENOCARCINOMA                                                    2
  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"
D70V10, binary
                                cls
clus                               0   1
  DEL PEAK 38(16Q23.1) MUTATED     9 146
  DEL PEAK 38(16Q23.1) WILD-TYPE  12 295
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(16Q23.1) MUTATED      9  146
  DEL PEAK 38(16Q23.1) WILD-TYPE   12  295
     clus
vv    DEL PEAK 38(16Q23.1) MUTATED DEL PEAK 38(16Q23.1) WILD-TYPE
  NO                             9                             12
  YES                          146                            295
[1] 2 2
[1] FALSE
D70V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 38(16Q23.1) MUTATED   106   2   1   7
  DEL PEAK 38(16Q23.1) WILD-TYPE 212   9   3  12
D70V12, multiclass
    clus
vv   DEL PEAK 38(16Q23.1) MUTATED DEL PEAK 38(16Q23.1) WILD-TYPE
  R0                          106                            212
  R1                            2                              9
  R2                            1                              3
  RX                            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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 38(16Q23.1) MUTATED                                  0     4
  DEL PEAK 38(16Q23.1) WILD-TYPE                                1     2
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 38(16Q23.1) MUTATED                           8   123
  DEL PEAK 38(16Q23.1) WILD-TYPE                        18   239
D70V13, multiclass
                                  clus
vv                                 DEL PEAK 38(16Q23.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                   8
  WHITE                                                     123
                                  clus
vv                                 DEL PEAK 38(16Q23.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         2
  BLACK OR AFRICAN AMERICAN                                    18
  WHITE                                                       239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V14, binary
                                cls
clus                               0   1
  DEL PEAK 38(16Q23.1) MUTATED     5 110
  DEL PEAK 38(16Q23.1) WILD-TYPE   2 222
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(16Q23.1) MUTATED      5  110
  DEL PEAK 38(16Q23.1) WILD-TYPE    2  222
                        clus
vv                       DEL PEAK 38(16Q23.1) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          110
                        clus
vv                       DEL PEAK 38(16Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            222
[1] 2 2
[1] FALSE

Clustering(71) Variable = DEL PEAK 39(17P13.3) MUTATION ANALYSIS
D71V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 39(17P13.3) MUTATED   174  38
  DEL PEAK 39(17P13.3) WILD-TYPE 147  44
  DEL PEAK 39(17P13.3) MUTATED DEL PEAK 39(17P13.3) WILD-TYPE 
                           212                            191 
  DEL PEAK 39(17P13.3) MUTATED DEL PEAK 39(17P13.3) WILD-TYPE 
                            38                             44 
$`DEL PEAK 39(17P13.3) MUTATED`
TCGA-05-4249 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 TCGA-05-4398 TCGA-05-4410 
        1523         1369         1126         1947         1431         1958 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 
        1997          455          912          669          791          791 
TCGA-05-4430 TCGA-05-4433 TCGA-05-5420 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
         761          730          457          882          670           30 
TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
         225          182         1952          354         1357          448 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 
        1429          400         1367          741         1280         1301 
TCGA-44-2668 TCGA-44-3396 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-6144 
         246         1130          190          722         1013          723 
TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 TCGA-44-7661 
         705         1942         1864         1978          592          366 
TCGA-44-7667 TCGA-44-7670 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A47B 
         557          882          385           99          260          287 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4507 TCGA-49-4510 TCGA-49-6743 TCGA-49-6744 
        1421          428          268          896          369          890 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5049 TCGA-50-5051 TCGA-50-5068 TCGA-50-5931 
         522          354         2146          455         1499          267 
TCGA-50-5941 TCGA-50-5944 TCGA-50-6597 TCGA-50-7109 TCGA-53-7624 TCGA-53-7626 
         567          764         1015          255         1986         1971 
TCGA-53-7813 TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-6712 
         424          701         1178         1479         1375           24 
TCGA-55-6972 TCGA-55-6980 TCGA-55-6985 TCGA-55-7281 TCGA-55-7573 TCGA-55-7574 
        1475           67         1233           18            4           95 
TCGA-55-7576 TCGA-55-7726 TCGA-55-7727 TCGA-55-7815 TCGA-55-7903 TCGA-55-7910 
          40           39           34           54           19          197 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8089 
          21            3           31            5           33          100 
TCGA-55-8091 TCGA-55-8094 TCGA-55-8097 TCGA-55-8205 TCGA-55-8207 TCGA-55-8302 
          43            4           15           33           66           23 
TCGA-55-8506 TCGA-55-8510 TCGA-55-8511 TCGA-55-8514 TCGA-55-8614 TCGA-55-8620 
          11          228            9          202          536           66 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 TCGA-62-8397 TCGA-62-A46U 
          33           42           29         1952         1289         2067 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
         910         1728         1189         1686         1968         1959 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 
        1305          864          866           31          610          573 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 
         427          174          422          202          186          414 
TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-8255 TCGA-69-A59K 
         165          184           70           89          129          214 
TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4668 TCGA-73-4670 TCGA-73-7499 
          61         1600          711          467          131          519 
TCGA-75-6214 TCGA-75-7025 TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
        1970         1967         1965         1973         1988         1950 
TCGA-78-7150 TCGA-78-7154 TCGA-78-7159 TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 
        1963         1948         1221         1972         1949          327 
TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8655 TCGA-80-5608 TCGA-86-6851 
         881         1952         1949         1981         1972         1959 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
          11          630          422          591         1963          508 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 TCGA-86-8278 
         745           10         1963           13          479          476 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8668 TCGA-86-8669 TCGA-91-6828 
         482           16           19           45           34          323 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-7771 
         310           79          417          372          842          492 
TCGA-91-A4BC TCGA-93-7347 TCGA-93-8067 TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 
          44          297          186           34          568          377 
TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-97-7554 TCGA-97-7937 TCGA-97-8175 
         477          476          121          775          181           87 
TCGA-97-8547 TCGA-99-7458 TCGA-99-8025 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-A4AD 
         148          392          427          170          154          287 
TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L9-A443 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
         282          578          116          285          622          353 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4TE TCGA-MP-A4TF 
        1946         1967         1954         1957         1970         1970 
TCGA-MP-A4TH TCGA-MP-A4TI 
         142         1955 

$`DEL PEAK 39(17P13.3) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4403 TCGA-05-4405 TCGA-05-4422 TCGA-05-4424 
         607          426          578          610          365          913 
TCGA-05-4432 TCGA-05-5423 TCGA-05-5715 TCGA-35-3615 TCGA-35-5375 TCGA-38-4626 
         761          151           62           14          264         1962 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-7271 TCGA-38-A44F 
        1147         1492          864         1073         1971          133 
TCGA-44-2655 TCGA-44-2666 TCGA-44-3398 TCGA-44-3918 TCGA-44-5644 TCGA-44-5645 
        1324           97         1163         1036          863          383 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6776 
         328          302          845          704          658         1938 
TCGA-44-7659 TCGA-44-7662 TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-A479 
         444          218         1970          535          719          486 
TCGA-44-A47A TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
         466          337          351          415           76         1932 
TCGA-49-4494 TCGA-49-4506 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-50-5045 
        1081          999          157         1700          445         2174 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 
         785          944          246          282         1091         2370 
TCGA-50-5935 TCGA-50-5942 TCGA-50-5946 TCGA-50-8460 TCGA-53-A4EZ TCGA-55-5899 
         653          883          686          105          280           87 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6969 TCGA-55-6971 TCGA-55-6983 TCGA-55-6986 
           2          993         1239           25         1826         2151 
TCGA-55-6987 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7724 TCGA-55-7725 
        1170           35          121            6         1958           39 
TCGA-55-7728 TCGA-55-7907 TCGA-55-8087 TCGA-55-8090 TCGA-55-8092 TCGA-55-8096 
          24           16           21            6           26           47 
TCGA-55-8206 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 
          46          216           44           29            8           15 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8621 
           3          146           15           48           49          106 
TCGA-55-A490 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
          48            1           28            5           47          162 
TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46V TCGA-62-A471 
        1216         1970         2696         1445         2199         1246 
TCGA-64-1677 TCGA-64-1680 TCGA-64-5775 TCGA-64-5781 TCGA-67-3774 TCGA-67-6216 
         628         1126           62         1559          385          141 
TCGA-69-7763 TCGA-69-7973 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-73-4662 
         690          230          382          100           77          912 
TCGA-73-4666 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-75-7027 
         800           40          164           38          621         1956 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7155 TCGA-78-7156 
        1944         1093         1202          760         1957         1961 
TCGA-78-7158 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
        1963          678          215         1940         1950         1934 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7537 TCGA-78-7633 TCGA-78-8648 TCGA-78-8660 
        1937         1965         1944          994         1971         1954 
TCGA-78-8662 TCGA-80-5607 TCGA-83-5908 TCGA-86-7714 TCGA-86-8074 TCGA-86-8076 
        1964         1965          824         1968           24          489 
TCGA-86-8281 TCGA-86-8359 TCGA-86-8585 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1955           26           35           18           15          455 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 
         405           10           30           14           39         1940 
TCGA-91-6830 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
          60          224           35          197          174           36 
TCGA-91-A4BD TCGA-93-7348 TCGA-95-7043 TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
         218          127            2          964         1965         1932 
TCGA-97-7553 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8177 
        1332           22          107          182         1965          147 
TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-8028 TCGA-99-8032 
          15          115          197          271          459           44 
TCGA-J2-8194 TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A444 TCGA-MP-A4T2 TCGA-MP-A4T7 
         114          238          435            6         1951         1954 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TK TCGA-MP-A5C7 
        1980         1951         1944         1971         1490 

  DEL PEAK 39(17P13.3) MUTATED DEL PEAK 39(17P13.3) WILD-TYPE 
                             3                              1 
  DEL PEAK 39(17P13.3) MUTATED DEL PEAK 39(17P13.3) WILD-TYPE 
                          2146                           2696 
  DEL PEAK 39(17P13.3) MUTATED DEL PEAK 39(17P13.3) WILD-TYPE 
                           478                            444 
[1] "3.0 - 2146.0 (478.0)" "1.0 - 2696.0 (444.0)"
[1] "hr=" "1.3"
D71V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 39(17P13.3) MUTATED         2       49       74        27        39
  DEL PEAK 39(17P13.3) WILD-TYPE       2       64       57        16        30
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 39(17P13.3) MUTATED           36          7       14
  DEL PEAK 39(17P13.3) WILD-TYPE         31          4        9
D71V3, multiclass
            clus
vv           DEL PEAK 39(17P13.3) MUTATED DEL PEAK 39(17P13.3) WILD-TYPE
  STAGE I                               2                              2
  STAGE IA                             49                             64
  STAGE IB                             74                             57
  STAGE IIA                            27                             16
  STAGE IIB                            39                             30
  STAGE IIIA                           36                             31
  STAGE IIIB                            7                              4
  STAGE IV                             14                              9
[1] 8 2
[1] TRUE
[1] "dimension of 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(17P13.3) MUTATED    67 152  18  10
  DEL PEAK 39(17P13.3) WILD-TYPE  76 107  22   8
D71V4, multiclass
    clus
vv   DEL PEAK 39(17P13.3) MUTATED DEL PEAK 39(17P13.3) WILD-TYPE
  T1                           67                             76
  T2                          152                            107
  T3                           18                             22
  T4                           10                              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 39(17P13.3) MUTATED   156  48    39
  DEL PEAK 39(17P13.3) WILD-TYPE 139  37    33
D71V5, multiclass
       clus
vv      DEL PEAK 39(17P13.3) MUTATED DEL PEAK 39(17P13.3) WILD-TYPE
  N0                             156                            139
  N1                              48                             37
  N2+N3                           39                             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"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 39(17P13.3) MUTATED   178  11   0   2  56
  DEL PEAK 39(17P13.3) WILD-TYPE 139   7   1   1  63
D71V6, multiclass
     clus
vv    DEL PEAK 39(17P13.3) MUTATED DEL PEAK 39(17P13.3) WILD-TYPE
  M0                           178                            139
  M1                            11                              7
  M1A                            0                              1
  M1B                            2                              1
  MX                            56                             63
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V7, binary
                                cls
clus                               0   1
  DEL PEAK 39(17P13.3) MUTATED   139 109
  DEL PEAK 39(17P13.3) WILD-TYPE 109 105
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(17P13.3) MUTATED    139  109
  DEL PEAK 39(17P13.3) WILD-TYPE  109  105
        clus
vv       DEL PEAK 39(17P13.3) MUTATED DEL PEAK 39(17P13.3) WILD-TYPE
  FEMALE                          139                            109
  MALE                            109                            105
[1] 2 2
[1] FALSE
D71V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 39(17P13.3) MUTATED                            7
  DEL PEAK 39(17P13.3) WILD-TYPE                          6
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 39(17P13.3) MUTATED                                  44
  DEL PEAK 39(17P13.3) WILD-TYPE                                49
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 39(17P13.3) MUTATED                                                  170
  DEL PEAK 39(17P13.3) WILD-TYPE                                                124
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 39(17P13.3) MUTATED                                            2
  DEL PEAK 39(17P13.3) WILD-TYPE                                          2
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 39(17P13.3) MUTATED                                               9
  DEL PEAK 39(17P13.3) WILD-TYPE                                            10
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 39(17P13.3) MUTATED                                2
  DEL PEAK 39(17P13.3) WILD-TYPE                              0
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 39(17P13.3) MUTATED                                    4
  DEL PEAK 39(17P13.3) WILD-TYPE                                  0
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 39(17P13.3) MUTATED                              0
  DEL PEAK 39(17P13.3) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 39(17P13.3) MUTATED                               5
  DEL PEAK 39(17P13.3) WILD-TYPE                            14
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 39(17P13.3) MUTATED                                 1
  DEL PEAK 39(17P13.3) WILD-TYPE                               0
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 39(17P13.3) MUTATED                                               3
  DEL PEAK 39(17P13.3) WILD-TYPE                                             1
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 39(17P13.3) MUTATED                              1
  DEL PEAK 39(17P13.3) WILD-TYPE                            6
D71V9, multiclass
                                                    clus
vv                                                   DEL PEAK 39(17P13.3) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            44
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          170
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 9
  LUNG CLEAR CELL ADENOCARCINOMA                                                2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            4
  LUNG MUCINOUS ADENOCARCINOMA                                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                                 5
  LUNG SIGNET RING ADENOCARCINOMA                                               1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 3
  MUCINOUS (COLLOID) CARCINOMA                                                  1
                                                    clus
vv                                                   DEL PEAK 39(17P13.3) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              49
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            124
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  10
  LUNG CLEAR CELL ADENOCARCINOMA                                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              0
  LUNG MUCINOUS ADENOCARCINOMA                                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                                  14
  LUNG SIGNET RING ADENOCARCINOMA                                                 0
  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"
D71V10, binary
                                cls
clus                               0   1
  DEL PEAK 39(17P13.3) MUTATED     8 240
  DEL PEAK 39(17P13.3) WILD-TYPE  13 201
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(17P13.3) MUTATED      8  240
  DEL PEAK 39(17P13.3) WILD-TYPE   13  201
     clus
vv    DEL PEAK 39(17P13.3) MUTATED DEL PEAK 39(17P13.3) WILD-TYPE
  NO                             8                             13
  YES                          240                            201
[1] 2 2
[1] FALSE
D71V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 39(17P13.3) MUTATED   177   4   1  12
  DEL PEAK 39(17P13.3) WILD-TYPE 141   7   3   7
D71V12, multiclass
    clus
vv   DEL PEAK 39(17P13.3) MUTATED DEL PEAK 39(17P13.3) WILD-TYPE
  R0                          177                            141
  R1                            4                              7
  R2                            1                              3
  RX                           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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 39(17P13.3) MUTATED                                  1     4
  DEL PEAK 39(17P13.3) WILD-TYPE                                0     2
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 39(17P13.3) MUTATED                          14   189
  DEL PEAK 39(17P13.3) WILD-TYPE                        12   173
D71V13, multiclass
                                  clus
vv                                 DEL PEAK 39(17P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  14
  WHITE                                                     189
                                  clus
vv                                 DEL PEAK 39(17P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         2
  BLACK OR AFRICAN AMERICAN                                    12
  WHITE                                                       173
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V14, binary
                                cls
clus                               0   1
  DEL PEAK 39(17P13.3) MUTATED     5 171
  DEL PEAK 39(17P13.3) WILD-TYPE   2 161
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(17P13.3) MUTATED      5  171
  DEL PEAK 39(17P13.3) WILD-TYPE    2  161
                        clus
vv                       DEL PEAK 39(17P13.3) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          171
                        clus
vv                       DEL PEAK 39(17P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            161
[1] 2 2
[1] FALSE

Clustering(72) Variable = DEL PEAK 40(17P11.2) MUTATION ANALYSIS
D72V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 40(17P11.2) MUTATED   145  29
  DEL PEAK 40(17P11.2) WILD-TYPE 176  53
  DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE 
                           174                            229 
  DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE 
                            29                             53 
$`DEL PEAK 40(17P11.2) MUTATED`
TCGA-05-4249 TCGA-05-4389 TCGA-05-4396 TCGA-05-4410 TCGA-05-4417 TCGA-05-4420 
        1523         1369         1947         1958          455          912 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4433 TCGA-05-5420 
         669          791          791          761          730          457 
TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 
         670           30           62          225          182         1952 
TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 
         354         1357          448         1429          400         1367 
TCGA-44-2662 TCGA-44-2665 TCGA-44-3396 TCGA-44-3919 TCGA-44-5643 TCGA-44-6144 
        1280         1301         1130          190         1013          723 
TCGA-44-6775 TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 TCGA-44-7662 TCGA-44-7670 
         705         1864         1978          592          218          882 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A47B TCGA-49-4505 TCGA-49-4507 
         385           99          260          287          428          268 
TCGA-49-4510 TCGA-49-4512 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
         896          157          369          890          522          354 
TCGA-50-5051 TCGA-50-5068 TCGA-50-5931 TCGA-50-5941 TCGA-50-5944 TCGA-50-7109 
         455         1499          267          567          764          255 
TCGA-53-7624 TCGA-53-7813 TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 
        1986          424          701         1178         1375           87 
TCGA-55-6712 TCGA-55-6971 TCGA-55-6972 TCGA-55-6985 TCGA-55-7281 TCGA-55-7570 
          24           25         1475         1233           18            6 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7726 TCGA-55-7727 TCGA-55-7911 
           4           95           40           39           34           21 
TCGA-55-7914 TCGA-55-7994 TCGA-55-8089 TCGA-55-8091 TCGA-55-8092 TCGA-55-8097 
           3           31          100           43           26           15 
TCGA-55-8205 TCGA-55-8302 TCGA-55-8510 TCGA-55-8511 TCGA-55-8514 TCGA-55-8614 
          33           23          228            9          202          536 
TCGA-55-8616 TCGA-55-A48Z TCGA-55-A491 TCGA-62-8397 TCGA-62-A46U TCGA-62-A472 
          48           29         1952         1289         2067          910 
TCGA-64-1676 TCGA-64-1679 TCGA-64-5774 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 
        1728         1686         1959          866           31          610 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 
         427          174          422          202          186          414 
TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-8255 TCGA-69-A59K 
         165          184           70           89          129          214 
TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4668 TCGA-73-4670 TCGA-73-7499 
          61         1600          711          467          131          519 
TCGA-75-6214 TCGA-75-7025 TCGA-75-7031 TCGA-78-7146 TCGA-78-7147 TCGA-78-7150 
        1970         1967         1965         1988         1950         1963 
TCGA-78-7154 TCGA-78-7159 TCGA-78-7535 TCGA-78-7536 TCGA-78-7540 TCGA-78-7542 
        1948         1221         1972         1949          881         1952 
TCGA-78-8640 TCGA-78-8655 TCGA-80-5608 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
        1949         1981         1972         1959           11          630 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
         591         1963          508           10         1963           13 
TCGA-86-8075 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8668 TCGA-86-8673 
         479          476          482           16           45          455 
TCGA-91-6828 TCGA-91-6831 TCGA-91-6836 TCGA-91-6840 TCGA-91-7771 TCGA-93-7347 
         323          310          417          372          492          297 
TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-7948 TCGA-95-A4VK TCGA-97-7554 
          34          568          377          476          121          775 
TCGA-97-7937 TCGA-97-8175 TCGA-97-8547 TCGA-99-8025 TCGA-99-8033 TCGA-J2-8192 
         181           87          148          427          170          154 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
         287          282          578          285          622          353 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T8 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
        1946         1967         1957         1970         1970          142 

$`DEL PEAK 40(17P11.2) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4390 TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 
         607          426         1126         1431          578          610 
TCGA-05-4415 TCGA-05-4422 TCGA-05-4424 TCGA-05-4432 TCGA-05-5423 TCGA-05-5425 
        1997          365          913          761          151          882 
TCGA-35-3615 TCGA-35-5375 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 
          14          264         1962         1147         1492          864 
TCGA-38-4630 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2661 TCGA-44-2666 
        1073         1971          133         1324          741           97 
TCGA-44-2668 TCGA-44-3398 TCGA-44-3918 TCGA-44-4112 TCGA-44-5644 TCGA-44-5645 
         246         1163         1036          722          863          383 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6776 
         328          302          845          704          658         1938 
TCGA-44-6777 TCGA-44-7659 TCGA-44-7661 TCGA-44-7667 TCGA-44-7669 TCGA-44-7671 
        1942          444          366          557         1970          535 
TCGA-44-7672 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
         719          486          466          337          351          415 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 TCGA-49-4506 TCGA-49-4514 
          76         1932         1081         1421          999         1700 
TCGA-49-6742 TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 
         445         2174         2146          785          944          246 
TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5942 TCGA-50-5946 
         282         1091         2370          653          883          686 
TCGA-50-6597 TCGA-50-8460 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1595 TCGA-55-6543 
        1015          105         1971          280         1479            2 
TCGA-55-6642 TCGA-55-6969 TCGA-55-6980 TCGA-55-6983 TCGA-55-6986 TCGA-55-6987 
         993         1239           67         1826         2151         1170 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7724 TCGA-55-7725 TCGA-55-7728 TCGA-55-7815 
          35          121         1958           39           24           54 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
          19           16          197            5           33           21 
TCGA-55-8090 TCGA-55-8094 TCGA-55-8096 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 
           6            4           47           46           66          216 
TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8512 
          44           29           11            8           15            3 
TCGA-55-8513 TCGA-55-8615 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
         146           15           49           66          106           33 
TCGA-55-A48Y TCGA-55-A490 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
          42           48            1           28            5           47 
TCGA-55-A4DG TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46V 
         162         1216         1970         2696         1445         2199 
TCGA-62-A471 TCGA-64-1677 TCGA-64-1678 TCGA-64-1680 TCGA-64-1681 TCGA-64-5775 
        1246          628         1189         1126         1968           62 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-67-3772 TCGA-67-3774 TCGA-67-6216 
        1305          864         1559          573          385          141 
TCGA-69-7763 TCGA-69-7973 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-73-4662 
         690          230          382          100           77          912 
TCGA-73-4666 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-75-7027 
         800           40          164           38          621         1956 
TCGA-78-7145 TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7155 
        1973         1944         1093         1202          760         1957 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        1961         1963          678          215         1940         1950 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7537 TCGA-78-7539 TCGA-78-7633 
        1934         1937         1965         1944          327          994 
TCGA-78-8648 TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 TCGA-83-5908 TCGA-86-7713 
        1971         1954         1964         1965          824          422 
TCGA-86-7714 TCGA-86-8054 TCGA-86-8074 TCGA-86-8076 TCGA-86-8281 TCGA-86-8358 
        1968          745           24          489         1955           19 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 
          26           35           34           18           15          405 
TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 
          10           30           14           39         1940           60 
TCGA-91-6835 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 
          79          842          224           35          197          174 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7348 TCGA-93-8067 TCGA-95-7043 
          36           44          218          127          186            2 
TCGA-95-7947 TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7941 
         477          964         1965         1932         1332           22 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 
         107          182         1965          147           15          115 
TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 TCGA-J2-8194 
         197          271          392          459           44          114 
TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MP-A4T2 TCGA-MP-A4T4 
         238          435          116            6         1951         1954 
TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TI TCGA-MP-A4TK 
        1954         1980         1951         1944         1955         1971 
TCGA-MP-A5C7 
        1490 

  DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE 
                             3                              1 
  DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE 
                          2067                           2696 
  DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE 
                           456                            477 
[1] "3.0 - 2067.0 (456.0)" "1.0 - 2696.0 (477.0)"
[1] "hr=" "1.2"
D72V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 40(17P11.2) MUTATED         2       38       64        17        34
  DEL PEAK 40(17P11.2) WILD-TYPE       2       75       67        26        35
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 40(17P11.2) MUTATED           36          3       11
  DEL PEAK 40(17P11.2) WILD-TYPE         31          8       12
D72V3, multiclass
            clus
vv           DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE
  STAGE I                               2                              2
  STAGE IA                             38                             75
  STAGE IB                             64                             67
  STAGE IIA                            17                             26
  STAGE IIB                            34                             35
  STAGE IIIA                           36                             31
  STAGE IIIB                            3                              8
  STAGE IV                             11                             12
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 40(17P11.2) MUTATED    54 128  18   4
  DEL PEAK 40(17P11.2) WILD-TYPE  89 131  22  14
D72V4, multiclass
    clus
vv   DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE
  T1                           54                             89
  T2                          128                            131
  T3                           18                             22
  T4                            4                             14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1 N2+N3
  DEL PEAK 40(17P11.2) MUTATED   125  41    35
  DEL PEAK 40(17P11.2) WILD-TYPE 170  44    37
D72V5, multiclass
       clus
vv      DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE
  N0                             125                            170
  N1                              41                             44
  N2+N3                           35                             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"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 40(17P11.2) MUTATED   144  10   0   0  50
  DEL PEAK 40(17P11.2) WILD-TYPE 173   8   1   3  69
D72V6, multiclass
     clus
vv    DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE
  M0                           144                            173
  M1                            10                              8
  M1A                            0                              1
  M1B                            0                              3
  MX                            50                             69
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V7, binary
                                cls
clus                               0   1
  DEL PEAK 40(17P11.2) MUTATED   116  89
  DEL PEAK 40(17P11.2) WILD-TYPE 132 125
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(17P11.2) MUTATED    116   89
  DEL PEAK 40(17P11.2) WILD-TYPE  132  125
        clus
vv       DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE
  FEMALE                          116                            132
  MALE                             89                            125
[1] 2 2
[1] FALSE
D72V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 40(17P11.2) MUTATED                            4
  DEL PEAK 40(17P11.2) WILD-TYPE                          9
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 40(17P11.2) MUTATED                                  37
  DEL PEAK 40(17P11.2) WILD-TYPE                                56
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 40(17P11.2) MUTATED                                                  142
  DEL PEAK 40(17P11.2) WILD-TYPE                                                152
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 40(17P11.2) MUTATED                                            2
  DEL PEAK 40(17P11.2) WILD-TYPE                                          2
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 40(17P11.2) MUTATED                                               7
  DEL PEAK 40(17P11.2) WILD-TYPE                                            12
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 40(17P11.2) MUTATED                                1
  DEL PEAK 40(17P11.2) WILD-TYPE                              1
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 40(17P11.2) MUTATED                                    4
  DEL PEAK 40(17P11.2) WILD-TYPE                                  0
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 40(17P11.2) MUTATED                              0
  DEL PEAK 40(17P11.2) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 40(17P11.2) MUTATED                               4
  DEL PEAK 40(17P11.2) WILD-TYPE                            15
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 40(17P11.2) MUTATED                                 0
  DEL PEAK 40(17P11.2) WILD-TYPE                               1
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 40(17P11.2) MUTATED                                               3
  DEL PEAK 40(17P11.2) WILD-TYPE                                             1
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 40(17P11.2) MUTATED                              1
  DEL PEAK 40(17P11.2) WILD-TYPE                            6
D72V9, multiclass
                                                    clus
vv                                                   DEL PEAK 40(17P11.2) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            37
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          142
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 7
  LUNG CLEAR CELL ADENOCARCINOMA                                                1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            4
  LUNG MUCINOUS ADENOCARCINOMA                                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                                 4
  LUNG SIGNET RING ADENOCARCINOMA                                               0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 3
  MUCINOUS (COLLOID) CARCINOMA                                                  1
                                                    clus
vv                                                   DEL PEAK 40(17P11.2) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              56
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            152
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  12
  LUNG CLEAR CELL ADENOCARCINOMA                                                  1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              0
  LUNG MUCINOUS ADENOCARCINOMA                                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                                  15
  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"
D72V10, binary
                                cls
clus                               0   1
  DEL PEAK 40(17P11.2) MUTATED     5 200
  DEL PEAK 40(17P11.2) WILD-TYPE  16 241
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(17P11.2) MUTATED      5  200
  DEL PEAK 40(17P11.2) WILD-TYPE   16  241
     clus
vv    DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE
  NO                             5                             16
  YES                          200                            241
[1] 2 2
[1] FALSE
D72V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 40(17P11.2) MUTATED   143   4   2  11
  DEL PEAK 40(17P11.2) WILD-TYPE 175   7   2   8
D72V12, multiclass
    clus
vv   DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE
  R0                          143                            175
  R1                            4                              7
  R2                            2                              2
  RX                           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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 40(17P11.2) MUTATED                                  1     2
  DEL PEAK 40(17P11.2) WILD-TYPE                                0     4
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 40(17P11.2) MUTATED                          14   152
  DEL PEAK 40(17P11.2) WILD-TYPE                        12   210
D72V13, multiclass
                                  clus
vv                                 DEL PEAK 40(17P11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  14
  WHITE                                                     152
                                  clus
vv                                 DEL PEAK 40(17P11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    12
  WHITE                                                       210
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V14, binary
                                cls
clus                               0   1
  DEL PEAK 40(17P11.2) MUTATED     5 136
  DEL PEAK 40(17P11.2) WILD-TYPE   2 196
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(17P11.2) MUTATED      5  136
  DEL PEAK 40(17P11.2) WILD-TYPE    2  196
                        clus
vv                       DEL PEAK 40(17P11.2) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          136
                        clus
vv                       DEL PEAK 40(17P11.2) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            196
[1] 2 2
[1] FALSE

Clustering(73) Variable = DEL PEAK 41(18Q21.32) MUTATION ANALYSIS
D73V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 41(18Q21.32) MUTATED   154  43
  DEL PEAK 41(18Q21.32) WILD-TYPE 167  39
  DEL PEAK 41(18Q21.32) MUTATED DEL PEAK 41(18Q21.32) WILD-TYPE 
                            197                             206 
  DEL PEAK 41(18Q21.32) MUTATED DEL PEAK 41(18Q21.32) WILD-TYPE 
                             43                              39 
$`DEL PEAK 41(18Q21.32) MUTATED`
TCGA-05-4249 TCGA-05-4396 TCGA-05-4398 TCGA-05-4405 TCGA-05-4410 TCGA-05-4417 
        1523         1947         1431          610         1958          455 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4433 
         365          913          669          791          791          730 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 
         151          882           30           62          225          182 
TCGA-35-5375 TCGA-38-4627 TCGA-38-4628 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
         264         1147         1492          354         1357          448 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2662 TCGA-44-2665 TCGA-44-2668 TCGA-44-3918 
        1429          400         1280         1301          246         1036 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6775 TCGA-44-6777 TCGA-44-6779 TCGA-44-7662 
         328          302          705         1942         1978          218 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7672 TCGA-44-A47F TCGA-44-A4SU 
         557         1970          882          719          337           76 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4512 TCGA-49-6742 
        1421          428          999          268          157          445 
TCGA-49-6743 TCGA-49-6761 TCGA-50-5051 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
         369          354          455          944         1499          246 
TCGA-50-5933 TCGA-50-5941 TCGA-50-5946 TCGA-50-6597 TCGA-53-7624 TCGA-53-7626 
        2370          567          686         1015         1986         1971 
TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-6712 TCGA-55-6971 
         280         1178         1479         1375           24           25 
TCGA-55-6972 TCGA-55-6980 TCGA-55-6985 TCGA-55-7281 TCGA-55-7283 TCGA-55-7573 
        1475           67         1233           18           35            4 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
          95           40           39           39           34           24 
TCGA-55-7910 TCGA-55-7994 TCGA-55-7995 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
         197           31            5           21          100            6 
TCGA-55-8091 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8207 TCGA-55-8301 
          43            4           47           15           66           44 
TCGA-55-8505 TCGA-55-8507 TCGA-55-8510 TCGA-55-8511 TCGA-55-8616 TCGA-55-A48Z 
          29            8          228            9           48           29 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A4DG TCGA-62-8397 
          48         1952            1           28          162         1289 
TCGA-62-A46U TCGA-62-A471 TCGA-62-A472 TCGA-64-1679 TCGA-64-1681 TCGA-64-5775 
        2067         1246          910         1686         1968           62 
TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 
        1305         1559          866           31          610          573 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7765 TCGA-69-7978 TCGA-69-7979 
         141          422          202          165           70           89 
TCGA-69-8254 TCGA-69-A59K TCGA-73-4662 TCGA-73-4666 TCGA-73-4670 TCGA-73-7498 
          77          214          912          800          131          621 
TCGA-73-7499 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 TCGA-78-7145 
         519         1970         1967         1956         1965         1973 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7150 TCGA-78-7155 TCGA-78-7161 TCGA-78-7535 
        1988         1950         1963         1957          215         1972 
TCGA-78-7536 TCGA-78-7539 TCGA-78-8660 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 
        1949          327         1954          824         1959           11 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7954 TCGA-86-8055 TCGA-86-8073 
         630          422         1968         1963           10           13 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
          24          479          476          482           16           19 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8672 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
          26           35           15         1940           60          310 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-7771 TCGA-91-A4BC 
         417          372          842          224          492           44 
TCGA-91-A4BD TCGA-93-7348 TCGA-95-7043 TCGA-95-7567 TCGA-95-7947 TCGA-97-7546 
         218          127            2          568          477          964 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7937 TCGA-97-7941 TCGA-97-8174 TCGA-97-8177 
        1965         1932          181           22         1965          147 
TCGA-97-8547 TCGA-97-8552 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
         148          115          170          154          114          287 
TCGA-J2-A4AE TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T2 
         282          285          622          353         1967         1951 
TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TK 
        1954         1954         1970         1955         1971 

$`DEL PEAK 41(18Q21.32) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4403 TCGA-05-4415 
         607          426         1369         1126          578         1997 
TCGA-05-4420 TCGA-05-4430 TCGA-05-4432 TCGA-05-5420 TCGA-05-5428 TCGA-35-3615 
         912          761          761          457          670           14 
TCGA-38-4625 TCGA-38-4626 TCGA-38-4629 TCGA-38-4630 TCGA-38-7271 TCGA-38-A44F 
        1952         1962          864         1073         1971          133 
TCGA-44-2655 TCGA-44-2659 TCGA-44-2661 TCGA-44-2666 TCGA-44-3396 TCGA-44-3398 
        1324         1367          741           97         1130         1163 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 
         190          722         1013          863          383          723 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6776 TCGA-44-6778 TCGA-44-7659 
         845          704          658         1938         1864          444 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7671 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
         592          366          535          385           99          260 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 
         486          466          287          351          415         1932 
TCGA-49-4494 TCGA-49-4510 TCGA-49-4514 TCGA-49-6744 TCGA-49-6745 TCGA-50-5045 
        1081          896         1700          890          522         2174 
TCGA-50-5049 TCGA-50-5055 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5935 
        2146          785          282          267         1091          653 
TCGA-50-5942 TCGA-50-5944 TCGA-50-7109 TCGA-50-8460 TCGA-53-7813 TCGA-55-1592 
         883          764          255          105          424          701 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6969 TCGA-55-6983 TCGA-55-6986 
          87            2          993         1239         1826         2151 
TCGA-55-6987 TCGA-55-7284 TCGA-55-7570 TCGA-55-7724 TCGA-55-7815 TCGA-55-7903 
        1170          121            6         1958           54           19 
TCGA-55-7907 TCGA-55-7911 TCGA-55-7914 TCGA-55-8085 TCGA-55-8092 TCGA-55-8205 
          16           21            3           33           26           33 
TCGA-55-8206 TCGA-55-8299 TCGA-55-8302 TCGA-55-8506 TCGA-55-8508 TCGA-55-8512 
          46          216           23           11           15            3 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8619 TCGA-55-8620 
         146          202          536           15           49           66 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A494 TCGA-55-A4DF TCGA-62-8395 
         106           33           42            5           47         1216 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46V TCGA-64-1676 TCGA-64-1677 
        1970         2696         1445         2199         1728          628 
TCGA-64-1678 TCGA-64-1680 TCGA-64-5774 TCGA-64-5779 TCGA-67-3773 TCGA-67-3774 
        1189         1126         1959          864          427          385 
TCGA-67-6215 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 TCGA-69-7974 
         174          186          690          414          230          184 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8255 TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 
         382          100          129           61         1600          711 
TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-78-7148 TCGA-78-7149 
         467           40          164           38         1944         1093 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
        1202          760         1948         1961         1963         1221 
TCGA-78-7160 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
         678         1940         1950         1934         1937         1965 
TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
        1944          881         1952          994         1949         1971 
TCGA-78-8655 TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 TCGA-86-7953 TCGA-86-7955 
        1981         1964         1965         1972          591          508 
TCGA-86-8054 TCGA-86-8056 TCGA-86-8076 TCGA-86-8281 TCGA-86-8668 TCGA-86-8669 
         745         1963          489         1955           45           34 
TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 
          18          455          405           10           30           14 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6835 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 
          39          323           79           35          197          174 
TCGA-91-8499 TCGA-93-7347 TCGA-93-8067 TCGA-95-7039 TCGA-95-7944 TCGA-95-7948 
          36          297          186           34          377          476 
TCGA-95-A4VK TCGA-97-7553 TCGA-97-7554 TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 
         121         1332          775          107          182           87 
TCGA-97-8179 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
          15          197          271          392          427          459 
TCGA-99-8032 TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
          44          238          578          435          116            6 
TCGA-MP-A4SV TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TE 
        1946         1957         1980         1951         1944         1970 
TCGA-MP-A4TH TCGA-MP-A5C7 
         142         1490 

  DEL PEAK 41(18Q21.32) MUTATED DEL PEAK 41(18Q21.32) WILD-TYPE 
                              1                               2 
  DEL PEAK 41(18Q21.32) MUTATED DEL PEAK 41(18Q21.32) WILD-TYPE 
                           2370                            2696 
  DEL PEAK 41(18Q21.32) MUTATED DEL PEAK 41(18Q21.32) WILD-TYPE 
                            422                             515 
[1] "1.0 - 2370.0 (422.0)" "2.0 - 2696.0 (515.0)"
[1] "hr=" "1.2"
D73V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 41(18Q21.32) MUTATED         1       42       66        26        41
  DEL PEAK 41(18Q21.32) WILD-TYPE       3       71       65        17        28
                                 vv
clus                              STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 41(18Q21.32) MUTATED           31          6       14
  DEL PEAK 41(18Q21.32) WILD-TYPE         36          5        9
D73V3, multiclass
            clus
vv           DEL PEAK 41(18Q21.32) MUTATED DEL PEAK 41(18Q21.32) WILD-TYPE
  STAGE I                                1                               3
  STAGE IA                              42                              71
  STAGE IB                              66                              65
  STAGE IIA                             26                              17
  STAGE IIB                             41                              28
  STAGE IIIA                            31                              36
  STAGE IIIB                             6                               5
  STAGE IV                              14                               9
[1] 8 2
[1] TRUE
[1] "dimension of 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(18Q21.32) MUTATED    61 135  21   9
  DEL PEAK 41(18Q21.32) WILD-TYPE  82 124  19   9
D73V4, multiclass
    clus
vv   DEL PEAK 41(18Q21.32) MUTATED DEL PEAK 41(18Q21.32) WILD-TYPE
  T1                            61                              82
  T2                           135                             124
  T3                            21                              19
  T4                             9                               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 41(18Q21.32) MUTATED   138  52    33
  DEL PEAK 41(18Q21.32) WILD-TYPE 157  33    39
D73V5, multiclass
       clus
vv      DEL PEAK 41(18Q21.32) MUTATED DEL PEAK 41(18Q21.32) WILD-TYPE
  N0                              138                             157
  N1                               52                              33
  N2+N3                            33                              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"
                                 vv
clus                               M0  M1 M1A M1B  MX
  DEL PEAK 41(18Q21.32) MUTATED   146  12   0   1  67
  DEL PEAK 41(18Q21.32) WILD-TYPE 171   6   1   2  52
D73V6, multiclass
     clus
vv    DEL PEAK 41(18Q21.32) MUTATED DEL PEAK 41(18Q21.32) WILD-TYPE
  M0                            146                             171
  M1                             12                               6
  M1A                             0                               1
  M1B                             1                               2
  MX                             67                              52
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V7, binary
                                 cls
clus                                0   1
  DEL PEAK 41(18Q21.32) MUTATED   129  99
  DEL PEAK 41(18Q21.32) WILD-TYPE 119 115
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 41(18Q21.32) MUTATED    129   99
  DEL PEAK 41(18Q21.32) WILD-TYPE  119  115
        clus
vv       DEL PEAK 41(18Q21.32) MUTATED DEL PEAK 41(18Q21.32) WILD-TYPE
  FEMALE                           129                             119
  MALE                              99                             115
[1] 2 2
[1] FALSE
D73V8, continuous
                                 vv
clus                              LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 41(18Q21.32) MUTATED                            7
  DEL PEAK 41(18Q21.32) WILD-TYPE                          6
                                 vv
clus                              LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 41(18Q21.32) MUTATED                                  45
  DEL PEAK 41(18Q21.32) WILD-TYPE                                48
                                 vv
clus                              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 41(18Q21.32) MUTATED                                                  149
  DEL PEAK 41(18Q21.32) WILD-TYPE                                                145
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 41(18Q21.32) MUTATED                                            1
  DEL PEAK 41(18Q21.32) WILD-TYPE                                          3
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 41(18Q21.32) MUTATED                                              10
  DEL PEAK 41(18Q21.32) WILD-TYPE                                             9
                                 vv
clus                              LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 41(18Q21.32) MUTATED                                2
  DEL PEAK 41(18Q21.32) WILD-TYPE                              0
                                 vv
clus                              LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 41(18Q21.32) MUTATED                                    3
  DEL PEAK 41(18Q21.32) WILD-TYPE                                  1
                                 vv
clus                              LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 41(18Q21.32) MUTATED                              1
  DEL PEAK 41(18Q21.32) WILD-TYPE                            1
                                 vv
clus                              LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 41(18Q21.32) MUTATED                               4
  DEL PEAK 41(18Q21.32) WILD-TYPE                            15
                                 vv
clus                              LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 41(18Q21.32) MUTATED                                 1
  DEL PEAK 41(18Q21.32) WILD-TYPE                               0
                                 vv
clus                              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 41(18Q21.32) MUTATED                                               2
  DEL PEAK 41(18Q21.32) WILD-TYPE                                             2
                                 vv
clus                              MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 41(18Q21.32) MUTATED                              3
  DEL PEAK 41(18Q21.32) WILD-TYPE                            4
D73V9, multiclass
                                                    clus
vv                                                   DEL PEAK 41(18Q21.32) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                     7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             45
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           149
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 10
  LUNG CLEAR CELL ADENOCARCINOMA                                                 2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             3
  LUNG MUCINOUS ADENOCARCINOMA                                                   1
  LUNG PAPILLARY ADENOCARCINOMA                                                  4
  LUNG SIGNET RING ADENOCARCINOMA                                                1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                  2
  MUCINOUS (COLLOID) CARCINOMA                                                   3
                                                    clus
vv                                                   DEL PEAK 41(18Q21.32) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                       6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                               48
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             145
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                       3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                    9
  LUNG CLEAR CELL ADENOCARCINOMA                                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                               1
  LUNG MUCINOUS ADENOCARCINOMA                                                     1
  LUNG PAPILLARY ADENOCARCINOMA                                                   15
  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"
D73V10, binary
                                 cls
clus                                0   1
  DEL PEAK 41(18Q21.32) MUTATED     7 221
  DEL PEAK 41(18Q21.32) WILD-TYPE  14 220
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 41(18Q21.32) MUTATED      7  221
  DEL PEAK 41(18Q21.32) WILD-TYPE   14  220
     clus
vv    DEL PEAK 41(18Q21.32) MUTATED DEL PEAK 41(18Q21.32) WILD-TYPE
  NO                              7                              14
  YES                           221                             220
[1] 2 2
[1] FALSE
D73V11, continuous
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 41(18Q21.32) MUTATED   156   8   3   5
  DEL PEAK 41(18Q21.32) WILD-TYPE 162   3   1  14
D73V12, multiclass
    clus
vv   DEL PEAK 41(18Q21.32) MUTATED DEL PEAK 41(18Q21.32) WILD-TYPE
  R0                           156                             162
  R1                             8                               3
  R2                             3                               1
  RX                             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                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 41(18Q21.32) MUTATED                                  0     2
  DEL PEAK 41(18Q21.32) WILD-TYPE                                1     4
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 41(18Q21.32) MUTATED                          11   178
  DEL PEAK 41(18Q21.32) WILD-TYPE                        15   184
D73V13, multiclass
                                  clus
vv                                 DEL PEAK 41(18Q21.32) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   11
  WHITE                                                      178
                                  clus
vv                                 DEL PEAK 41(18Q21.32) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          4
  BLACK OR AFRICAN AMERICAN                                     15
  WHITE                                                        184
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V14, binary
                                 cls
clus                                0   1
  DEL PEAK 41(18Q21.32) MUTATED     5 161
  DEL PEAK 41(18Q21.32) WILD-TYPE   2 171
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 41(18Q21.32) MUTATED      5  161
  DEL PEAK 41(18Q21.32) WILD-TYPE    2  171
                        clus
vv                       DEL PEAK 41(18Q21.32) MUTATED
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           161
                        clus
vv                       DEL PEAK 41(18Q21.32) WILD-TYPE
  HISPANIC OR LATINO                                   2
  NOT HISPANIC OR LATINO                             171
[1] 2 2
[1] FALSE

Clustering(74) Variable = DEL PEAK 42(18Q23) MUTATION ANALYSIS
D74V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 42(18Q23) MUTATED   155  43
  DEL PEAK 42(18Q23) WILD-TYPE 166  39
  DEL PEAK 42(18Q23) MUTATED DEL PEAK 42(18Q23) WILD-TYPE 
                         198                          205 
  DEL PEAK 42(18Q23) MUTATED DEL PEAK 42(18Q23) WILD-TYPE 
                          43                           39 
$`DEL PEAK 42(18Q23) MUTATED`
TCGA-05-4249 TCGA-05-4398 TCGA-05-4405 TCGA-05-4410 TCGA-05-4417 TCGA-05-4422 
        1523         1431          610         1958          455          365 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4433 TCGA-05-5423 
         913          669          791          791          730          151 
TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 
         882           30           62          225          182          264 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-44-2656 
        1147         1492          354         1357          448         1429 
TCGA-44-2657 TCGA-44-2662 TCGA-44-2665 TCGA-44-2668 TCGA-44-3918 TCGA-44-5644 
         400         1280         1301          246         1036          863 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6775 TCGA-44-6777 TCGA-44-6779 TCGA-44-7662 
         328          302          705         1942         1978          218 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7672 TCGA-44-A47F TCGA-44-A4SU 
         557         1970          882          719          337           76 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4512 TCGA-49-6742 
        1421          428          999          268          157          445 
TCGA-49-6743 TCGA-49-6761 TCGA-50-5051 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
         369          354          455          944         1499          246 
TCGA-50-5933 TCGA-50-5941 TCGA-50-5946 TCGA-50-6597 TCGA-53-7624 TCGA-53-7626 
        2370          567          686         1015         1986         1971 
TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-6712 TCGA-55-6971 
         280         1178         1479         1375           24           25 
TCGA-55-6972 TCGA-55-6980 TCGA-55-6985 TCGA-55-7281 TCGA-55-7283 TCGA-55-7573 
        1475           67         1233           18           35            4 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
          95           40           39           39           34           24 
TCGA-55-7910 TCGA-55-7994 TCGA-55-7995 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
         197           31            5           21          100            6 
TCGA-55-8091 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8207 TCGA-55-8301 
          43            4           47           15           66           44 
TCGA-55-8505 TCGA-55-8507 TCGA-55-8510 TCGA-55-8511 TCGA-55-8616 TCGA-55-A48Z 
          29            8          228            9           48           29 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A4DG TCGA-62-8397 
          48         1952            1           28          162         1289 
TCGA-62-A46U TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1679 TCGA-64-1681 
        2067         1246          910         1728         1686         1968 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 
          62         1305         1559          866           31          610 
TCGA-67-3772 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7765 TCGA-69-7978 
         573          141          422          202          165           70 
TCGA-69-7979 TCGA-69-8254 TCGA-69-A59K TCGA-73-4662 TCGA-73-4666 TCGA-73-4670 
          89           77          214          912          800          131 
TCGA-73-7498 TCGA-73-7499 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 
         621          519         1970         1967         1956         1965 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7150 TCGA-78-7155 TCGA-78-7161 
        1973         1988         1950         1963         1957          215 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
        1972         1949          327         1954         1964          824 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 TCGA-86-7954 TCGA-86-8054 
        1959           11          630         1968         1963          745 
TCGA-86-8055 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8278 TCGA-86-8279 
          10           13           24          479          476          482 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8672 TCGA-91-6829 
          16           19           26           35           15         1940 
TCGA-91-6830 TCGA-91-6836 TCGA-91-6840 TCGA-91-6848 TCGA-91-7771 TCGA-91-8499 
          60          417          372          224          492           36 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7348 TCGA-95-7039 TCGA-95-7567 TCGA-95-7947 
          44          218          127           34          568          477 
TCGA-97-7546 TCGA-97-7552 TCGA-97-7937 TCGA-97-7941 TCGA-97-8174 TCGA-97-8177 
         964         1932          181           22         1965          147 
TCGA-97-8547 TCGA-99-8025 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
         148          427          170          154          114          287 
TCGA-J2-A4AE TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T2 
         282          285          622          353         1967         1951 
TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
        1954         1954         1970          142         1955         1971 

$`DEL PEAK 42(18Q23) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 TCGA-05-4403 
         607          426         1369         1126         1947          578 
TCGA-05-4415 TCGA-05-4420 TCGA-05-4430 TCGA-05-4432 TCGA-05-5420 TCGA-05-5428 
        1997          912          761          761          457          670 
TCGA-35-3615 TCGA-38-4625 TCGA-38-4626 TCGA-38-4629 TCGA-38-4630 TCGA-38-7271 
          14         1952         1962          864         1073         1971 
TCGA-38-A44F TCGA-44-2655 TCGA-44-2659 TCGA-44-2661 TCGA-44-2666 TCGA-44-3396 
         133         1324         1367          741           97         1130 
TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 
        1163          190          722         1013          383          723 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6776 TCGA-44-6778 TCGA-44-7659 
         845          704          658         1938         1864          444 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7671 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
         592          366          535          385           99          260 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 
         486          466          287          351          415         1932 
TCGA-49-4494 TCGA-49-4510 TCGA-49-4514 TCGA-49-6744 TCGA-49-6745 TCGA-50-5045 
        1081          896         1700          890          522         2174 
TCGA-50-5049 TCGA-50-5055 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5935 
        2146          785          282          267         1091          653 
TCGA-50-5942 TCGA-50-5944 TCGA-50-7109 TCGA-50-8460 TCGA-53-7813 TCGA-55-1592 
         883          764          255          105          424          701 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6969 TCGA-55-6983 TCGA-55-6986 
          87            2          993         1239         1826         2151 
TCGA-55-6987 TCGA-55-7284 TCGA-55-7570 TCGA-55-7724 TCGA-55-7815 TCGA-55-7903 
        1170          121            6         1958           54           19 
TCGA-55-7907 TCGA-55-7911 TCGA-55-7914 TCGA-55-8085 TCGA-55-8092 TCGA-55-8205 
          16           21            3           33           26           33 
TCGA-55-8206 TCGA-55-8299 TCGA-55-8302 TCGA-55-8506 TCGA-55-8508 TCGA-55-8512 
          46          216           23           11           15            3 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8619 TCGA-55-8620 
         146          202          536           15           49           66 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A494 TCGA-55-A4DF TCGA-62-8395 
         106           33           42            5           47         1216 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46V TCGA-64-1677 TCGA-64-1678 
        1970         2696         1445         2199          628         1189 
TCGA-64-1680 TCGA-64-5774 TCGA-64-5779 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 
        1126         1959          864          427          385          174 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 TCGA-69-7974 TCGA-69-7980 
         186          690          414          230          184          382 
TCGA-69-8253 TCGA-69-8255 TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4668 
         100          129           61         1600          711          467 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 
          40          164           38         1944         1093         1202 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
         760         1948         1961         1963         1221          678 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7537 
        1940         1950         1934         1937         1965         1944 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
         881         1952          994         1949         1971         1981 
TCGA-80-5607 TCGA-80-5608 TCGA-86-7713 TCGA-86-7953 TCGA-86-7955 TCGA-86-8056 
        1965         1972          422          591          508         1963 
TCGA-86-8076 TCGA-86-8281 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 
         489         1955           45           34           18          455 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
         405           10           30           14           39          323 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6847 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 
         310           79          842           35          197          174 
TCGA-93-7347 TCGA-93-8067 TCGA-95-7043 TCGA-95-7944 TCGA-95-7948 TCGA-95-A4VK 
         297          186            2          377          476          121 
TCGA-97-7547 TCGA-97-7553 TCGA-97-7554 TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 
        1965         1332          775          107          182           87 
TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8028 
          15          115          197          271          392          459 
TCGA-99-8032 TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
          44          238          578          435          116            6 
TCGA-MP-A4SV TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TE 
        1946         1957         1980         1951         1944         1970 
TCGA-MP-A5C7 
        1490 

  DEL PEAK 42(18Q23) MUTATED DEL PEAK 42(18Q23) WILD-TYPE 
                           1                            2 
  DEL PEAK 42(18Q23) MUTATED DEL PEAK 42(18Q23) WILD-TYPE 
                        2370                         2696 
  DEL PEAK 42(18Q23) MUTATED DEL PEAK 42(18Q23) WILD-TYPE 
                       427.5                        508.0 
[1] "1.0 - 2370.0 (427.5)" "2.0 - 2696.0 (508.0)"
[1] "hr=" "1.2"
D74V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 42(18Q23) MUTATED         0       42       63        25        43
  DEL PEAK 42(18Q23) WILD-TYPE       4       71       68        18        26
                              vv
clus                           STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 42(18Q23) MUTATED           32          5       13
  DEL PEAK 42(18Q23) WILD-TYPE         35          6       10
D74V3, multiclass
            clus
vv           DEL PEAK 42(18Q23) MUTATED DEL PEAK 42(18Q23) WILD-TYPE
  STAGE I                             0                            4
  STAGE IA                           42                           71
  STAGE IB                           63                           68
  STAGE IIA                          25                           18
  STAGE IIB                          43                           26
  STAGE IIIA                         32                           35
  STAGE IIIB                          5                            6
  STAGE IV                           13                           10
[1] 8 2
[1] TRUE
[1] "dimension of 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(18Q23) MUTATED    60 132  23   8
  DEL PEAK 42(18Q23) WILD-TYPE  83 127  17  10
D74V4, multiclass
    clus
vv   DEL PEAK 42(18Q23) MUTATED DEL PEAK 42(18Q23) WILD-TYPE
  T1                         60                           83
  T2                        132                          127
  T3                         23                           17
  T4                          8                           10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            N0  N1 N2+N3
  DEL PEAK 42(18Q23) MUTATED   133  52    34
  DEL PEAK 42(18Q23) WILD-TYPE 162  33    38
D74V5, multiclass
       clus
vv      DEL PEAK 42(18Q23) MUTATED DEL PEAK 42(18Q23) WILD-TYPE
  N0                           133                          162
  N1                            52                           33
  N2+N3                         34                           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"
                              vv
clus                            M0  M1 M1A M1B  MX
  DEL PEAK 42(18Q23) MUTATED   146  11   0   1  63
  DEL PEAK 42(18Q23) WILD-TYPE 171   7   1   2  56
D74V6, multiclass
     clus
vv    DEL PEAK 42(18Q23) MUTATED DEL PEAK 42(18Q23) WILD-TYPE
  M0                         146                          171
  M1                          11                            7
  M1A                          0                            1
  M1B                          1                            2
  MX                          63                           56
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V7, binary
                              cls
clus                             0   1
  DEL PEAK 42(18Q23) MUTATED   128  96
  DEL PEAK 42(18Q23) WILD-TYPE 120 118
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 42(18Q23) MUTATED    128   96
  DEL PEAK 42(18Q23) WILD-TYPE  120  118
        clus
vv       DEL PEAK 42(18Q23) MUTATED DEL PEAK 42(18Q23) WILD-TYPE
  FEMALE                        128                          120
  MALE                           96                          118
[1] 2 2
[1] FALSE
D74V8, continuous
                              vv
clus                           LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 42(18Q23) MUTATED                            8
  DEL PEAK 42(18Q23) WILD-TYPE                          5
                              vv
clus                           LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 42(18Q23) MUTATED                                  44
  DEL PEAK 42(18Q23) WILD-TYPE                                49
                              vv
clus                           LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 42(18Q23) MUTATED                                                  149
  DEL PEAK 42(18Q23) WILD-TYPE                                                145
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 42(18Q23) MUTATED                                            1
  DEL PEAK 42(18Q23) WILD-TYPE                                          3
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 42(18Q23) MUTATED                                               8
  DEL PEAK 42(18Q23) WILD-TYPE                                            11
                              vv
clus                           LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 42(18Q23) MUTATED                                2
  DEL PEAK 42(18Q23) WILD-TYPE                              0
                              vv
clus                           LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 42(18Q23) MUTATED                                    3
  DEL PEAK 42(18Q23) WILD-TYPE                                  1
                              vv
clus                           LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 42(18Q23) MUTATED                              1
  DEL PEAK 42(18Q23) WILD-TYPE                            1
                              vv
clus                           LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 42(18Q23) MUTATED                               3
  DEL PEAK 42(18Q23) WILD-TYPE                            16
                              vv
clus                           LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 42(18Q23) MUTATED                                 1
  DEL PEAK 42(18Q23) WILD-TYPE                               0
                              vv
clus                           LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 42(18Q23) MUTATED                                               1
  DEL PEAK 42(18Q23) WILD-TYPE                                             3
                              vv
clus                           MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 42(18Q23) MUTATED                              3
  DEL PEAK 42(18Q23) WILD-TYPE                            4
D74V9, multiclass
                                                    clus
vv                                                   DEL PEAK 42(18Q23) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                  8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                          44
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                        149
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                  1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                               8
  LUNG CLEAR CELL ADENOCARCINOMA                                              2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                          3
  LUNG MUCINOUS ADENOCARCINOMA                                                1
  LUNG PAPILLARY ADENOCARCINOMA                                               3
  LUNG SIGNET RING ADENOCARCINOMA                                             1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                               1
  MUCINOUS (COLLOID) CARCINOMA                                                3
                                                    clus
vv                                                   DEL PEAK 42(18Q23) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                    5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            49
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          145
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                11
  LUNG CLEAR CELL ADENOCARCINOMA                                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            1
  LUNG MUCINOUS ADENOCARCINOMA                                                  1
  LUNG PAPILLARY ADENOCARCINOMA                                                16
  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"
D74V10, binary
                              cls
clus                             0   1
  DEL PEAK 42(18Q23) MUTATED     7 217
  DEL PEAK 42(18Q23) WILD-TYPE  14 224
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 42(18Q23) MUTATED      7  217
  DEL PEAK 42(18Q23) WILD-TYPE   14  224
     clus
vv    DEL PEAK 42(18Q23) MUTATED DEL PEAK 42(18Q23) WILD-TYPE
  NO                           7                           14
  YES                        217                          224
[1] 2 2
[1] FALSE
D74V11, continuous
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 42(18Q23) MUTATED   155   8   3   5
  DEL PEAK 42(18Q23) WILD-TYPE 163   3   1  14
D74V12, multiclass
    clus
vv   DEL PEAK 42(18Q23) MUTATED DEL PEAK 42(18Q23) WILD-TYPE
  R0                        155                          163
  R1                          8                            3
  R2                          3                            1
  RX                          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                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 42(18Q23) MUTATED                                  0     2
  DEL PEAK 42(18Q23) WILD-TYPE                                1     4
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 42(18Q23) MUTATED                          12   174
  DEL PEAK 42(18Q23) WILD-TYPE                        14   188
D74V13, multiclass
                                  clus
vv                                 DEL PEAK 42(18Q23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     2
  BLACK OR AFRICAN AMERICAN                                12
  WHITE                                                   174
                                  clus
vv                                 DEL PEAK 42(18Q23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  14
  WHITE                                                     188
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V14, binary
                              cls
clus                             0   1
  DEL PEAK 42(18Q23) MUTATED     5 159
  DEL PEAK 42(18Q23) WILD-TYPE   2 173
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 42(18Q23) MUTATED      5  159
  DEL PEAK 42(18Q23) WILD-TYPE    2  173
                        clus
vv                       DEL PEAK 42(18Q23) MUTATED
  HISPANIC OR LATINO                              5
  NOT HISPANIC OR LATINO                        159
                        clus
vv                       DEL PEAK 42(18Q23) WILD-TYPE
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          173
[1] 2 2
[1] FALSE

Clustering(75) Variable = DEL PEAK 43(19P13.3) MUTATION ANALYSIS
D75V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 43(19P13.3) MUTATED   166  52
  DEL PEAK 43(19P13.3) WILD-TYPE 155  30
  DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE 
                           218                            185 
  DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE 
                            52                             30 
$`DEL PEAK 43(19P13.3) MUTATED`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 TCGA-05-4398 
         607          426         1369         1126         1947         1431 
TCGA-05-4410 TCGA-05-4415 TCGA-05-4422 TCGA-05-4424 TCGA-05-4427 TCGA-05-4433 
        1958         1997          365          913          791          730 
TCGA-05-5420 TCGA-05-5425 TCGA-05-5428 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 
         457          882          670          225          182          264 
TCGA-38-4628 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-44-2655 
        1492         1073          354         1357          448         1324 
TCGA-44-2656 TCGA-44-2657 TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 TCGA-44-6146 
        1429          400         1013          863          723          302 
TCGA-44-6774 TCGA-44-6776 TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 TCGA-44-7667 
         658         1938         1864         1978          592          557 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 
        1970          882          535           99          260          486 
TCGA-44-A47F TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4501 TCGA-49-4505 
         337          415           76         1932         1421          428 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
         268          896         1700          445          369          890 
TCGA-49-6745 TCGA-50-5049 TCGA-50-5051 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
         522         2146          455          944         1499          246 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 
         282          267         1091         2370          653          567 
TCGA-50-5944 TCGA-50-6597 TCGA-50-7109 TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ 
         764         1015          255         1986          424          280 
TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6971 TCGA-55-6972 
         701         1178         1375           87           25         1475 
TCGA-55-7570 TCGA-55-7576 TCGA-55-7727 TCGA-55-7907 TCGA-55-7910 TCGA-55-7914 
           6           40           34           16          197            3 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 
          31            5           33          100           26            4 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8508 TCGA-55-8512 TCGA-55-8614 TCGA-55-8616 
          23           29           15            3          536           48 
TCGA-55-A48X TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
          33           48         1952            1           28            5 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
          47          162         1216         1289         1970         2696 
TCGA-62-8402 TCGA-62-A46U TCGA-62-A471 TCGA-64-1676 TCGA-64-1681 TCGA-64-5774 
        1445         2067         1246         1728         1968         1959 
TCGA-64-5778 TCGA-64-5779 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3774 
        1305          864           31          610          573          385 
TCGA-67-6217 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 TCGA-69-7978 
         422          186          690          414          230           70 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 
         382          100          129          214           61          711 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4677 TCGA-73-7498 
         800          467          131           40           38          621 
TCGA-73-7499 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 TCGA-78-7145 
         519         1970         1967         1956         1965         1973 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7153 
        1988         1950         1944         1093         1963          760 
TCGA-78-7156 TCGA-78-7160 TCGA-78-7162 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        1961          678         1940         1934         1937         1965 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 TCGA-78-7633 TCGA-80-5608 TCGA-83-5908 
        1972         1949          327          994         1972          824 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
          11          630          422          591         1963          508 
TCGA-86-8055 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 TCGA-86-8280 
          10           13           24          479          482           16 
TCGA-86-8281 TCGA-86-8358 TCGA-86-8669 TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 
        1955           19           34           15          405           10 
TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6836 
          30          323         1940           60          310          417 
TCGA-91-6840 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8497 TCGA-93-8067 
         372          224           35          492          174          186 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7944 TCGA-95-7948 TCGA-95-A4VK TCGA-97-7937 
          34            2          377          476          121          181 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-99-7458 TCGA-99-8033 TCGA-J2-8192 
         107          182         1965          392          170          154 
TCGA-J2-A4AD TCGA-L4-A4E5 TCGA-L9-A443 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4T4 
         287          578          116          622         1946         1954 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        1954         1957         1951         1970          142         1955 
TCGA-MP-A4TK TCGA-MP-A5C7 
        1971         1490 

$`DEL PEAK 43(19P13.3) WILD-TYPE`
TCGA-05-4249 TCGA-05-4403 TCGA-05-4405 TCGA-05-4417 TCGA-05-4420 TCGA-05-4425 
        1523          578          610          455          912          669 
TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-5423 TCGA-05-5429 TCGA-05-5715 
         791          761          761          151           30           62 
TCGA-35-3615 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4629 TCGA-38-7271 
          14         1952         1962         1147          864         1971 
TCGA-38-A44F TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 
         133         1367          741         1280         1301           97 
TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
         246         1130         1163         1036          190          722 
TCGA-44-5645 TCGA-44-6145 TCGA-44-6147 TCGA-44-6148 TCGA-44-6775 TCGA-44-6777 
         383          328          845          704          705         1942 
TCGA-44-7659 TCGA-44-7661 TCGA-44-7662 TCGA-44-7672 TCGA-44-8117 TCGA-44-A47A 
         444          366          218          719          385          466 
TCGA-44-A47B TCGA-44-A47G TCGA-49-4494 TCGA-49-4506 TCGA-49-4512 TCGA-49-6761 
         287          351         1081          999          157          354 
TCGA-50-5045 TCGA-50-5055 TCGA-50-5942 TCGA-50-5946 TCGA-50-8460 TCGA-53-7626 
        2174          785          883          686          105         1971 
TCGA-55-1595 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6980 
        1479            2          993           24         1239           67 
TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 
        1826         1233         2151         1170           18           35 
TCGA-55-7284 TCGA-55-7573 TCGA-55-7574 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
         121            4           95         1958           39           39 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 TCGA-55-8087 TCGA-55-8090 
          24           54           19           21           21            6 
TCGA-55-8091 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
          43           47           15           33           46           66 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 TCGA-55-8511 
         216           44           11            8          228            9 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8615 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
         146          202           15           49           66          106 
TCGA-55-A48Y TCGA-55-A48Z TCGA-62-A46V TCGA-62-A472 TCGA-64-1677 TCGA-64-1678 
          42           29         2199          910          628         1189 
TCGA-64-1679 TCGA-64-1680 TCGA-64-5775 TCGA-64-5781 TCGA-64-5815 TCGA-67-3773 
        1686         1126           62         1559          866          427 
TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7765 TCGA-69-7974 TCGA-69-7979 
         174          141          202          165          184           89 
TCGA-69-8254 TCGA-73-4658 TCGA-73-4662 TCGA-73-4676 TCGA-78-7152 TCGA-78-7154 
          77         1600          912          164         1202         1948 
TCGA-78-7155 TCGA-78-7158 TCGA-78-7159 TCGA-78-7161 TCGA-78-7163 TCGA-78-7537 
        1957         1963         1221          215         1950         1944 
TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
         881         1952         1949         1971         1981         1954 
TCGA-78-8662 TCGA-80-5607 TCGA-86-6851 TCGA-86-7714 TCGA-86-8054 TCGA-86-8056 
        1964         1965         1959         1968          745         1963 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 
         489          476           26           35           45           18 
TCGA-86-8673 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6835 TCGA-91-6847 TCGA-91-8496 
         455           14           39           79          842          197 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-95-7567 
          36           44          218          297          127          568 
TCGA-95-7947 TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
         477          964         1965         1932         1332          775 
TCGA-97-7941 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
          22           87          147           15          148          115 
TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-J2-8194 
         197          271          427          459           44          114 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N5 
         282          238          435            6          285          353 
TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T9 TCGA-MP-A4TC TCGA-MP-A4TE 
        1967         1951         1980         1944         1970 

  DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE 
                             1                              2 
  DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE 
                          2696                           2199 
  DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE 
                         513.5                          427.0 
[1] "1.0 - 2696.0 (513.5)" "2.0 - 2199.0 (427.0)"
[1] "hr=" "1.2"
D75V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 43(19P13.3) MUTATED         3       52       64        28        40
  DEL PEAK 43(19P13.3) WILD-TYPE       1       61       67        15        29
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 43(19P13.3) MUTATED           39          8       16
  DEL PEAK 43(19P13.3) WILD-TYPE         28          3        7
D75V3, multiclass
            clus
vv           DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE
  STAGE I                               3                              1
  STAGE IA                             52                             61
  STAGE IB                             64                             67
  STAGE IIA                            28                             15
  STAGE IIB                            40                             29
  STAGE IIIA                           39                             28
  STAGE IIIB                            8                              3
  STAGE IV                             16                              7
[1] 8 2
[1] TRUE
[1] "dimension of 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(19P13.3) MUTATED    66 151  19  12
  DEL PEAK 43(19P13.3) WILD-TYPE  77 108  21   6
D75V4, multiclass
    clus
vv   DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE
  T1                           66                             77
  T2                          151                            108
  T3                           19                             21
  T4                           12                              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 43(19P13.3) MUTATED   149  55    42
  DEL PEAK 43(19P13.3) WILD-TYPE 146  30    30
D75V5, multiclass
       clus
vv      DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE
  N0                             149                            146
  N1                              55                             30
  N2+N3                           42                             30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 43(19P13.3) MUTATED   180  13   1   2  52
  DEL PEAK 43(19P13.3) WILD-TYPE 137   5   0   1  67
D75V6, multiclass
     clus
vv    DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE
  M0                           180                            137
  M1                            13                              5
  M1A                            1                              0
  M1B                            2                              1
  MX                            52                             67
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V7, binary
                                cls
clus                               0   1
  DEL PEAK 43(19P13.3) MUTATED   120 130
  DEL PEAK 43(19P13.3) WILD-TYPE 128  84
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(19P13.3) MUTATED    120  130
  DEL PEAK 43(19P13.3) WILD-TYPE  128   84
        clus
vv       DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE
  FEMALE                          120                            128
  MALE                            130                             84
[1] 2 2
[1] FALSE
D75V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 43(19P13.3) MUTATED                            6
  DEL PEAK 43(19P13.3) WILD-TYPE                          7
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 43(19P13.3) MUTATED                                  52
  DEL PEAK 43(19P13.3) WILD-TYPE                                41
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 43(19P13.3) MUTATED                                                  160
  DEL PEAK 43(19P13.3) WILD-TYPE                                                134
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 43(19P13.3) MUTATED                                            0
  DEL PEAK 43(19P13.3) WILD-TYPE                                          4
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 43(19P13.3) MUTATED                                               9
  DEL PEAK 43(19P13.3) WILD-TYPE                                            10
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 43(19P13.3) MUTATED                                1
  DEL PEAK 43(19P13.3) WILD-TYPE                              1
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 43(19P13.3) MUTATED                                    3
  DEL PEAK 43(19P13.3) WILD-TYPE                                  1
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 43(19P13.3) MUTATED                              1
  DEL PEAK 43(19P13.3) WILD-TYPE                            1
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 43(19P13.3) MUTATED                              12
  DEL PEAK 43(19P13.3) WILD-TYPE                             7
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 43(19P13.3) MUTATED                                 1
  DEL PEAK 43(19P13.3) WILD-TYPE                               0
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 43(19P13.3) MUTATED                                               2
  DEL PEAK 43(19P13.3) WILD-TYPE                                             2
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 43(19P13.3) MUTATED                              3
  DEL PEAK 43(19P13.3) WILD-TYPE                            4
D75V9, multiclass
                                                    clus
vv                                                   DEL PEAK 43(19P13.3) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            52
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          160
  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                                                12
  LUNG SIGNET RING ADENOCARCINOMA                                               1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 2
  MUCINOUS (COLLOID) CARCINOMA                                                  3
                                                    clus
vv                                                   DEL PEAK 43(19P13.3) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              41
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            134
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  10
  LUNG CLEAR CELL ADENOCARCINOMA                                                  1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              1
  LUNG MUCINOUS ADENOCARCINOMA                                                    1
  LUNG PAPILLARY ADENOCARCINOMA                                                   7
  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"
D75V10, binary
                                cls
clus                               0   1
  DEL PEAK 43(19P13.3) MUTATED    13 237
  DEL PEAK 43(19P13.3) WILD-TYPE   8 204
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(19P13.3) MUTATED     13  237
  DEL PEAK 43(19P13.3) WILD-TYPE    8  204
     clus
vv    DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE
  NO                            13                              8
  YES                          237                            204
[1] 2 2
[1] FALSE
D75V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 43(19P13.3) MUTATED   169   4   2  12
  DEL PEAK 43(19P13.3) WILD-TYPE 149   7   2   7
D75V12, multiclass
    clus
vv   DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE
  R0                          169                            149
  R1                            4                              7
  R2                            2                              2
  RX                           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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 43(19P13.3) MUTATED                                  1     5
  DEL PEAK 43(19P13.3) WILD-TYPE                                0     1
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 43(19P13.3) MUTATED                          18   188
  DEL PEAK 43(19P13.3) WILD-TYPE                         8   174
D75V13, multiclass
                                  clus
vv                                 DEL PEAK 43(19P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  18
  WHITE                                                     188
                                  clus
vv                                 DEL PEAK 43(19P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         1
  BLACK OR AFRICAN AMERICAN                                     8
  WHITE                                                       174
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V14, binary
                                cls
clus                               0   1
  DEL PEAK 43(19P13.3) MUTATED     5 176
  DEL PEAK 43(19P13.3) WILD-TYPE   2 156
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(19P13.3) MUTATED      5  176
  DEL PEAK 43(19P13.3) WILD-TYPE    2  156
                        clus
vv                       DEL PEAK 43(19P13.3) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          176
                        clus
vv                       DEL PEAK 43(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            156
[1] 2 2
[1] FALSE

Clustering(76) Variable = DEL PEAK 44(19P13.2) MUTATION ANALYSIS
D76V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 44(19P13.2) MUTATED   164  49
  DEL PEAK 44(19P13.2) WILD-TYPE 157  33
  DEL PEAK 44(19P13.2) MUTATED DEL PEAK 44(19P13.2) WILD-TYPE 
                           213                            190 
  DEL PEAK 44(19P13.2) MUTATED DEL PEAK 44(19P13.2) WILD-TYPE 
                            49                             33 
$`DEL PEAK 44(19P13.2) MUTATED`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 TCGA-05-4398 
         607          426         1369         1126         1947         1431 
TCGA-05-4410 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4427 TCGA-05-4432 
        1958          912          365          913          791          761 
TCGA-05-4433 TCGA-05-5420 TCGA-05-5425 TCGA-05-5428 TCGA-35-4122 TCGA-35-4123 
         730          457          882          670          225          182 
TCGA-35-5375 TCGA-38-4628 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-44-2655 
         264         1492          354         1357          448         1324 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2662 TCGA-44-5644 TCGA-44-6144 TCGA-44-6146 
        1429          400         1280          863          723          302 
TCGA-44-6774 TCGA-44-6776 TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 TCGA-44-7667 
         658         1938         1864         1978          592          557 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
        1970          882          535          385           99          260 
TCGA-44-A47F TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4501 TCGA-49-4505 
         337          415           76         1932         1421          428 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
         268          896         1700          445          369          890 
TCGA-49-6745 TCGA-50-5049 TCGA-50-5051 TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 
         522         2146          455          944          246          282 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5941 TCGA-50-5944 TCGA-50-6597 
         267         1091         2370          567          764         1015 
TCGA-50-7109 TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 
         255         1986          424          280          701         1178 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6971 TCGA-55-6972 TCGA-55-7570 TCGA-55-7576 
        1375           87           25         1475            6           40 
TCGA-55-7727 TCGA-55-7907 TCGA-55-7910 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
          34           16          197            3           31            5 
TCGA-55-8085 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8302 TCGA-55-8505 
          33          100           26            4           23           29 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8512 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
           8           15            3          536           15           48 
TCGA-55-A48X TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
          33           48         1952            1           28            5 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
          47          162         1216         1289         1970         2696 
TCGA-62-8402 TCGA-62-A46U TCGA-62-A471 TCGA-64-1676 TCGA-64-1681 TCGA-64-5774 
        1445         2067         1246         1728         1968         1959 
TCGA-64-5778 TCGA-64-5779 TCGA-67-3770 TCGA-67-3772 TCGA-67-3774 TCGA-69-7761 
        1305          864           31          573          385          186 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 
         690          414          230           70          382          100 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 
         129          214           61          711          800          467 
TCGA-73-4670 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-75-6214 TCGA-75-7025 
         131           38          621          519         1970         1967 
TCGA-75-7027 TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
        1956         1965         1973         1988         1950         1944 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7153 TCGA-78-7156 TCGA-78-7159 TCGA-78-7160 
        1093         1963          760         1961         1221          678 
TCGA-78-7162 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
        1940         1934         1937         1965         1972         1949 
TCGA-78-7539 TCGA-78-7633 TCGA-80-5608 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
         327          994         1972           11          630          422 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8073 
         591         1963          508          745           10           13 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 TCGA-86-8280 TCGA-86-8281 TCGA-86-8669 
          24          479          482           16         1955           34 
TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6829 
          15          405           10           30          323         1940 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6836 TCGA-91-6849 TCGA-91-7771 TCGA-91-A4BC 
          60          310          417           35          492           44 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-95-7948 TCGA-95-A4VK TCGA-97-8171 
          34            2          568          476          121          107 
TCGA-97-8172 TCGA-97-8174 TCGA-99-7458 TCGA-99-8025 TCGA-99-8033 TCGA-J2-8192 
         182         1965          392          427          170          154 
TCGA-J2-A4AD TCGA-L4-A4E5 TCGA-L9-A443 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
         287          578          116          622          353         1946 
TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TF 
        1954         1954         1957         1951         1944         1970 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
         142         1955         1971 

$`DEL PEAK 44(19P13.2) WILD-TYPE`
TCGA-05-4249 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4425 
        1523          578          610         1997          455          669 
TCGA-05-4426 TCGA-05-4430 TCGA-05-5423 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
         791          761          151           30           62           14 
TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4629 TCGA-38-4630 TCGA-38-7271 
        1952         1962         1147          864         1073         1971 
TCGA-38-A44F TCGA-44-2659 TCGA-44-2661 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
         133         1367          741         1301           97          246 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
        1130         1163         1036          190          722         1013 
TCGA-44-5645 TCGA-44-6145 TCGA-44-6147 TCGA-44-6148 TCGA-44-6775 TCGA-44-6777 
         383          328          845          704          705         1942 
TCGA-44-7659 TCGA-44-7661 TCGA-44-7662 TCGA-44-7672 TCGA-44-A479 TCGA-44-A47A 
         444          366          218          719          486          466 
TCGA-44-A47B TCGA-44-A47G TCGA-49-4494 TCGA-49-4506 TCGA-49-4512 TCGA-49-6761 
         287          351         1081          999          157          354 
TCGA-50-5045 TCGA-50-5055 TCGA-50-5068 TCGA-50-5935 TCGA-50-5942 TCGA-50-5946 
        2174          785         1499          653          883          686 
TCGA-50-8460 TCGA-53-7626 TCGA-55-1595 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
         105         1971         1479            2          993           24 
TCGA-55-6969 TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
        1239           67         1826         1233         2151         1170 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7573 TCGA-55-7574 TCGA-55-7724 
          18           35          121            4           95         1958 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 
          39           39           24           54           19           21 
TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 
          21            6           43           47           15           33 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8506 TCGA-55-8510 
          46           66          216           44           11          228 
TCGA-55-8511 TCGA-55-8513 TCGA-55-8514 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
           9          146          202           49           66          106 
TCGA-55-A48Y TCGA-55-A48Z TCGA-62-A46V TCGA-62-A472 TCGA-64-1677 TCGA-64-1678 
          42           29         2199          910          628         1189 
TCGA-64-1679 TCGA-64-1680 TCGA-64-5775 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        1686         1126           62         1559          866          610 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7765 
         427          174          141          422          202          165 
TCGA-69-7974 TCGA-69-7979 TCGA-69-8254 TCGA-73-4658 TCGA-73-4662 TCGA-73-4675 
         184           89           77         1600          912           40 
TCGA-73-4676 TCGA-78-7152 TCGA-78-7154 TCGA-78-7155 TCGA-78-7158 TCGA-78-7161 
         164         1202         1948         1957         1963          215 
TCGA-78-7163 TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 
        1950         1944          881         1952         1949         1971 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 TCGA-83-5908 TCGA-86-6851 
        1981         1954         1964         1965          824         1959 
TCGA-86-7714 TCGA-86-8056 TCGA-86-8076 TCGA-86-8278 TCGA-86-8358 TCGA-86-8359 
        1968         1963          489          476           19           26 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8673 TCGA-86-A4P7 TCGA-86-A4P8 
          35           45           18          455           14           39 
TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-8496 TCGA-91-8497 
          79          372          842          224          197          174 
TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7944 
          36          218          297          127          186          377 
TCGA-95-7947 TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
         477          964         1965         1932         1332          775 
TCGA-97-7937 TCGA-97-7941 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
         181           22           87          147           15          148 
TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-8028 TCGA-99-8032 TCGA-J2-8194 
         115          197          271          459           44          114 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4SW 
         282          238          435            6          285         1967 
TCGA-MP-A4T2 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A5C7 
        1951         1980         1970         1490 

  DEL PEAK 44(19P13.2) MUTATED DEL PEAK 44(19P13.2) WILD-TYPE 
                             1                              2 
  DEL PEAK 44(19P13.2) MUTATED DEL PEAK 44(19P13.2) WILD-TYPE 
                          2696                           2199 
  DEL PEAK 44(19P13.2) MUTATED DEL PEAK 44(19P13.2) WILD-TYPE 
                         522.0                          402.5 
[1] "1.0 - 2696.0 (522.0)" "2.0 - 2199.0 (402.5)"
[1] "hr=" "1.1"
D76V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 44(19P13.2) MUTATED         3       49       61        28        41
  DEL PEAK 44(19P13.2) WILD-TYPE       1       64       70        15        28
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 44(19P13.2) MUTATED           40          7       16
  DEL PEAK 44(19P13.2) WILD-TYPE         27          4        7
D76V3, multiclass
            clus
vv           DEL PEAK 44(19P13.2) MUTATED DEL PEAK 44(19P13.2) WILD-TYPE
  STAGE I                               3                              1
  STAGE IA                             49                             64
  STAGE IB                             61                             70
  STAGE IIA                            28                             15
  STAGE IIB                            41                             28
  STAGE IIIA                           40                             27
  STAGE IIIB                            7                              4
  STAGE IV                             16                              7
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 44(19P13.2) MUTATED    66 146  20  11
  DEL PEAK 44(19P13.2) WILD-TYPE  77 113  20   7
D76V4, multiclass
    clus
vv   DEL PEAK 44(19P13.2) MUTATED DEL PEAK 44(19P13.2) WILD-TYPE
  T1                           66                             77
  T2                          146                            113
  T3                           20                             20
  T4                           11                              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 44(19P13.2) MUTATED   143  54    43
  DEL PEAK 44(19P13.2) WILD-TYPE 152  31    29
D76V5, multiclass
       clus
vv      DEL PEAK 44(19P13.2) MUTATED DEL PEAK 44(19P13.2) WILD-TYPE
  N0                             143                            152
  N1                              54                             31
  N2+N3                           43                             29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 44(19P13.2) MUTATED   178  13   1   2  49
  DEL PEAK 44(19P13.2) WILD-TYPE 139   5   0   1  70
D76V6, multiclass
     clus
vv    DEL PEAK 44(19P13.2) MUTATED DEL PEAK 44(19P13.2) WILD-TYPE
  M0                           178                            139
  M1                            13                              5
  M1A                            1                              0
  M1B                            2                              1
  MX                            49                             70
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V7, binary
                                cls
clus                               0   1
  DEL PEAK 44(19P13.2) MUTATED   112 133
  DEL PEAK 44(19P13.2) WILD-TYPE 136  81
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(19P13.2) MUTATED    112  133
  DEL PEAK 44(19P13.2) WILD-TYPE  136   81
        clus
vv       DEL PEAK 44(19P13.2) MUTATED DEL PEAK 44(19P13.2) WILD-TYPE
  FEMALE                          112                            136
  MALE                            133                             81
[1] 2 2
[1] FALSE
D76V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 44(19P13.2) MUTATED                            7
  DEL PEAK 44(19P13.2) WILD-TYPE                          6
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 44(19P13.2) MUTATED                                  56
  DEL PEAK 44(19P13.2) WILD-TYPE                                37
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 44(19P13.2) MUTATED                                                  152
  DEL PEAK 44(19P13.2) WILD-TYPE                                                142
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 44(19P13.2) MUTATED                                            0
  DEL PEAK 44(19P13.2) WILD-TYPE                                          4
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 44(19P13.2) MUTATED                                               9
  DEL PEAK 44(19P13.2) WILD-TYPE                                            10
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 44(19P13.2) MUTATED                                1
  DEL PEAK 44(19P13.2) WILD-TYPE                              1
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 44(19P13.2) MUTATED                                    2
  DEL PEAK 44(19P13.2) WILD-TYPE                                  2
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 44(19P13.2) MUTATED                              1
  DEL PEAK 44(19P13.2) WILD-TYPE                            1
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 44(19P13.2) MUTATED                              11
  DEL PEAK 44(19P13.2) WILD-TYPE                             8
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 44(19P13.2) MUTATED                                 1
  DEL PEAK 44(19P13.2) WILD-TYPE                               0
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 44(19P13.2) MUTATED                                               2
  DEL PEAK 44(19P13.2) WILD-TYPE                                             2
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 44(19P13.2) MUTATED                              3
  DEL PEAK 44(19P13.2) WILD-TYPE                            4
D76V9, multiclass
                                                    clus
vv                                                   DEL PEAK 44(19P13.2) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            56
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          152
  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                                                11
  LUNG SIGNET RING ADENOCARCINOMA                                               1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 2
  MUCINOUS (COLLOID) CARCINOMA                                                  3
                                                    clus
vv                                                   DEL PEAK 44(19P13.2) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              37
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            142
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  10
  LUNG CLEAR CELL ADENOCARCINOMA                                                  1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              2
  LUNG MUCINOUS ADENOCARCINOMA                                                    1
  LUNG PAPILLARY ADENOCARCINOMA                                                   8
  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"
D76V10, binary
                                cls
clus                               0   1
  DEL PEAK 44(19P13.2) MUTATED    11 234
  DEL PEAK 44(19P13.2) WILD-TYPE  10 207
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(19P13.2) MUTATED     11  234
  DEL PEAK 44(19P13.2) WILD-TYPE   10  207
     clus
vv    DEL PEAK 44(19P13.2) MUTATED DEL PEAK 44(19P13.2) WILD-TYPE
  NO                            11                             10
  YES                          234                            207
[1] 2 2
[1] FALSE
D76V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 44(19P13.2) MUTATED   171   3   2  10
  DEL PEAK 44(19P13.2) WILD-TYPE 147   8   2   9
D76V12, multiclass
    clus
vv   DEL PEAK 44(19P13.2) MUTATED DEL PEAK 44(19P13.2) WILD-TYPE
  R0                          171                            147
  R1                            3                              8
  R2                            2                              2
  RX                           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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 44(19P13.2) MUTATED                                  1     4
  DEL PEAK 44(19P13.2) WILD-TYPE                                0     2
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 44(19P13.2) MUTATED                          16   186
  DEL PEAK 44(19P13.2) WILD-TYPE                        10   176
D76V13, multiclass
                                  clus
vv                                 DEL PEAK 44(19P13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  16
  WHITE                                                     186
                                  clus
vv                                 DEL PEAK 44(19P13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         2
  BLACK OR AFRICAN AMERICAN                                    10
  WHITE                                                       176
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V14, binary
                                cls
clus                               0   1
  DEL PEAK 44(19P13.2) MUTATED     5 170
  DEL PEAK 44(19P13.2) WILD-TYPE   2 162
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(19P13.2) MUTATED      5  170
  DEL PEAK 44(19P13.2) WILD-TYPE    2  162
                        clus
vv                       DEL PEAK 44(19P13.2) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          170
                        clus
vv                       DEL PEAK 44(19P13.2) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            162
[1] 2 2
[1] FALSE

Clustering(77) Variable = DEL PEAK 45(19Q13.33) MUTATION ANALYSIS
D77V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 45(19Q13.33) MUTATED   113  35
  DEL PEAK 45(19Q13.33) WILD-TYPE 208  47
  DEL PEAK 45(19Q13.33) MUTATED DEL PEAK 45(19Q13.33) WILD-TYPE 
                            148                             255 
  DEL PEAK 45(19Q13.33) MUTATED DEL PEAK 45(19Q13.33) WILD-TYPE 
                             35                              47 
$`DEL PEAK 45(19Q13.33) MUTATED`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4396 TCGA-05-4398 TCGA-05-4410 
         607          426         1369         1947         1431         1958 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4426 TCGA-05-5420 TCGA-05-5425 TCGA-05-5715 
         912          365          791          457          882           62 
TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 
         225          182         1952         1073         1357          448 
TCGA-44-2655 TCGA-44-2656 TCGA-44-2662 TCGA-44-2665 TCGA-44-3918 TCGA-44-5644 
        1324         1429         1280         1301         1036          863 
TCGA-44-6144 TCGA-44-6778 TCGA-44-6779 TCGA-44-7670 TCGA-44-7671 TCGA-44-8117 
         723         1864         1978          882          535          385 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A4SU TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
          99          260           76          428          999          268 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6745 TCGA-50-5051 TCGA-50-5072 TCGA-50-5932 
        1700          445          522          455          246         1091 
TCGA-50-5935 TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 TCGA-50-6597 TCGA-55-1592 
         653          567          764          686         1015          701 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6972 TCGA-55-6985 TCGA-55-7283 TCGA-55-7570 
        1375           87         1475         1233           35            6 
TCGA-55-7727 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8091 TCGA-55-8094 
          34           31            5           33           43            4 
TCGA-55-8507 TCGA-55-8511 TCGA-55-8514 TCGA-55-8615 TCGA-55-8616 TCGA-55-A48X 
           8            9          202           15           48           33 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8402 
        1952            1          162         1216         1289         1445 
TCGA-62-A46V TCGA-62-A471 TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 
        2199         1246         1728         1189         1686         1968 
TCGA-67-3770 TCGA-67-3772 TCGA-69-7760 TCGA-69-7764 TCGA-69-7978 TCGA-69-7979 
          31          573          202          414           70           89 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
         129          214           61          711          912          800 
TCGA-73-4670 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-75-6214 TCGA-75-7031 
         131           38          621          519         1970         1965 
TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 TCGA-78-7153 TCGA-78-7156 TCGA-78-7161 
        1988         1944         1093          760         1961          215 
TCGA-78-7162 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7542 
        1940         1937         1965         1972         1949         1952 
TCGA-86-7701 TCGA-86-7954 TCGA-86-7955 TCGA-86-8074 TCGA-86-8279 TCGA-86-8669 
          11         1963          508           24          482           34 
TCGA-86-8672 TCGA-86-A456 TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
          15           10           30          323         1940           60 
TCGA-91-6831 TCGA-91-6836 TCGA-91-6848 TCGA-91-7771 TCGA-91-8499 TCGA-91-A4BC 
         310          417          224          492           36           44 
TCGA-95-7039 TCGA-95-7567 TCGA-95-7948 TCGA-95-A4VK TCGA-97-8171 TCGA-97-8174 
          34          568          476          121          107         1965 
TCGA-97-8547 TCGA-99-7458 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-A4AD TCGA-L4-A4E5 
         148          392          170          154          287          578 
TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T8 
         285          353         1946         1967         1951         1957 
TCGA-MP-A4TA TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
        1951         1955         1971         1490 

$`DEL PEAK 45(19Q13.33) WILD-TYPE`
TCGA-05-4249 TCGA-05-4390 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 
        1523         1126          578          610         1997          455 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
         913          669          791          761          761          730 
TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 TCGA-35-3615 TCGA-35-5375 TCGA-38-4626 
         151          670           30           14          264         1962 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4631 TCGA-38-7271 TCGA-38-A44F 
        1147         1492          864          354         1971          133 
TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 
         400         1367          741           97          246         1130 
TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6145 
        1163          190          722         1013          383          328 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
         302          845          704          658          705         1938 
TCGA-44-6777 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
        1942          444          592          366          218          557 
TCGA-44-7669 TCGA-44-7672 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        1970          719          486          466          287          337 
TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 TCGA-49-4510 
         351          415         1932         1081         1421          896 
TCGA-49-4512 TCGA-49-6743 TCGA-49-6744 TCGA-49-6761 TCGA-50-5045 TCGA-50-5049 
         157          369          890          354         2174         2146 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 
         785          944         1499          282          267         2370 
TCGA-50-5942 TCGA-50-7109 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
         883          255          105         1986         1971          424 
TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1595 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
         280         1178         1479            2          993           24 
TCGA-55-6969 TCGA-55-6971 TCGA-55-6980 TCGA-55-6983 TCGA-55-6986 TCGA-55-6987 
        1239           25           67         1826         2151         1170 
TCGA-55-7281 TCGA-55-7284 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
          18          121            4           95           40         1958 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 
          39           39           24           54           19           16 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
         197           21            3           21          100            6 
TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
          26           47           15           33           46           66 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 
         216           44           23           29           11           15 
TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-8619 TCGA-55-8620 
         228            3          146          536           49           66 
TCGA-55-8621 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 
         106           42           29           48           28            5 
TCGA-55-A4DF TCGA-62-8398 TCGA-62-8399 TCGA-62-A46U TCGA-62-A472 TCGA-64-1677 
          47         1970         2696         2067          910          628 
TCGA-64-1680 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
        1126         1959           62         1305          864         1559 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 
         866          610          427          385          174          141 
TCGA-67-6217 TCGA-69-7761 TCGA-69-7763 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
         422          186          690          165          230          184 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-73-4658 TCGA-73-4668 TCGA-73-4675 
         382          100           77         1600          467           40 
TCGA-73-4676 TCGA-75-7025 TCGA-75-7027 TCGA-78-7145 TCGA-78-7147 TCGA-78-7150 
         164         1967         1956         1973         1950         1963 
TCGA-78-7152 TCGA-78-7154 TCGA-78-7155 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
        1202         1948         1957         1963         1221          678 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7633 
        1950         1934         1944          327          881          994 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 
        1949         1971         1981         1954         1964         1965 
TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
        1972          824         1959          630          422         1968 
TCGA-86-7953 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 
         591          745           10         1963           13          479 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8281 TCGA-86-8358 TCGA-86-8359 
         489          476           16         1955           19           26 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4P7 
          35           45           18          455          405           14 
TCGA-86-A4P8 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6849 TCGA-91-8496 
          39           79          372          842           35          197 
TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7043 
         174          218          297          127          186            2 
TCGA-95-7944 TCGA-95-7947 TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
         377          477          964         1965         1932         1332 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 TCGA-97-8172 TCGA-97-8175 TCGA-97-8177 
         775          181           22          182           87          147 
TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-8025 TCGA-99-8028 
          15          115          197          271          427          459 
TCGA-99-8032 TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 
          44          114          282          238          435          116 
TCGA-L9-A444 TCGA-MN-A4N4 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TC 
           6          622         1954         1954         1980         1944 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
        1970         1970          142 

  DEL PEAK 45(19Q13.33) MUTATED DEL PEAK 45(19Q13.33) WILD-TYPE 
                              1                               2 
  DEL PEAK 45(19Q13.33) MUTATED DEL PEAK 45(19Q13.33) WILD-TYPE 
                           2199                            2696 
  DEL PEAK 45(19Q13.33) MUTATED DEL PEAK 45(19Q13.33) WILD-TYPE 
                            551                             427 
[1] "1.0 - 2199.0 (551.0)" "2.0 - 2696.0 (427.0)"
[1] "hr=" "1.5"
D77V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 45(19Q13.33) MUTATED         1       39       45        14        30
  DEL PEAK 45(19Q13.33) WILD-TYPE       3       74       86        29        39
                                 vv
clus                              STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 45(19Q13.33) MUTATED           30          5       12
  DEL PEAK 45(19Q13.33) WILD-TYPE         37          6       11
D77V3, multiclass
            clus
vv           DEL PEAK 45(19Q13.33) MUTATED DEL PEAK 45(19Q13.33) WILD-TYPE
  STAGE I                                1                               3
  STAGE IA                              39                              74
  STAGE IB                              45                              86
  STAGE IIA                             14                              29
  STAGE IIB                             30                              39
  STAGE IIIA                            30                              37
  STAGE IIIB                             5                               6
  STAGE IV                              12                              11
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  DEL PEAK 45(19Q13.33) MUTATED    47 103  17   8
  DEL PEAK 45(19Q13.33) WILD-TYPE  96 156  23  10
D77V4, multiclass
    clus
vv   DEL PEAK 45(19Q13.33) MUTATED DEL PEAK 45(19Q13.33) WILD-TYPE
  T1                            47                              96
  T2                           103                             156
  T3                            17                              23
  T4                             8                              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 45(19Q13.33) MUTATED   108  35    31
  DEL PEAK 45(19Q13.33) WILD-TYPE 187  50    41
D77V5, multiclass
       clus
vv      DEL PEAK 45(19Q13.33) MUTATED DEL PEAK 45(19Q13.33) WILD-TYPE
  N0                              108                             187
  N1                               35                              50
  N2+N3                            31                              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"
                                 vv
clus                               M0  M1 M1A M1B  MX
  DEL PEAK 45(19Q13.33) MUTATED   126  10   1   1  36
  DEL PEAK 45(19Q13.33) WILD-TYPE 191   8   0   2  83
D77V6, multiclass
     clus
vv    DEL PEAK 45(19Q13.33) MUTATED DEL PEAK 45(19Q13.33) WILD-TYPE
  M0                            126                             191
  M1                             10                               8
  M1A                             1                               0
  M1B                             1                               2
  MX                             36                              83
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V7, binary
                                 cls
clus                                0   1
  DEL PEAK 45(19Q13.33) MUTATED    89  87
  DEL PEAK 45(19Q13.33) WILD-TYPE 159 127
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 45(19Q13.33) MUTATED     89   87
  DEL PEAK 45(19Q13.33) WILD-TYPE  159  127
        clus
vv       DEL PEAK 45(19Q13.33) MUTATED DEL PEAK 45(19Q13.33) WILD-TYPE
  FEMALE                            89                             159
  MALE                              87                             127
[1] 2 2
[1] FALSE
D77V8, continuous
                                 vv
clus                              LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 45(19Q13.33) MUTATED                            4
  DEL PEAK 45(19Q13.33) WILD-TYPE                          9
                                 vv
clus                              LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 45(19Q13.33) MUTATED                                  42
  DEL PEAK 45(19Q13.33) WILD-TYPE                                51
                                 vv
clus                              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 45(19Q13.33) MUTATED                                                  111
  DEL PEAK 45(19Q13.33) WILD-TYPE                                                183
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 45(19Q13.33) MUTATED                                            0
  DEL PEAK 45(19Q13.33) WILD-TYPE                                          4
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 45(19Q13.33) MUTATED                                               5
  DEL PEAK 45(19Q13.33) WILD-TYPE                                            14
                                 vv
clus                              LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 45(19Q13.33) MUTATED                                0
  DEL PEAK 45(19Q13.33) WILD-TYPE                              2
                                 vv
clus                              LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 45(19Q13.33) MUTATED                                    2
  DEL PEAK 45(19Q13.33) WILD-TYPE                                  2
                                 vv
clus                              LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 45(19Q13.33) MUTATED                              0
  DEL PEAK 45(19Q13.33) WILD-TYPE                            2
                                 vv
clus                              LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 45(19Q13.33) MUTATED                               9
  DEL PEAK 45(19Q13.33) WILD-TYPE                            10
                                 vv
clus                              LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 45(19Q13.33) MUTATED                                 0
  DEL PEAK 45(19Q13.33) WILD-TYPE                               1
                                 vv
clus                              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 45(19Q13.33) MUTATED                                               2
  DEL PEAK 45(19Q13.33) WILD-TYPE                                             2
                                 vv
clus                              MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 45(19Q13.33) MUTATED                              1
  DEL PEAK 45(19Q13.33) WILD-TYPE                            6
D77V9, multiclass
                                                    clus
vv                                                   DEL PEAK 45(19Q13.33) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                     4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             42
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           111
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  5
  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                                  2
  MUCINOUS (COLLOID) CARCINOMA                                                   1
                                                    clus
vv                                                   DEL PEAK 45(19Q13.33) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                       9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                               51
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             183
  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                                                   10
  LUNG SIGNET RING ADENOCARCINOMA                                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                    2
  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"
D77V10, binary
                                 cls
clus                                0   1
  DEL PEAK 45(19Q13.33) MUTATED     6 170
  DEL PEAK 45(19Q13.33) WILD-TYPE  15 271
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 45(19Q13.33) MUTATED      6  170
  DEL PEAK 45(19Q13.33) WILD-TYPE   15  271
     clus
vv    DEL PEAK 45(19Q13.33) MUTATED DEL PEAK 45(19Q13.33) WILD-TYPE
  NO                              6                              15
  YES                           170                             271
[1] 2 2
[1] FALSE
D77V11, continuous
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 45(19Q13.33) MUTATED   117   4   3   8
  DEL PEAK 45(19Q13.33) WILD-TYPE 201   7   1  11
D77V12, multiclass
    clus
vv   DEL PEAK 45(19Q13.33) MUTATED DEL PEAK 45(19Q13.33) WILD-TYPE
  R0                           117                             201
  R1                             4                               7
  R2                             3                               1
  RX                             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                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 45(19Q13.33) MUTATED                                  0     4
  DEL PEAK 45(19Q13.33) WILD-TYPE                                1     2
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 45(19Q13.33) MUTATED                           9   135
  DEL PEAK 45(19Q13.33) WILD-TYPE                        17   227
D77V13, multiclass
                                  clus
vv                                 DEL PEAK 45(19Q13.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                    9
  WHITE                                                      135
                                  clus
vv                                 DEL PEAK 45(19Q13.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          2
  BLACK OR AFRICAN AMERICAN                                     17
  WHITE                                                        227
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V14, binary
                                 cls
clus                                0   1
  DEL PEAK 45(19Q13.33) MUTATED     2 121
  DEL PEAK 45(19Q13.33) WILD-TYPE   5 211
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 45(19Q13.33) MUTATED      2  121
  DEL PEAK 45(19Q13.33) WILD-TYPE    5  211
                        clus
vv                       DEL PEAK 45(19Q13.33) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           121
                        clus
vv                       DEL PEAK 45(19Q13.33) WILD-TYPE
  HISPANIC OR LATINO                                   5
  NOT HISPANIC OR LATINO                             211
[1] 2 2
[1] FALSE

Clustering(78) Variable = DEL PEAK 46(20P13) MUTATION ANALYSIS
D78V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 46(20P13) MUTATED    76  26
  DEL PEAK 46(20P13) WILD-TYPE 245  56
  DEL PEAK 46(20P13) MUTATED DEL PEAK 46(20P13) WILD-TYPE 
                         102                          301 
  DEL PEAK 46(20P13) MUTATED DEL PEAK 46(20P13) WILD-TYPE 
                          26                           56 
$`DEL PEAK 46(20P13) MUTATED`
TCGA-05-4398 TCGA-05-4415 TCGA-05-5423 TCGA-38-4629 TCGA-38-6178 TCGA-44-2656 
        1431         1997          151          864          448         1429 
TCGA-44-2662 TCGA-44-2665 TCGA-44-2668 TCGA-44-3919 TCGA-44-6779 TCGA-44-8117 
        1280         1301          246          190         1978          385 
TCGA-44-A47A TCGA-44-A47G TCGA-49-4501 TCGA-49-4505 TCGA-49-4512 TCGA-49-6743 
         466          351         1421          428          157          369 
TCGA-49-6745 TCGA-50-5051 TCGA-50-5072 TCGA-50-5933 TCGA-50-5944 TCGA-50-6597 
         522          455          246         2370          764         1015 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-55-1594 TCGA-55-1595 TCGA-55-6712 
         105         1986         1971         1178         1479           24 
TCGA-55-6980 TCGA-55-7283 TCGA-55-7576 TCGA-55-7725 TCGA-55-7727 TCGA-55-7903 
          67           35           40           39           34           19 
TCGA-55-7907 TCGA-55-7994 TCGA-55-8090 TCGA-55-8092 TCGA-55-8094 TCGA-55-8207 
          16           31            6           26            4           66 
TCGA-55-8506 TCGA-55-8616 TCGA-55-A491 TCGA-55-A493 TCGA-62-8397 TCGA-62-A46U 
          11           48         1952           28         1289         2067 
TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 TCGA-64-1681 
        2199         1246          910         1728         1189         1968 
TCGA-64-5781 TCGA-67-3773 TCGA-67-6216 TCGA-69-7761 TCGA-69-7974 TCGA-69-A59K 
        1559          427          141          186          184          214 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4670 TCGA-73-7499 TCGA-75-6214 TCGA-75-7031 
         912          800          131          519         1970         1965 
TCGA-78-7145 TCGA-78-7148 TCGA-78-7158 TCGA-78-7159 TCGA-78-7535 TCGA-78-8660 
        1973         1944         1963         1221         1972         1954 
TCGA-78-8662 TCGA-80-5608 TCGA-86-6851 TCGA-86-7953 TCGA-86-7955 TCGA-86-8278 
        1964         1972         1959          591          508          476 
TCGA-86-8280 TCGA-86-8673 TCGA-91-6828 TCGA-91-6835 TCGA-93-7347 TCGA-95-7039 
          16          455          323           79          297           34 
TCGA-95-7043 TCGA-95-7567 TCGA-97-7554 TCGA-99-7458 TCGA-99-8033 TCGA-J2-8192 
           2          568          775          392          170          154 
TCGA-J2-A4AD TCGA-L4-A4E5 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4SV 
         287          578            6          285          622         1946 
TCGA-MP-A4SW TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TI TCGA-MP-A4TK 
        1967         1957         1951         1944         1955         1971 

$`DEL PEAK 46(20P13) WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 
        1523          607          426         1369         1126         1947 
TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 
         578          610         1958          455          912          365 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
         913          669          791          791          761          761 
TCGA-05-4433 TCGA-05-5420 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
         730          457          882          670           30           62 
TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
          14          225          182          264         1952         1962 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-7271 
        1147         1492         1073          354         1357         1971 
TCGA-38-A44F TCGA-44-2655 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2666 
         133         1324          400         1367          741           97 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
        1130         1163         1036          722         1013          863 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
         383          723          328          302          845          704 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-7659 
         658          705         1938         1942         1864          444 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
         592          366          218          557         1970          882 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B 
         535          719           99          260          486          287 
TCGA-44-A47F TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 TCGA-49-4506 
         337          415           76         1932         1081          999 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4514 TCGA-49-6742 TCGA-49-6744 TCGA-49-6761 
         268          896         1700          445          890          354 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 
        2174         2146          785          944         1499          282 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 TCGA-50-5946 
         267         1091          653          567          883          686 
TCGA-50-7109 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1596 TCGA-55-5899 
         255          424          280          701         1375           87 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6983 
           2          993         1239           25         1475         1826 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7284 TCGA-55-7570 
        1233         2151         1170           18          121            6 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7724 TCGA-55-7726 TCGA-55-7728 TCGA-55-7815 
           4           95         1958           39           24           54 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
         197           21            3            5           33           21 
TCGA-55-8089 TCGA-55-8091 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 
         100           43           47           15           33           46 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 
         216           44           23           29            8           15 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
         228            9            3          146          202          536 
TCGA-55-8615 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
          15           49           66          106           33           42 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A492 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
          29           48            1            5           47          162 
TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-64-1677 TCGA-64-1679 
        1216         1970         2696         1445          628         1686 
TCGA-64-1680 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 
        1126         1959           62         1305          864          866 
TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3774 TCGA-67-6215 TCGA-67-6217 
          31          610          573          385          174          422 
TCGA-69-7760 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7978 
         202          690          414          165          230           70 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-71-6725 
          89          382          100           77          129           61 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
        1600          711          467           40          164           38 
TCGA-73-7498 TCGA-75-7025 TCGA-75-7027 TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 
         621         1967         1956         1988         1950         1093 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
        1963         1202          760         1948         1957         1961 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
         678          215         1940         1950         1934         1937 
TCGA-78-7220 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
        1965         1949         1944          327          881         1952 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-80-5607 TCGA-83-5908 
         994         1949         1971         1981         1965          824 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7954 TCGA-86-8054 
          11          630          422         1968         1963          745 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
          10         1963           13           24          479          489 
TCGA-86-8279 TCGA-86-8281 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
         482         1955           19           26           35           45 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 
          34           18           15          405           10           30 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6836 
          14           39         1940           60          310          417 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
         372          842          224           35          492          197 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7348 TCGA-93-8067 
         174           36           44          218          127          186 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 
         377          477          476          121          964         1965 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
        1932         1332          181           22          107          182 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
        1965           87          147           15          148          115 
TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-J2-8194 
         197          271          427          459           44          114 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 TCGA-MN-A4N5 TCGA-MP-A4T2 
         282          238          435          116          353         1951 
TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
        1954         1954         1980         1970         1970          142 
TCGA-MP-A5C7 
        1490 

  DEL PEAK 46(20P13) MUTATED DEL PEAK 46(20P13) WILD-TYPE 
                           2                            1 
  DEL PEAK 46(20P13) MUTATED DEL PEAK 46(20P13) WILD-TYPE 
                        2370                         2696 
  DEL PEAK 46(20P13) MUTATED DEL PEAK 46(20P13) WILD-TYPE 
                       520.5                        445.0 
[1] "2.0 - 2370.0 (520.5)" "1.0 - 2696.0 (445.0)"
[1] "hr=" "1.3"
D78V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 46(20P13) MUTATED         1       26       26        12        23
  DEL PEAK 46(20P13) WILD-TYPE       3       87      105        31        46
                              vv
clus                           STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 46(20P13) MUTATED           21          5        6
  DEL PEAK 46(20P13) WILD-TYPE         46          6       17
D78V3, multiclass
            clus
vv           DEL PEAK 46(20P13) MUTATED DEL PEAK 46(20P13) WILD-TYPE
  STAGE I                             1                            3
  STAGE IA                           26                           87
  STAGE IB                           26                          105
  STAGE IIA                          12                           31
  STAGE IIB                          23                           46
  STAGE IIIA                         21                           46
  STAGE IIIB                          5                            6
  STAGE IV                            6                           17
[1] 8 2
[1] TRUE
[1] "dimension of 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(20P13) MUTATED    33  67  11   7
  DEL PEAK 46(20P13) WILD-TYPE 110 192  29  11
D78V4, multiclass
    clus
vv   DEL PEAK 46(20P13) MUTATED DEL PEAK 46(20P13) WILD-TYPE
  T1                         33                          110
  T2                         67                          192
  T3                         11                           29
  T4                          7                           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 46(20P13) MUTATED    68  25    25
  DEL PEAK 46(20P13) WILD-TYPE 227  60    47
D78V5, multiclass
       clus
vv      DEL PEAK 46(20P13) MUTATED DEL PEAK 46(20P13) WILD-TYPE
  N0                            68                          227
  N1                            25                           60
  N2+N3                         25                           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"
                              vv
clus                            M0  M1 M1A M1B  MX
  DEL PEAK 46(20P13) MUTATED    88   5   0   1  25
  DEL PEAK 46(20P13) WILD-TYPE 229  13   1   2  94
D78V6, multiclass
     clus
vv    DEL PEAK 46(20P13) MUTATED DEL PEAK 46(20P13) WILD-TYPE
  M0                          88                          229
  M1                           5                           13
  M1A                          0                            1
  M1B                          1                            2
  MX                          25                           94
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V7, binary
                              cls
clus                             0   1
  DEL PEAK 46(20P13) MUTATED    72  48
  DEL PEAK 46(20P13) WILD-TYPE 176 166
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 46(20P13) MUTATED     72   48
  DEL PEAK 46(20P13) WILD-TYPE  176  166
        clus
vv       DEL PEAK 46(20P13) MUTATED DEL PEAK 46(20P13) WILD-TYPE
  FEMALE                         72                          176
  MALE                           48                          166
[1] 2 2
[1] FALSE
D78V8, continuous
                              vv
clus                           LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 46(20P13) MUTATED                            3
  DEL PEAK 46(20P13) WILD-TYPE                         10
                              vv
clus                           LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 46(20P13) MUTATED                                  23
  DEL PEAK 46(20P13) WILD-TYPE                                70
                              vv
clus                           LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 46(20P13) MUTATED                                                   80
  DEL PEAK 46(20P13) WILD-TYPE                                                214
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 46(20P13) MUTATED                                            0
  DEL PEAK 46(20P13) WILD-TYPE                                          4
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 46(20P13) MUTATED                                               6
  DEL PEAK 46(20P13) WILD-TYPE                                            13
                              vv
clus                           LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 46(20P13) MUTATED                                2
  DEL PEAK 46(20P13) WILD-TYPE                              0
                              vv
clus                           LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 46(20P13) MUTATED                                    1
  DEL PEAK 46(20P13) WILD-TYPE                                  3
                              vv
clus                           LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 46(20P13) MUTATED                              0
  DEL PEAK 46(20P13) WILD-TYPE                            2
                              vv
clus                           LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 46(20P13) MUTATED                               3
  DEL PEAK 46(20P13) WILD-TYPE                            16
                              vv
clus                           LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 46(20P13) MUTATED                                 1
  DEL PEAK 46(20P13) WILD-TYPE                               0
                              vv
clus                           LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 46(20P13) MUTATED                                               0
  DEL PEAK 46(20P13) WILD-TYPE                                             4
                              vv
clus                           MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 46(20P13) MUTATED                              1
  DEL PEAK 46(20P13) WILD-TYPE                            6
D78V9, multiclass
                                                    clus
vv                                                   DEL PEAK 46(20P13) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                  3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                          23
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         80
  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                                               3
  LUNG SIGNET RING ADENOCARCINOMA                                             1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                               0
  MUCINOUS (COLLOID) CARCINOMA                                                1
                                                    clus
vv                                                   DEL PEAK 46(20P13) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                   10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            70
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          214
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                13
  LUNG CLEAR CELL ADENOCARCINOMA                                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            3
  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"
D78V10, binary
                              cls
clus                             0   1
  DEL PEAK 46(20P13) MUTATED     4 116
  DEL PEAK 46(20P13) WILD-TYPE  17 325
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 46(20P13) MUTATED      4  116
  DEL PEAK 46(20P13) WILD-TYPE   17  325
     clus
vv    DEL PEAK 46(20P13) MUTATED DEL PEAK 46(20P13) WILD-TYPE
  NO                           4                           17
  YES                        116                          325
[1] 2 2
[1] FALSE
D78V11, continuous
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 46(20P13) MUTATED    88   4   1   3
  DEL PEAK 46(20P13) WILD-TYPE 230   7   3  16
D78V12, multiclass
    clus
vv   DEL PEAK 46(20P13) MUTATED DEL PEAK 46(20P13) WILD-TYPE
  R0                         88                          230
  R1                          4                            7
  R2                          1                            3
  RX                          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                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 46(20P13) MUTATED                                  0     1
  DEL PEAK 46(20P13) WILD-TYPE                                1     5
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 46(20P13) MUTATED                           4    97
  DEL PEAK 46(20P13) WILD-TYPE                        22   265
D78V13, multiclass
                                  clus
vv                                 DEL PEAK 46(20P13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     1
  BLACK OR AFRICAN AMERICAN                                 4
  WHITE                                                    97
                                  clus
vv                                 DEL PEAK 46(20P13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  22
  WHITE                                                     265
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V14, binary
                              cls
clus                             0   1
  DEL PEAK 46(20P13) MUTATED     1  88
  DEL PEAK 46(20P13) WILD-TYPE   6 244
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 46(20P13) MUTATED      1   88
  DEL PEAK 46(20P13) WILD-TYPE    6  244
                        clus
vv                       DEL PEAK 46(20P13) MUTATED
  HISPANIC OR LATINO                              1
  NOT HISPANIC OR LATINO                         88
                        clus
vv                       DEL PEAK 46(20P13) WILD-TYPE
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          244
[1] 2 2
[1] FALSE

Clustering(79) Variable = DEL PEAK 47(20Q13.12) MUTATION ANALYSIS
D79V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 47(20Q13.12) MUTATED    51  16
  DEL PEAK 47(20Q13.12) WILD-TYPE 270  66
  DEL PEAK 47(20Q13.12) MUTATED DEL PEAK 47(20Q13.12) WILD-TYPE 
                             67                             336 
  DEL PEAK 47(20Q13.12) MUTATED DEL PEAK 47(20Q13.12) WILD-TYPE 
                             16                              66 
$`DEL PEAK 47(20Q13.12) MUTATED`
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4422 TCGA-05-5715 TCGA-38-4628 
         610         1997          455          365           62         1492 
TCGA-44-2656 TCGA-44-3918 TCGA-44-3919 TCGA-44-6779 TCGA-44-A47B TCGA-44-A47G 
        1429         1036          190         1978          287          351 
TCGA-49-4501 TCGA-49-4506 TCGA-49-6743 TCGA-49-6745 TCGA-50-5051 TCGA-50-5072 
        1421          999          369          522          455          246 
TCGA-50-8460 TCGA-53-7624 TCGA-53-A4EZ TCGA-55-1595 TCGA-55-8087 TCGA-55-8090 
         105         1986          280         1479           21            6 
TCGA-55-8508 TCGA-55-8512 TCGA-55-8615 TCGA-55-A494 TCGA-62-8397 TCGA-62-A46U 
          15            3           15            5         1289         2067 
TCGA-62-A471 TCGA-62-A472 TCGA-67-3770 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 
        1246          910           31          427          385          174 
TCGA-67-6216 TCGA-69-7763 TCGA-69-8253 TCGA-69-A59K TCGA-73-4675 TCGA-75-7031 
         141          690          100          214           40         1965 
TCGA-78-7146 TCGA-78-7152 TCGA-78-7158 TCGA-78-7160 TCGA-78-7167 TCGA-78-7537 
        1988         1202         1963          678         1937         1944 
TCGA-86-7953 TCGA-86-8054 TCGA-86-8358 TCGA-91-6828 TCGA-91-6831 TCGA-93-7347 
         591          745           19          323          310          297 
TCGA-95-A4VK TCGA-97-8172 TCGA-97-8174 TCGA-97-8547 TCGA-99-7458 TCGA-99-8025 
         121          182         1965          148          392          427 
TCGA-99-8033 TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-MP-A4SW TCGA-MP-A4TC TCGA-MP-A4TH 
         170          282          578         1967         1944          142 
TCGA-MP-A4TI 
        1955 

$`DEL PEAK 47(20Q13.12) WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 
        1523          607          426         1369         1126         1947 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4410 TCGA-05-4420 TCGA-05-4424 TCGA-05-4425 
        1431          578         1958          912          913          669 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 
         791          791          761          761          730          457 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-35-3615 TCGA-35-4122 
         151          882          670           30           14          225 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4629 
         182          264         1952         1962         1147          864 
TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F 
        1073          354         1357          448         1971          133 
TCGA-44-2655 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 
        1324          400         1367          741         1280         1301 
TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-4112 TCGA-44-5643 
          97          246         1130         1163          722         1013 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
         863          383          723          328          302          845 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
         704          658          705         1938         1942         1864 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
         444          592          366          218          557         1970 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
         882          535          719          385           99          260 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47F TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
         486          466          337          415           76         1932 
TCGA-49-4494 TCGA-49-4505 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
        1081          428          268          896          157         1700 
TCGA-49-6742 TCGA-49-6744 TCGA-49-6761 TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 
         445          890          354         2174         2146          785 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
         944         1499          282          267         1091         2370 
TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6597 
         653          567          883          764          686         1015 
TCGA-50-7109 TCGA-53-7626 TCGA-53-7813 TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 
         255         1971          424          701         1178         1375 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6971 
          87            2          993           24         1239           25 
TCGA-55-6972 TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
        1475           67         1826         1233         2151         1170 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
          18           35          121            6            4           95 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
          40         1958           39           39           34           24 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
          54           19           16          197           21            3 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8089 TCGA-55-8091 TCGA-55-8092 
          31            5           33          100           43           26 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
           4           47           15           33           46           66 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
         216           44           23           29           11            8 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 
         228            9          146          202          536           48 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
          49           66          106           33           42           29 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A4DF TCGA-55-A4DG 
          48         1952            1           28           47          162 
TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46V TCGA-64-1676 
        1216         1970         2696         1445         2199         1728 
TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 
         628         1189         1686         1126         1968         1959 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
          62         1305          864         1559          866          610 
TCGA-67-3772 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 
         573          422          202          186          414          165 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8254 
         230          184           70           89          382           77 
TCGA-69-8255 TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
         129           61         1600          711          912          800 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
         467          131          164           38          621          519 
TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 
        1970         1967         1956         1973         1950         1944 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
        1093         1963          760         1948         1957         1961 
TCGA-78-7159 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7220 
        1221          215         1940         1950         1934         1965 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        1972         1949          327          881         1952          994 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 
        1949         1971         1981         1954         1964         1965 
TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
        1972          824         1959           11          630          422 
TCGA-86-7714 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
        1968         1963          508           10         1963           13 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
          24          479          489          476          482           16 
TCGA-86-8281 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
        1955           26           35           45           34           18 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 
          15          455          405           10           30           14 
TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
          39         1940           60           79          417          372 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
         842          224           35          492          197          174 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 
          36           44          218          127          186           34 
TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-97-7546 
           2          568          377          477          476          964 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 
        1965         1932         1332          775          181           22 
TCGA-97-8171 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M2 
         107           87          147           15          115          197 
TCGA-97-A4M7 TCGA-99-8028 TCGA-99-8032 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
         271          459           44          154          114          287 
TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
         238          435          116            6          285          622 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 
         353         1946         1951         1954         1954         1957 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TK TCGA-MP-A5C7 
        1980         1951         1970         1970         1971         1490 

  DEL PEAK 47(20Q13.12) MUTATED DEL PEAK 47(20Q13.12) WILD-TYPE 
                              3                               1 
  DEL PEAK 47(20Q13.12) MUTATED DEL PEAK 47(20Q13.12) WILD-TYPE 
                           2067                            2696 
  DEL PEAK 47(20Q13.12) MUTATED DEL PEAK 47(20Q13.12) WILD-TYPE 
                          427.0                           476.5 
[1] "3.0 - 2067.0 (427.0)" "1.0 - 2696.0 (476.5)"
[1] "hr=" "1"  
D79V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 47(20Q13.12) MUTATED         1       14       23         5        11
  DEL PEAK 47(20Q13.12) WILD-TYPE       3       99      108        38        58
                                 vv
clus                              STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 47(20Q13.12) MUTATED           16          2        7
  DEL PEAK 47(20Q13.12) WILD-TYPE         51          9       16
D79V3, multiclass
            clus
vv           DEL PEAK 47(20Q13.12) MUTATED DEL PEAK 47(20Q13.12) WILD-TYPE
  STAGE I                                1                               3
  STAGE IA                              14                              99
  STAGE IB                              23                             108
  STAGE IIA                              5                              38
  STAGE IIB                             11                              58
  STAGE IIIA                            16                              51
  STAGE IIIB                             2                               9
  STAGE IV                               7                              16
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  DEL PEAK 47(20Q13.12) MUTATED    20  47   7   4
  DEL PEAK 47(20Q13.12) WILD-TYPE 123 212  33  14
D79V4, multiclass
    clus
vv   DEL PEAK 47(20Q13.12) MUTATED DEL PEAK 47(20Q13.12) WILD-TYPE
  T1                            20                             123
  T2                            47                             212
  T3                             7                              33
  T4                             4                              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 47(20Q13.12) MUTATED    45  14    18
  DEL PEAK 47(20Q13.12) WILD-TYPE 250  71    54
D79V5, multiclass
       clus
vv      DEL PEAK 47(20Q13.12) MUTATED DEL PEAK 47(20Q13.12) WILD-TYPE
  N0                               45                             250
  N1                               14                              71
  N2+N3                            18                              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"
                                 vv
clus                               M0  M1 M1A M1B  MX
  DEL PEAK 47(20Q13.12) MUTATED    60   6   0   1  12
  DEL PEAK 47(20Q13.12) WILD-TYPE 257  12   1   2 107
D79V6, multiclass
     clus
vv    DEL PEAK 47(20Q13.12) MUTATED DEL PEAK 47(20Q13.12) WILD-TYPE
  M0                             60                             257
  M1                              6                              12
  M1A                             0                               1
  M1B                             1                               2
  MX                             12                             107
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V7, binary
                                 cls
clus                                0   1
  DEL PEAK 47(20Q13.12) MUTATED    46  33
  DEL PEAK 47(20Q13.12) WILD-TYPE 202 181
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 47(20Q13.12) MUTATED     46   33
  DEL PEAK 47(20Q13.12) WILD-TYPE  202  181
        clus
vv       DEL PEAK 47(20Q13.12) MUTATED DEL PEAK 47(20Q13.12) WILD-TYPE
  FEMALE                            46                             202
  MALE                              33                             181
[1] 2 2
[1] FALSE
D79V8, continuous
                                 vv
clus                              LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 47(20Q13.12) MUTATED                            3
  DEL PEAK 47(20Q13.12) WILD-TYPE                         10
                                 vv
clus                              LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 47(20Q13.12) MUTATED                                  20
  DEL PEAK 47(20Q13.12) WILD-TYPE                                73
                                 vv
clus                              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 47(20Q13.12) MUTATED                                                   43
  DEL PEAK 47(20Q13.12) WILD-TYPE                                                251
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 47(20Q13.12) MUTATED                                            0
  DEL PEAK 47(20Q13.12) WILD-TYPE                                          4
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 47(20Q13.12) MUTATED                                               3
  DEL PEAK 47(20Q13.12) WILD-TYPE                                            16
                                 vv
clus                              LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 47(20Q13.12) MUTATED                                2
  DEL PEAK 47(20Q13.12) WILD-TYPE                              0
                                 vv
clus                              LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 47(20Q13.12) MUTATED                                    2
  DEL PEAK 47(20Q13.12) WILD-TYPE                                  2
                                 vv
clus                              LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 47(20Q13.12) MUTATED                              0
  DEL PEAK 47(20Q13.12) WILD-TYPE                            2
                                 vv
clus                              LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 47(20Q13.12) MUTATED                               4
  DEL PEAK 47(20Q13.12) WILD-TYPE                            15
                                 vv
clus                              LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 47(20Q13.12) MUTATED                                 0
  DEL PEAK 47(20Q13.12) WILD-TYPE                               1
                                 vv
clus                              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 47(20Q13.12) MUTATED                                               0
  DEL PEAK 47(20Q13.12) WILD-TYPE                                             4
                                 vv
clus                              MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 47(20Q13.12) MUTATED                              2
  DEL PEAK 47(20Q13.12) WILD-TYPE                            5
D79V9, multiclass
                                                    clus
vv                                                   DEL PEAK 47(20Q13.12) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                     3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             20
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            43
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  3
  LUNG CLEAR CELL ADENOCARCINOMA                                                 2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             2
  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 47(20Q13.12) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                               73
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             251
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                   16
  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                                    4
  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"
D79V10, binary
                                 cls
clus                                0   1
  DEL PEAK 47(20Q13.12) MUTATED     1  78
  DEL PEAK 47(20Q13.12) WILD-TYPE  20 363
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 47(20Q13.12) MUTATED      1   78
  DEL PEAK 47(20Q13.12) WILD-TYPE   20  363
     clus
vv    DEL PEAK 47(20Q13.12) MUTATED DEL PEAK 47(20Q13.12) WILD-TYPE
  NO                              1                              20
  YES                            78                             363
[1] 2 2
[1] FALSE
D79V11, continuous
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 47(20Q13.12) MUTATED    56   2   1   6
  DEL PEAK 47(20Q13.12) WILD-TYPE 262   9   3  13
D79V12, multiclass
    clus
vv   DEL PEAK 47(20Q13.12) MUTATED DEL PEAK 47(20Q13.12) WILD-TYPE
  R0                            56                             262
  R1                             2                               9
  R2                             1                               3
  RX                             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                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 47(20Q13.12) MUTATED                                  0     1
  DEL PEAK 47(20Q13.12) WILD-TYPE                                1     5
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 47(20Q13.12) MUTATED                           4    59
  DEL PEAK 47(20Q13.12) WILD-TYPE                        22   303
D79V13, multiclass
                                  clus
vv                                 DEL PEAK 47(20Q13.12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                    4
  WHITE                                                       59
                                  clus
vv                                 DEL PEAK 47(20Q13.12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          5
  BLACK OR AFRICAN AMERICAN                                     22
  WHITE                                                        303
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V14, binary
                                 cls
clus                                0   1
  DEL PEAK 47(20Q13.12) MUTATED     2  52
  DEL PEAK 47(20Q13.12) WILD-TYPE   5 280
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 47(20Q13.12) MUTATED      2   52
  DEL PEAK 47(20Q13.12) WILD-TYPE    5  280
                        clus
vv                       DEL PEAK 47(20Q13.12) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            52
                        clus
vv                       DEL PEAK 47(20Q13.12) WILD-TYPE
  HISPANIC OR LATINO                                   5
  NOT HISPANIC OR LATINO                             280
[1] 2 2
[1] FALSE

Clustering(80) Variable = DEL PEAK 48(21Q11.2) MUTATION ANALYSIS
D80V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 48(21Q11.2) MUTATED   111  32
  DEL PEAK 48(21Q11.2) WILD-TYPE 210  50
  DEL PEAK 48(21Q11.2) MUTATED DEL PEAK 48(21Q11.2) WILD-TYPE 
                           143                            260 
  DEL PEAK 48(21Q11.2) MUTATED DEL PEAK 48(21Q11.2) WILD-TYPE 
                            32                             50 
$`DEL PEAK 48(21Q11.2) MUTATED`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 TCGA-05-4398 
        1523          607         1369         1126         1947         1431 
TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4427 TCGA-05-4430 
         455          912          365          913          791          761 
TCGA-05-4432 TCGA-05-5420 TCGA-05-5425 TCGA-05-5429 TCGA-35-4122 TCGA-35-4123 
         761          457          882           30          225          182 
TCGA-38-4627 TCGA-38-4630 TCGA-44-2659 TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 
        1147         1073         1367         1013          863          723 
TCGA-44-6145 TCGA-44-6778 TCGA-44-6779 TCGA-44-7661 TCGA-44-7667 TCGA-44-7670 
         328         1864         1978          366          557          882 
TCGA-44-7672 TCGA-44-8117 TCGA-44-A479 TCGA-44-A47B TCGA-44-A47F TCGA-44-A4SS 
         719          385          486          287          337          415 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4514 TCGA-49-6745 TCGA-49-6761 
         999          268          896         1700          522          354 
TCGA-50-5045 TCGA-50-5051 TCGA-50-5068 TCGA-50-5072 TCGA-50-5932 TCGA-50-5933 
        2174          455         1499          246         1091         2370 
TCGA-50-5935 TCGA-50-5944 TCGA-50-5946 TCGA-50-7109 TCGA-53-7813 TCGA-55-1592 
         653          764          686          255          424          701 
TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6972 TCGA-55-6983 TCGA-55-6985 
        1178         1375           87         1475         1826         1233 
TCGA-55-6986 TCGA-55-7570 TCGA-55-7576 TCGA-55-7724 TCGA-55-7728 TCGA-55-7815 
        2151            6           40         1958           24           54 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7994 TCGA-55-8089 TCGA-55-8090 
          16          197           21           31          100            6 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8205 TCGA-55-8302 TCGA-55-8506 TCGA-55-8507 
          26            4           33           23           11            8 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8514 TCGA-55-8615 TCGA-55-A490 TCGA-55-A491 
          15          228          202           15           48         1952 
TCGA-55-A4DF TCGA-62-8402 TCGA-62-A471 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
          47         1445         1246          628         1686         1968 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5781 TCGA-69-7760 TCGA-69-7761 TCGA-69-7765 
        1959           62         1559          202          186          165 
TCGA-69-7974 TCGA-69-7979 TCGA-69-7980 TCGA-73-4658 TCGA-73-4659 TCGA-73-4666 
         184           89          382         1600          711          800 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-75-7027 TCGA-75-7031 TCGA-78-7146 
         467          131           40         1956         1965         1988 
TCGA-78-7148 TCGA-78-7153 TCGA-78-7154 TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 
        1944          760         1948         1937         1965         1949 
TCGA-78-8640 TCGA-78-8660 TCGA-80-5608 TCGA-86-7701 TCGA-86-7711 TCGA-86-7953 
        1949         1954         1972           11          630          591 
TCGA-86-8054 TCGA-86-8278 TCGA-86-8359 TCGA-86-8585 TCGA-86-8669 TCGA-91-6828 
         745          476           26           35           34          323 
TCGA-91-6831 TCGA-91-6836 TCGA-91-6840 TCGA-91-7771 TCGA-95-7043 TCGA-95-7948 
         310          417          372          492            2          476 
TCGA-97-7547 TCGA-97-8172 TCGA-97-8175 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
        1965          182           87          427          459           44 
TCGA-99-8033 TCGA-J2-A4AE TCGA-MP-A4SV TCGA-MP-A4T8 TCGA-MP-A4TE 
         170          282         1946         1957         1970 

$`DEL PEAK 48(21Q11.2) WILD-TYPE`
TCGA-05-4384 TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4425 
         426          578          610         1958         1997          669 
TCGA-05-4426 TCGA-05-4433 TCGA-05-5423 TCGA-05-5428 TCGA-05-5715 TCGA-35-3615 
         791          730          151          670           62           14 
TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4628 TCGA-38-4629 TCGA-38-4631 
         264         1952         1962         1492          864          354 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 
        1357          448         1971          133         1324         1429 
TCGA-44-2657 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
         400          741         1280         1301           97          246 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5645 
        1130         1163         1036          190          722          383 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
         302          845          704          658          705         1938 
TCGA-44-6777 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7669 TCGA-44-7671 
        1942          444          592          218         1970          535 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A47A TCGA-44-A47G TCGA-44-A4SU TCGA-49-4486 
          99          260          466          351           76         1932 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4512 TCGA-49-6742 TCGA-49-6743 
        1081         1421          428          157          445          369 
TCGA-49-6744 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5930 TCGA-50-5931 
         890         2146          785          944          282          267 
TCGA-50-5941 TCGA-50-5942 TCGA-50-6597 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
         567          883         1015          105         1986         1971 
TCGA-53-A4EZ TCGA-55-1595 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 
         280         1479            2          993           24         1239 
TCGA-55-6971 TCGA-55-6980 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
          25           67         1170           18           35          121 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7903 
           4           95           39           39           34           19 
TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8091 TCGA-55-8096 
           3            5           33           21           43           47 
TCGA-55-8097 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 
          15           46           66          216           44           29 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 
           9            3          146          536           48           49 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A492 
          66          106           33           42           29            1 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
          28            5          162         1216         1289         1970 
TCGA-62-8399 TCGA-62-A46U TCGA-62-A46V TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 
        2696         2067         2199          910         1728         1189 
TCGA-64-1680 TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 
        1126         1305          864          866           31          610 
TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
         573          427          385          174          141          422 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 TCGA-69-7978 TCGA-69-8253 TCGA-69-8254 
         690          414          230           70          100           77 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-73-4662 TCGA-73-4676 TCGA-73-4677 
         129          214           61          912          164           38 
TCGA-73-7498 TCGA-73-7499 TCGA-75-6214 TCGA-75-7025 TCGA-78-7145 TCGA-78-7147 
         621          519         1970         1967         1973         1950 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
        1093         1963         1202         1957         1961         1963 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
        1221          678          215         1940         1950         1934 
TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        1972         1944          327          881         1952          994 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5607 TCGA-83-5908 TCGA-86-6851 
        1971         1981         1964         1965          824         1959 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 
         422         1968         1963          508           10         1963 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8279 TCGA-86-8280 
          13           24          479          489          482           16 
TCGA-86-8281 TCGA-86-8358 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1955           19           45           18           15          455 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 
         405           10           30           14           39         1940 
TCGA-91-6830 TCGA-91-6835 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 
          60           79          842          224           35          197 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
         174           36           44          218          297          127 
TCGA-93-8067 TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-A4VK 
         186           34          568          377          477          121 
TCGA-97-7546 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 
         964         1932         1332          775          181           22 
TCGA-97-8171 TCGA-97-8174 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
         107         1965          147           15          148          115 
TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
         197          271          392          154          114          287 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
         238          578          435          116            6          285 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 
         622          353         1967         1951         1954         1954 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        1980         1951         1944         1970          142         1955 
TCGA-MP-A4TK TCGA-MP-A5C7 
        1971         1490 

  DEL PEAK 48(21Q11.2) MUTATED DEL PEAK 48(21Q11.2) WILD-TYPE 
                             2                              1 
  DEL PEAK 48(21Q11.2) MUTATED DEL PEAK 48(21Q11.2) WILD-TYPE 
                          2370                           2696 
  DEL PEAK 48(21Q11.2) MUTATED DEL PEAK 48(21Q11.2) WILD-TYPE 
                         522.0                          431.5 
[1] "2.0 - 2370.0 (522.0)" "1.0 - 2696.0 (431.5)"
[1] "hr=" "1.2"
D80V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 48(21Q11.2) MUTATED         2       33       44        10        30
  DEL PEAK 48(21Q11.2) WILD-TYPE       2       80       87        33        39
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 48(21Q11.2) MUTATED           25          5        9
  DEL PEAK 48(21Q11.2) WILD-TYPE         42          6       14
D80V3, multiclass
            clus
vv           DEL PEAK 48(21Q11.2) MUTATED DEL PEAK 48(21Q11.2) WILD-TYPE
  STAGE I                               2                              2
  STAGE IA                             33                             80
  STAGE IB                             44                             87
  STAGE IIA                            10                             33
  STAGE IIB                            30                             39
  STAGE IIIA                           25                             42
  STAGE IIIB                            5                              6
  STAGE IV                              9                             14
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 48(21Q11.2) MUTATED    40  93  16   7
  DEL PEAK 48(21Q11.2) WILD-TYPE 103 166  24  11
D80V4, multiclass
    clus
vv   DEL PEAK 48(21Q11.2) MUTATED DEL PEAK 48(21Q11.2) WILD-TYPE
  T1                           40                            103
  T2                           93                            166
  T3                           16                             24
  T4                            7                             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 48(21Q11.2) MUTATED   100  31    25
  DEL PEAK 48(21Q11.2) WILD-TYPE 195  54    47
D80V5, multiclass
       clus
vv      DEL PEAK 48(21Q11.2) MUTATED DEL PEAK 48(21Q11.2) WILD-TYPE
  N0                             100                            195
  N1                              31                             54
  N2+N3                           25                             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"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 48(21Q11.2) MUTATED   108   7   0   1  41
  DEL PEAK 48(21Q11.2) WILD-TYPE 209  11   1   2  78
D80V6, multiclass
     clus
vv    DEL PEAK 48(21Q11.2) MUTATED DEL PEAK 48(21Q11.2) WILD-TYPE
  M0                           108                            209
  M1                             7                             11
  M1A                            0                              1
  M1B                            1                              2
  MX                            41                             78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V7, binary
                                cls
clus                               0   1
  DEL PEAK 48(21Q11.2) MUTATED    78  80
  DEL PEAK 48(21Q11.2) WILD-TYPE 170 134
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 48(21Q11.2) MUTATED     78   80
  DEL PEAK 48(21Q11.2) WILD-TYPE  170  134
        clus
vv       DEL PEAK 48(21Q11.2) MUTATED DEL PEAK 48(21Q11.2) WILD-TYPE
  FEMALE                           78                            170
  MALE                             80                            134
[1] 2 2
[1] FALSE
D80V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 48(21Q11.2) MUTATED                            7
  DEL PEAK 48(21Q11.2) WILD-TYPE                          6
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 48(21Q11.2) MUTATED                                  26
  DEL PEAK 48(21Q11.2) WILD-TYPE                                67
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 48(21Q11.2) MUTATED                                                  110
  DEL PEAK 48(21Q11.2) WILD-TYPE                                                184
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 48(21Q11.2) MUTATED                                            0
  DEL PEAK 48(21Q11.2) WILD-TYPE                                          4
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 48(21Q11.2) MUTATED                                               2
  DEL PEAK 48(21Q11.2) WILD-TYPE                                            17
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 48(21Q11.2) MUTATED                                0
  DEL PEAK 48(21Q11.2) WILD-TYPE                              2
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 48(21Q11.2) MUTATED                                    1
  DEL PEAK 48(21Q11.2) WILD-TYPE                                  3
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 48(21Q11.2) MUTATED                              0
  DEL PEAK 48(21Q11.2) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 48(21Q11.2) MUTATED                               6
  DEL PEAK 48(21Q11.2) WILD-TYPE                            13
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 48(21Q11.2) MUTATED                                 1
  DEL PEAK 48(21Q11.2) WILD-TYPE                               0
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 48(21Q11.2) MUTATED                                               2
  DEL PEAK 48(21Q11.2) WILD-TYPE                                             2
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 48(21Q11.2) MUTATED                              3
  DEL PEAK 48(21Q11.2) WILD-TYPE                            4
D80V9, multiclass
                                                    clus
vv                                                   DEL PEAK 48(21Q11.2) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            26
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          110
  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                                                  3
                                                    clus
vv                                                   DEL PEAK 48(21Q11.2) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              67
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            184
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  17
  LUNG CLEAR CELL ADENOCARCINOMA                                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              3
  LUNG MUCINOUS ADENOCARCINOMA                                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                                  13
  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"
D80V10, binary
                                cls
clus                               0   1
  DEL PEAK 48(21Q11.2) MUTATED    10 148
  DEL PEAK 48(21Q11.2) WILD-TYPE  11 293
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 48(21Q11.2) MUTATED     10  148
  DEL PEAK 48(21Q11.2) WILD-TYPE   11  293
     clus
vv    DEL PEAK 48(21Q11.2) MUTATED DEL PEAK 48(21Q11.2) WILD-TYPE
  NO                            10                             11
  YES                          148                            293
[1] 2 2
[1] FALSE
D80V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 48(21Q11.2) MUTATED   109   3   1   4
  DEL PEAK 48(21Q11.2) WILD-TYPE 209   8   3  15
D80V12, multiclass
    clus
vv   DEL PEAK 48(21Q11.2) MUTATED DEL PEAK 48(21Q11.2) WILD-TYPE
  R0                          109                            209
  R1                            3                              8
  R2                            1                              3
  RX                            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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 48(21Q11.2) MUTATED                                  1     1
  DEL PEAK 48(21Q11.2) WILD-TYPE                                0     5
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 48(21Q11.2) MUTATED                          13   114
  DEL PEAK 48(21Q11.2) WILD-TYPE                        13   248
D80V13, multiclass
                                  clus
vv                                 DEL PEAK 48(21Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                  13
  WHITE                                                     114
                                  clus
vv                                 DEL PEAK 48(21Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         5
  BLACK OR AFRICAN AMERICAN                                    13
  WHITE                                                       248
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V14, binary
                                cls
clus                               0   1
  DEL PEAK 48(21Q11.2) MUTATED     2 109
  DEL PEAK 48(21Q11.2) WILD-TYPE   5 223
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 48(21Q11.2) MUTATED      2  109
  DEL PEAK 48(21Q11.2) WILD-TYPE    5  223
                        clus
vv                       DEL PEAK 48(21Q11.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          109
                        clus
vv                       DEL PEAK 48(21Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            223
[1] 2 2
[1] FALSE

Clustering(81) Variable = DEL PEAK 49(22Q13.32) MUTATION ANALYSIS
D81V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 49(22Q13.32) MUTATED   157  39
  DEL PEAK 49(22Q13.32) WILD-TYPE 164  43
  DEL PEAK 49(22Q13.32) MUTATED DEL PEAK 49(22Q13.32) WILD-TYPE 
                            196                             207 
  DEL PEAK 49(22Q13.32) MUTATED DEL PEAK 49(22Q13.32) WILD-TYPE 
                             39                              43 
$`DEL PEAK 49(22Q13.32) MUTATED`
TCGA-05-4249 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 TCGA-05-4415 TCGA-05-4420 
        1523         1369         1126         1947         1997          912 
TCGA-05-4424 TCGA-05-4426 TCGA-05-4427 TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 
         913          791          791          761          730          457 
TCGA-05-5425 TCGA-05-5428 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4628 
         882          670          225          182          264         1492 
TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 TCGA-44-2656 TCGA-44-2659 TCGA-44-2662 
        1073         1357          448         1429         1367         1280 
TCGA-44-2668 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
         246         1036          190          722         1013          863 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6147 TCGA-44-6774 TCGA-44-6778 TCGA-44-7662 
         723          328          845          658         1864          218 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7671 TCGA-44-8117 TCGA-44-8120 TCGA-44-A4SS 
         557         1970          535          385          260          415 
TCGA-44-A4SU TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
          76         1421          428          999          268          896 
TCGA-49-6744 TCGA-49-6761 TCGA-50-5051 TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 
         890          354          455          282         1091         2370 
TCGA-50-5935 TCGA-50-5941 TCGA-50-6597 TCGA-50-7109 TCGA-53-7624 TCGA-53-7813 
         653          567         1015          255         1986          424 
TCGA-53-A4EZ TCGA-55-1594 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6971 
         280         1178          993           24         1239           25 
TCGA-55-6972 TCGA-55-6980 TCGA-55-6985 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 
        1475           67         1233           18           35            6 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 
          95           40           34           19          197           21 
TCGA-55-7994 TCGA-55-8092 TCGA-55-8094 TCGA-55-8205 TCGA-55-8207 TCGA-55-8505 
          31           26            4           33           66           29 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
          11            8           15          228            9            3 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
          15           48           66           42           29           48 
TCGA-55-A493 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8399 TCGA-62-A46U TCGA-62-A472 
          28           47          162         2696         2067          910 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
        1728          628         1189         1686         1968         1959 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-67-3771 TCGA-67-6217 
          62         1305          864         1559          610          422 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 TCGA-69-7978 
         202          186          690          414          230           70 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
          89          382          100          129          214           61 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4668 TCGA-73-4670 TCGA-75-6214 TCGA-75-7027 
         711          912          467          131         1970         1956 
TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 TCGA-78-7152 TCGA-78-7159 TCGA-78-7163 
        1965         1973         1988         1202         1221         1950 
TCGA-78-7167 TCGA-78-7535 TCGA-78-7536 TCGA-78-8640 TCGA-78-8660 TCGA-78-8662 
        1937         1972         1949         1949         1954         1964 
TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7953 
        1972          824         1959           11          630          591 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8056 TCGA-86-8074 TCGA-86-8279 
        1963          508          745         1963           24          482 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8672 TCGA-86-A4D0 TCGA-91-6828 
          19           26           35           15           30          323 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1940           60          310          417          372          842 
TCGA-91-7771 TCGA-91-8499 TCGA-91-A4BC TCGA-93-8067 TCGA-95-7039 TCGA-95-7567 
         492           36           44          186           34          568 
TCGA-95-7944 TCGA-97-7546 TCGA-97-7552 TCGA-97-7554 TCGA-97-7937 TCGA-99-7458 
         377          964         1932          775          181          392 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L9-A444 
         459           44          170          238          578            6 
TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4T2 TCGA-MP-A4T8 TCGA-MP-A4TA 
         285          353         1946         1951         1957         1951 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TK 
        1970         1970          142         1971 

$`DEL PEAK 49(22Q13.32) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 
         607          426         1431          578          610         1958 
TCGA-05-4417 TCGA-05-4422 TCGA-05-4425 TCGA-05-4430 TCGA-05-5423 TCGA-05-5429 
         455          365          669          761          151           30 
TCGA-05-5715 TCGA-35-3615 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4629 
          62           14         1952         1962         1147          864 
TCGA-38-4631 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2657 TCGA-44-2661 
         354         1971          133         1324          400          741 
TCGA-44-2665 TCGA-44-2666 TCGA-44-3396 TCGA-44-3398 TCGA-44-5645 TCGA-44-6146 
        1301           97         1130         1163          383          302 
TCGA-44-6148 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 
         704          705         1938         1942         1978          444 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7670 TCGA-44-7672 TCGA-44-8119 TCGA-44-A479 
         592          366          882          719           99          486 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-49-4486 TCGA-49-4494 
         466          287          337          351         1932         1081 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6745 TCGA-50-5045 
         157         1700          445          369          522         2174 
TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 
        2146          785          944         1499          246          267 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-8460 TCGA-53-7626 TCGA-55-1592 
         883          764          686          105         1971          701 
TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6983 TCGA-55-6986 
        1479         1375           87            2         1826         2151 
TCGA-55-6987 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        1170          121            4         1958           39           39 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7907 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 
          24           54           16            3            5           33 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8096 TCGA-55-8097 
          21          100            6           43           47           15 
TCGA-55-8206 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8513 TCGA-55-8514 
          46          216           44           23          146          202 
TCGA-55-8614 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 
         536           49          106           33         1952            1 
TCGA-55-A494 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8402 TCGA-62-A46V 
           5         1216         1289         1970         1445         2199 
TCGA-62-A471 TCGA-64-1680 TCGA-64-5815 TCGA-67-3770 TCGA-67-3772 TCGA-67-3773 
        1246         1126          866           31          573          427 
TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-69-7765 TCGA-69-7974 TCGA-69-8254 
         385          174          141          165          184           77 
TCGA-73-4658 TCGA-73-4666 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
        1600          800           40          164           38          621 
TCGA-73-7499 TCGA-75-7025 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
         519         1967         1950         1944         1093         1963 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 
         760         1948         1957         1961         1963          678 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7166 TCGA-78-7220 TCGA-78-7537 TCGA-78-7539 
         215         1940         1934         1965         1944          327 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 TCGA-80-5607 
         881         1952          994         1971         1981         1965 
TCGA-86-7713 TCGA-86-7714 TCGA-86-8055 TCGA-86-8073 TCGA-86-8075 TCGA-86-8076 
         422         1968           10           13          479          489 
TCGA-86-8278 TCGA-86-8280 TCGA-86-8281 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
         476           16         1955           45           34           18 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6835 
         455          405           10           14           39           79 
TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 
         224           35          197          174          218          297 
TCGA-93-7348 TCGA-95-7043 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-97-7547 
         127            2          477          476          121         1965 
TCGA-97-7553 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        1332           22          107          182         1965           87 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 
         147           15          148          115          197          271 
TCGA-99-8025 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E6 
         427          154          114          287          282          435 
TCGA-L9-A443 TCGA-MN-A4N4 TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T9 
         116          622         1967         1954         1954         1980 
TCGA-MP-A4TC TCGA-MP-A4TI TCGA-MP-A5C7 
        1944         1955         1490 

  DEL PEAK 49(22Q13.32) MUTATED DEL PEAK 49(22Q13.32) WILD-TYPE 
                              3                               1 
  DEL PEAK 49(22Q13.32) MUTATED DEL PEAK 49(22Q13.32) WILD-TYPE 
                           2696                            2199 
  DEL PEAK 49(22Q13.32) MUTATED DEL PEAK 49(22Q13.32) WILD-TYPE 
                            500                             445 
[1] "3.0 - 2696.0 (500.0)" "1.0 - 2199.0 (445.0)"
[1] "hr=" "1.1"
D81V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 49(22Q13.32) MUTATED         3       48       62        22        34
  DEL PEAK 49(22Q13.32) WILD-TYPE       1       65       69        21        35
                                 vv
clus                              STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 49(22Q13.32) MUTATED           35          6       13
  DEL PEAK 49(22Q13.32) WILD-TYPE         32          5       10
D81V3, multiclass
            clus
vv           DEL PEAK 49(22Q13.32) MUTATED DEL PEAK 49(22Q13.32) WILD-TYPE
  STAGE I                                3                               1
  STAGE IA                              48                              65
  STAGE IB                              62                              69
  STAGE IIA                             22                              21
  STAGE IIB                             34                              35
  STAGE IIIA                            35                              32
  STAGE IIIB                             6                               5
  STAGE IV                              13                              10
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  DEL PEAK 49(22Q13.32) MUTATED    69 125  19   9
  DEL PEAK 49(22Q13.32) WILD-TYPE  74 134  21   9
D81V4, multiclass
    clus
vv   DEL PEAK 49(22Q13.32) MUTATED DEL PEAK 49(22Q13.32) WILD-TYPE
  T1                            69                              74
  T2                           125                             134
  T3                            19                              21
  T4                             9                               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 49(22Q13.32) MUTATED   144  40    36
  DEL PEAK 49(22Q13.32) WILD-TYPE 151  45    36
D81V5, multiclass
       clus
vv      DEL PEAK 49(22Q13.32) MUTATED DEL PEAK 49(22Q13.32) WILD-TYPE
  N0                              144                             151
  N1                               40                              45
  N2+N3                            36                              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"
                                 vv
clus                               M0  M1 M1A M1B  MX
  DEL PEAK 49(22Q13.32) MUTATED   152  10   0   3  56
  DEL PEAK 49(22Q13.32) WILD-TYPE 165   8   1   0  63
D81V6, multiclass
     clus
vv    DEL PEAK 49(22Q13.32) MUTATED DEL PEAK 49(22Q13.32) WILD-TYPE
  M0                            152                             165
  M1                             10                               8
  M1A                             0                               1
  M1B                             3                               0
  MX                             56                              63
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V7, binary
                                 cls
clus                                0   1
  DEL PEAK 49(22Q13.32) MUTATED   106 117
  DEL PEAK 49(22Q13.32) WILD-TYPE 142  97
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 49(22Q13.32) MUTATED    106  117
  DEL PEAK 49(22Q13.32) WILD-TYPE  142   97
        clus
vv       DEL PEAK 49(22Q13.32) MUTATED DEL PEAK 49(22Q13.32) WILD-TYPE
  FEMALE                           106                             142
  MALE                             117                              97
[1] 2 2
[1] FALSE
D81V8, continuous
                                 vv
clus                              LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 49(22Q13.32) MUTATED                            8
  DEL PEAK 49(22Q13.32) WILD-TYPE                          5
                                 vv
clus                              LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 49(22Q13.32) MUTATED                                  38
  DEL PEAK 49(22Q13.32) WILD-TYPE                                55
                                 vv
clus                              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 49(22Q13.32) MUTATED                                                  150
  DEL PEAK 49(22Q13.32) WILD-TYPE                                                144
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 49(22Q13.32) MUTATED                                            1
  DEL PEAK 49(22Q13.32) WILD-TYPE                                          3
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 49(22Q13.32) MUTATED                                              10
  DEL PEAK 49(22Q13.32) WILD-TYPE                                             9
                                 vv
clus                              LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 49(22Q13.32) MUTATED                                0
  DEL PEAK 49(22Q13.32) WILD-TYPE                              2
                                 vv
clus                              LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 49(22Q13.32) MUTATED                                    2
  DEL PEAK 49(22Q13.32) WILD-TYPE                                  2
                                 vv
clus                              LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 49(22Q13.32) MUTATED                              0
  DEL PEAK 49(22Q13.32) WILD-TYPE                            2
                                 vv
clus                              LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 49(22Q13.32) MUTATED                               8
  DEL PEAK 49(22Q13.32) WILD-TYPE                            11
                                 vv
clus                              LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 49(22Q13.32) MUTATED                                 1
  DEL PEAK 49(22Q13.32) WILD-TYPE                               0
                                 vv
clus                              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 49(22Q13.32) MUTATED                                               3
  DEL PEAK 49(22Q13.32) WILD-TYPE                                             1
                                 vv
clus                              MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 49(22Q13.32) MUTATED                              2
  DEL PEAK 49(22Q13.32) WILD-TYPE                            5
D81V9, multiclass
                                                    clus
vv                                                   DEL PEAK 49(22Q13.32) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                     8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             38
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           150
  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                                                  8
  LUNG SIGNET RING ADENOCARCINOMA                                                1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                  3
  MUCINOUS (COLLOID) CARCINOMA                                                   2
                                                    clus
vv                                                   DEL PEAK 49(22Q13.32) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                       5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                               55
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             144
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                       3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                    9
  LUNG CLEAR CELL ADENOCARCINOMA                                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                               2
  LUNG MUCINOUS ADENOCARCINOMA                                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                                   11
  LUNG SIGNET RING ADENOCARCINOMA                                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                    1
  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"
D81V10, binary
                                 cls
clus                                0   1
  DEL PEAK 49(22Q13.32) MUTATED     9 214
  DEL PEAK 49(22Q13.32) WILD-TYPE  12 227
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 49(22Q13.32) MUTATED      9  214
  DEL PEAK 49(22Q13.32) WILD-TYPE   12  227
     clus
vv    DEL PEAK 49(22Q13.32) MUTATED DEL PEAK 49(22Q13.32) WILD-TYPE
  NO                              9                              12
  YES                           214                             227
[1] 2 2
[1] FALSE
D81V11, continuous
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 49(22Q13.32) MUTATED   154   6   1   8
  DEL PEAK 49(22Q13.32) WILD-TYPE 164   5   3  11
D81V12, multiclass
    clus
vv   DEL PEAK 49(22Q13.32) MUTATED DEL PEAK 49(22Q13.32) WILD-TYPE
  R0                           154                             164
  R1                             6                               5
  R2                             1                               3
  RX                             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                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 49(22Q13.32) MUTATED                                  1     2
  DEL PEAK 49(22Q13.32) WILD-TYPE                                0     4
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 49(22Q13.32) MUTATED                          16   170
  DEL PEAK 49(22Q13.32) WILD-TYPE                        10   192
D81V13, multiclass
                                  clus
vv                                 DEL PEAK 49(22Q13.32) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   16
  WHITE                                                      170
                                  clus
vv                                 DEL PEAK 49(22Q13.32) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          4
  BLACK OR AFRICAN AMERICAN                                     10
  WHITE                                                        192
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V14, binary
                                 cls
clus                                0   1
  DEL PEAK 49(22Q13.32) MUTATED     4 164
  DEL PEAK 49(22Q13.32) WILD-TYPE   3 168
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 49(22Q13.32) MUTATED      4  164
  DEL PEAK 49(22Q13.32) WILD-TYPE    3  168
                        clus
vv                       DEL PEAK 49(22Q13.32) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           164
                        clus
vv                       DEL PEAK 49(22Q13.32) WILD-TYPE
  HISPANIC OR LATINO                                   3
  NOT HISPANIC OR LATINO                             168
[1] 2 2
[1] FALSE

Clustering(82) Variable = DEL PEAK 50(XP22.2) MUTATION ANALYSIS
D82V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 50(XP22.2) MUTATED    89  22
  DEL PEAK 50(XP22.2) WILD-TYPE 232  60
  DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE 
                          111                           292 
  DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE 
                           22                            60 
$`DEL PEAK 50(XP22.2) MUTATED`
TCGA-05-4382 TCGA-05-4389 TCGA-05-4396 TCGA-05-4405 TCGA-05-4426 TCGA-05-4427 
         607         1369         1947          610          791          791 
TCGA-05-5428 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-38-6178 TCGA-44-2659 
         670           62          225          182          448         1367 
TCGA-44-5643 TCGA-44-5644 TCGA-44-6146 TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 
        1013          863          302         1864         1978          592 
TCGA-44-8117 TCGA-44-8120 TCGA-49-4505 TCGA-49-4512 TCGA-50-5066 TCGA-50-5068 
         385          260          428          157          944         1499 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5941 TCGA-50-5946 TCGA-50-6597 TCGA-50-7109 
        1091         2370          567          686         1015          255 
TCGA-53-7624 TCGA-53-7626 TCGA-55-1592 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 
        1986         1971          701         1375           87            2 
TCGA-55-6987 TCGA-55-7281 TCGA-55-7570 TCGA-55-7726 TCGA-55-7903 TCGA-55-7994 
        1170           18            6           39           19           31 
TCGA-55-8090 TCGA-55-8094 TCGA-55-8301 TCGA-55-8510 TCGA-55-8616 TCGA-55-A48X 
           6            4           44          228           48           33 
TCGA-55-A48Z TCGA-55-A492 TCGA-55-A4DG TCGA-62-8397 TCGA-62-A46U TCGA-62-A472 
          29            1          162         1289         2067          910 
TCGA-64-1676 TCGA-64-1678 TCGA-64-5778 TCGA-64-5815 TCGA-67-3770 TCGA-67-3772 
        1728         1189         1305          866           31          573 
TCGA-67-3773 TCGA-67-6217 TCGA-69-7764 TCGA-69-7765 TCGA-69-7979 TCGA-69-A59K 
         427          422          414          165           89          214 
TCGA-71-6725 TCGA-73-4666 TCGA-73-4668 TCGA-73-7499 TCGA-75-7025 TCGA-75-7031 
          61          800          467          519         1967         1965 
TCGA-78-7146 TCGA-78-7154 TCGA-78-7160 TCGA-78-7166 TCGA-78-7535 TCGA-78-7542 
        1988         1948          678         1934         1972         1952 
TCGA-78-8640 TCGA-78-8655 TCGA-78-8660 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
        1949         1981         1954         1963          508          745 
TCGA-86-8055 TCGA-86-8075 TCGA-86-8281 TCGA-86-8358 TCGA-86-8359 TCGA-86-8673 
          10          479         1955           19           26          455 
TCGA-86-A4P7 TCGA-91-6848 TCGA-91-7771 TCGA-91-8496 TCGA-95-7039 TCGA-95-7043 
          14          224          492          197           34            2 
TCGA-95-7567 TCGA-97-7554 TCGA-97-7937 TCGA-97-8172 TCGA-97-8179 TCGA-97-8547 
         568          775          181          182           15          148 
TCGA-97-A4M7 TCGA-L4-A4E5 TCGA-L9-A444 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
         271          578            6          353         1946         1967 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4TI 
        1951         1954         1955 

$`DEL PEAK 50(XP22.2) WILD-TYPE`
TCGA-05-4249 TCGA-05-4384 TCGA-05-4390 TCGA-05-4398 TCGA-05-4403 TCGA-05-4410 
        1523          426         1126         1431          578         1958 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
        1997          455          912          365          913          669 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 
         761          761          730          457          151          882 
TCGA-05-5429 TCGA-35-3615 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
          30           14          264         1952         1962         1147 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-7271 
        1492          864         1073          354         1357         1971 
TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2662 
         133         1324         1429          400          741         1280 
TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 
        1301           97          246         1130         1163         1036 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6147 
         190          722          383          723          328          845 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-7659 
         704          658          705         1938         1942          444 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 
         366          218          557         1970          882          535 
TCGA-44-7672 TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
         719           99          486          466          287          337 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 
         351          415           76         1932         1081         1421 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
         999          268          896         1700          445          369 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
         890          522          354         2174         2146          455 
TCGA-50-5055 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5935 TCGA-50-5942 
         785          246          282          267          653          883 
TCGA-50-5944 TCGA-50-8460 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1595 
         764          105          424          280         1178         1479 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 
         993           24         1239           25         1475           67 
TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 TCGA-55-7283 TCGA-55-7284 TCGA-55-7573 
        1826         1233         2151           35          121            4 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7727 TCGA-55-7728 
          95           40         1958           39           34           24 
TCGA-55-7815 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 
          54           16          197           21            3            5 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8091 TCGA-55-8092 TCGA-55-8096 
          33           21          100           43           26           47 
TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8302 
          15           33           46           66          216           23 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8511 TCGA-55-8512 
          29           11            8           15            9            3 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8619 TCGA-55-8620 
         146          202          536           15           49           66 
TCGA-55-8621 TCGA-55-A48Y TCGA-55-A490 TCGA-55-A491 TCGA-55-A493 TCGA-55-A494 
         106           42           48         1952           28            5 
TCGA-55-A4DF TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46V 
          47         1216         1970         2696         1445         2199 
TCGA-62-A471 TCGA-64-1677 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 
        1246          628         1686         1126         1968         1959 
TCGA-64-5775 TCGA-64-5779 TCGA-64-5781 TCGA-67-3771 TCGA-67-3774 TCGA-67-6215 
          62          864         1559          610          385          174 
TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7973 TCGA-69-7974 
         141          202          186          690          230          184 
TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-73-4658 
          70          382          100           77          129         1600 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
         711          912          131           40          164           38 
TCGA-73-7498 TCGA-75-6214 TCGA-75-7027 TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 
         621         1970         1956         1973         1950         1944 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7155 TCGA-78-7156 
        1093         1963         1202          760         1957         1961 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 
        1963         1221          215         1940         1950         1937 
TCGA-78-7220 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7633 
        1965         1949         1944          327          881          994 
TCGA-78-8648 TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 
        1971         1964         1965         1972          824         1959 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-8056 
          11          630          422         1968          591         1963 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
          13           24          489          476          482           16 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 
          35           45           34           18           15          405 
TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
          10           30           39          323         1940           60 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6849 
         310           79          417          372          842           35 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
         174           36           44          218          297          127 
TCGA-93-8067 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-97-7546 
         186          377          477          476          121          964 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 
        1965         1932         1332           22          107         1965 
TCGA-97-8175 TCGA-97-8177 TCGA-97-8552 TCGA-97-A4M2 TCGA-99-7458 TCGA-99-8025 
          87          147          115          197          392          427 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
         459           44          170          154          114          287 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 TCGA-MN-A4N1 TCGA-MN-A4N4 
         282          238          435          116          285          622 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TE 
        1954         1957         1980         1951         1944         1970 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TK TCGA-MP-A5C7 
        1970          142         1971         1490 

  DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE 
                            1                             3 
  DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE 
                         2370                          2696 
  DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE 
                        567.0                         444.5 
[1] "1.0 - 2370.0 (567.0)" "3.0 - 2696.0 (444.5)"
[1] "hr=" "1.3"
D82V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 50(XP22.2) MUTATED         2       27       36         8        27
  DEL PEAK 50(XP22.2) WILD-TYPE       2       86       95        35        42
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 50(XP22.2) MUTATED           15          3        8
  DEL PEAK 50(XP22.2) WILD-TYPE         52          8       15
D82V3, multiclass
            clus
vv           DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE
  STAGE I                              2                             2
  STAGE IA                            27                            86
  STAGE IB                            36                            95
  STAGE IIA                            8                            35
  STAGE IIB                           27                            42
  STAGE IIIA                          15                            52
  STAGE IIIB                           3                             8
  STAGE IV                             8                            15
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 50(XP22.2) MUTATED    36  71  13   5
  DEL PEAK 50(XP22.2) WILD-TYPE 107 188  27  13
D82V4, multiclass
    clus
vv   DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE
  T1                          36                           107
  T2                          71                           188
  T3                          13                            27
  T4                           5                            13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1 N2+N3
  DEL PEAK 50(XP22.2) MUTATED    76  29    19
  DEL PEAK 50(XP22.2) WILD-TYPE 219  56    53
D82V5, multiclass
       clus
vv      DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE
  N0                             76                           219
  N1                             29                            56
  N2+N3                          19                            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"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK 50(XP22.2) MUTATED    89   6   0   1  28
  DEL PEAK 50(XP22.2) WILD-TYPE 228  12   1   2  91
D82V6, multiclass
     clus
vv    DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE
  M0                           89                           228
  M1                            6                            12
  M1A                           0                             1
  M1B                           1                             2
  MX                           28                            91
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V7, binary
                               cls
clus                              0   1
  DEL PEAK 50(XP22.2) MUTATED    58  68
  DEL PEAK 50(XP22.2) WILD-TYPE 190 146
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 50(XP22.2) MUTATED     58   68
  DEL PEAK 50(XP22.2) WILD-TYPE  190  146
        clus
vv       DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE
  FEMALE                          58                           190
  MALE                            68                           146
[1] 2 2
[1] FALSE
D82V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 50(XP22.2) MUTATED                            4
  DEL PEAK 50(XP22.2) WILD-TYPE                          9
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 50(XP22.2) MUTATED                                  28
  DEL PEAK 50(XP22.2) WILD-TYPE                                65
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 50(XP22.2) MUTATED                                                   82
  DEL PEAK 50(XP22.2) WILD-TYPE                                                212
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 50(XP22.2) MUTATED                                            1
  DEL PEAK 50(XP22.2) WILD-TYPE                                          3
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 50(XP22.2) MUTATED                                               4
  DEL PEAK 50(XP22.2) WILD-TYPE                                            15
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 50(XP22.2) MUTATED                                0
  DEL PEAK 50(XP22.2) WILD-TYPE                              2
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 50(XP22.2) MUTATED                                    3
  DEL PEAK 50(XP22.2) WILD-TYPE                                  1
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 50(XP22.2) MUTATED                              1
  DEL PEAK 50(XP22.2) WILD-TYPE                            1
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 50(XP22.2) MUTATED                               2
  DEL PEAK 50(XP22.2) WILD-TYPE                            17
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 50(XP22.2) MUTATED                                 0
  DEL PEAK 50(XP22.2) WILD-TYPE                               1
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 50(XP22.2) MUTATED                                               0
  DEL PEAK 50(XP22.2) WILD-TYPE                                             4
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 50(XP22.2) MUTATED                              1
  DEL PEAK 50(XP22.2) WILD-TYPE                            6
D82V9, multiclass
                                                    clus
vv                                                   DEL PEAK 50(XP22.2) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           28
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          82
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                   1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                4
  LUNG CLEAR CELL ADENOCARCINOMA                                               0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                           3
  LUNG MUCINOUS ADENOCARCINOMA                                                 1
  LUNG PAPILLARY ADENOCARCINOMA                                                2
  LUNG SIGNET RING ADENOCARCINOMA                                              0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                0
  MUCINOUS (COLLOID) CARCINOMA                                                 1
                                                    clus
vv                                                   DEL PEAK 50(XP22.2) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             65
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           212
  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                                                 17
  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"
D82V10, binary
                               cls
clus                              0   1
  DEL PEAK 50(XP22.2) MUTATED     4 122
  DEL PEAK 50(XP22.2) WILD-TYPE  17 319
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 50(XP22.2) MUTATED      4  122
  DEL PEAK 50(XP22.2) WILD-TYPE   17  319
     clus
vv    DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE
  NO                            4                            17
  YES                         122                           319
[1] 2 2
[1] FALSE
D82V11, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 50(XP22.2) MUTATED    83   2   1   3
  DEL PEAK 50(XP22.2) WILD-TYPE 235   9   3  16
D82V12, multiclass
    clus
vv   DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE
  R0                          83                           235
  R1                           2                             9
  R2                           1                             3
  RX                           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                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 50(XP22.2) MUTATED                                  1     2
  DEL PEAK 50(XP22.2) WILD-TYPE                                0     4
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 50(XP22.2) MUTATED                           8    94
  DEL PEAK 50(XP22.2) WILD-TYPE                        18   268
D82V13, multiclass
                                  clus
vv                                 DEL PEAK 50(XP22.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                  8
  WHITE                                                     94
                                  clus
vv                                 DEL PEAK 50(XP22.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   18
  WHITE                                                      268
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V14, binary
                               cls
clus                              0   1
  DEL PEAK 50(XP22.2) MUTATED     1  88
  DEL PEAK 50(XP22.2) WILD-TYPE   6 244
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 50(XP22.2) MUTATED      1   88
  DEL PEAK 50(XP22.2) WILD-TYPE    6  244
                        clus
vv                       DEL PEAK 50(XP22.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          88
                        clus
vv                       DEL PEAK 50(XP22.2) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           244
[1] 2 2
[1] FALSE
