[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/11541582/LUAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LUAD-TP/11548107/transformed.cor.cli.txt"

nPatients in clinical file=483, in cluster file=515, common to both=476
[1]  74 476
[1] "AMP PEAK  1(1P34.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1P34.3) MUTATED AMP PEAK  1(1P34.3) WILD-TYPE 
                          131                           345 
  AMP PEAK  1(1P34.3) MUTATED AMP PEAK  1(1P34.3) WILD-TYPE 
                          131                           345 
[1] "AMP PEAK  2(1P22.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(1P22.3) MUTATED AMP PEAK  2(1P22.3) WILD-TYPE 
                          129                           347 
  AMP PEAK  2(1P22.3) MUTATED AMP PEAK  2(1P22.3) WILD-TYPE 
                          129                           347 
[1] "AMP PEAK  3(1Q21.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE 
                          344                           132 
  AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE 
                          344                           132 
[1] "AMP PEAK  4(3Q26.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE 
                          160                           316 
  AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE 
                          160                           316 
[1] "AMP PEAK  5(4Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                         93                         383 
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                         93                         383 
[1] "AMP PEAK  6(5P15.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                           312                            164 
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                           312                            164 
[1] "AMP PEAK  7(5P13.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(5P13.1) MUTATED AMP PEAK  7(5P13.1) WILD-TYPE 
                          287                           189 
  AMP PEAK  7(5P13.1) MUTATED AMP PEAK  7(5P13.1) WILD-TYPE 
                          287                           189 
[1] "AMP PEAK  8(6P21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(6P21.1) MUTATED AMP PEAK  8(6P21.1) WILD-TYPE 
                          178                           298 
  AMP PEAK  8(6P21.1) MUTATED AMP PEAK  8(6P21.1) WILD-TYPE 
                          178                           298 
[1] "AMP PEAK  9(7P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(7P11.2) MUTATED AMP PEAK  9(7P11.2) WILD-TYPE 
                          259                           217 
  AMP PEAK  9(7P11.2) MUTATED AMP PEAK  9(7P11.2) WILD-TYPE 
                          259                           217 
[1] "AMP PEAK 10(7Q31.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(7Q31.2) MUTATED AMP PEAK 10(7Q31.2) WILD-TYPE 
                          205                           271 
  AMP PEAK 10(7Q31.2) MUTATED AMP PEAK 10(7Q31.2) WILD-TYPE 
                          205                           271 
[1] "AMP PEAK 11(8P11.23) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(8P11.23) MUTATED AMP PEAK 11(8P11.23) WILD-TYPE 
                           127                            349 
  AMP PEAK 11(8P11.23) MUTATED AMP PEAK 11(8P11.23) WILD-TYPE 
                           127                            349 
[1] "AMP PEAK 12(8P11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE 
                           163                            313 
  AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE 
                           163                            313 
[1] "AMP PEAK 13(8Q11.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(8Q11.1) MUTATED AMP PEAK 13(8Q11.1) WILD-TYPE 
                          219                           257 
  AMP PEAK 13(8Q11.1) MUTATED AMP PEAK 13(8Q11.1) WILD-TYPE 
                          219                           257 
[1] "AMP PEAK 14(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(8Q24.21) MUTATED AMP PEAK 14(8Q24.21) WILD-TYPE 
                           303                            173 
  AMP PEAK 14(8Q24.21) MUTATED AMP PEAK 14(8Q24.21) WILD-TYPE 
                           303                            173 
[1] "AMP PEAK 15(10P15.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(10P15.1) MUTATED AMP PEAK 15(10P15.1) WILD-TYPE 
                           134                            342 
  AMP PEAK 15(10P15.1) MUTATED AMP PEAK 15(10P15.1) WILD-TYPE 
                           134                            342 
[1] "AMP PEAK 16(11Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(11Q13.3) MUTATED AMP PEAK 16(11Q13.3) WILD-TYPE 
                           165                            311 
  AMP PEAK 16(11Q13.3) MUTATED AMP PEAK 16(11Q13.3) WILD-TYPE 
                           165                            311 
[1] "AMP PEAK 17(12P12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(12P12.1) MUTATED AMP PEAK 17(12P12.1) WILD-TYPE 
                           171                            305 
  AMP PEAK 17(12P12.1) MUTATED AMP PEAK 17(12P12.1) WILD-TYPE 
                           171                            305 
[1] "AMP PEAK 18(12Q14.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(12Q14.1) MUTATED AMP PEAK 18(12Q14.1) WILD-TYPE 
                           159                            317 
  AMP PEAK 18(12Q14.1) MUTATED AMP PEAK 18(12Q14.1) WILD-TYPE 
                           159                            317 
[1] "AMP PEAK 19(12Q15) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(12Q15) MUTATED AMP PEAK 19(12Q15) WILD-TYPE 
                         162                          314 
  AMP PEAK 19(12Q15) MUTATED AMP PEAK 19(12Q15) WILD-TYPE 
                         162                          314 
[1] "AMP PEAK 20(13Q33.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(13Q33.3) MUTATED AMP PEAK 20(13Q33.3) WILD-TYPE 
                            76                            400 
  AMP PEAK 20(13Q33.3) MUTATED AMP PEAK 20(13Q33.3) WILD-TYPE 
                            76                            400 
[1] "AMP PEAK 21(14Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(14Q13.3) MUTATED AMP PEAK 21(14Q13.3) WILD-TYPE 
                           211                            265 
  AMP PEAK 21(14Q13.3) MUTATED AMP PEAK 21(14Q13.3) WILD-TYPE 
                           211                            265 
[1] "AMP PEAK 22(16P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(16P11.2) MUTATED AMP PEAK 22(16P11.2) WILD-TYPE 
                           153                            323 
  AMP PEAK 22(16P11.2) MUTATED AMP PEAK 22(16P11.2) WILD-TYPE 
                           153                            323 
[1] "AMP PEAK 23(17Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(17Q12) MUTATED AMP PEAK 23(17Q12) WILD-TYPE 
                         217                          259 
  AMP PEAK 23(17Q12) MUTATED AMP PEAK 23(17Q12) WILD-TYPE 
                         217                          259 
[1] "AMP PEAK 24(17Q23.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(17Q23.1) MUTATED AMP PEAK 24(17Q23.1) WILD-TYPE 
                           234                            242 
  AMP PEAK 24(17Q23.1) MUTATED AMP PEAK 24(17Q23.1) WILD-TYPE 
                           234                            242 
[1] "AMP PEAK 25(18Q11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 25(18Q11.2) MUTATED AMP PEAK 25(18Q11.2) WILD-TYPE 
                            98                            378 
  AMP PEAK 25(18Q11.2) MUTATED AMP PEAK 25(18Q11.2) WILD-TYPE 
                            98                            378 
[1] "AMP PEAK 26(19Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 26(19Q12) MUTATED AMP PEAK 26(19Q12) WILD-TYPE 
                         131                          345 
  AMP PEAK 26(19Q12) MUTATED AMP PEAK 26(19Q12) WILD-TYPE 
                         131                          345 
[1] "AMP PEAK 27(20Q13.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 27(20Q13.33) MUTATED AMP PEAK 27(20Q13.33) WILD-TYPE 
                            232                             244 
  AMP PEAK 27(20Q13.33) MUTATED AMP PEAK 27(20Q13.33) WILD-TYPE 
                            232                             244 
[1] "AMP PEAK 28(22Q11.22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 28(22Q11.22) MUTATED AMP PEAK 28(22Q11.22) WILD-TYPE 
                             87                             389 
  AMP PEAK 28(22Q11.22) MUTATED AMP PEAK 28(22Q11.22) WILD-TYPE 
                             87                             389 
[1] "AMP PEAK 29(XQ28) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE 
                        147                         329 
  AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE 
                        147                         329 
[1] "DEL PEAK  1(1P36.13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE 
                           111                            365 
  DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE 
                           111                            365 
[1] "DEL PEAK  2(1P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                          144                           332 
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                          144                           332 
[1] "DEL PEAK  3(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           44                           432 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           44                           432 
[1] "DEL PEAK  4(3P26.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(3P26.2) MUTATED DEL PEAK  4(3P26.2) WILD-TYPE 
                          214                           262 
  DEL PEAK  4(3P26.2) MUTATED DEL PEAK  4(3P26.2) WILD-TYPE 
                          214                           262 
[1] "DEL PEAK  5(3P21.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                           228                            248 
  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                           228                            248 
[1] "DEL PEAK  6(3Q11.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(3Q11.1) MUTATED DEL PEAK  6(3Q11.1) WILD-TYPE 
                          132                           344 
  DEL PEAK  6(3Q11.1) MUTATED DEL PEAK  6(3Q11.1) WILD-TYPE 
                          132                           344 
[1] "DEL PEAK  7(3Q29) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE 
                        128                         348 
  DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE 
                        128                         348 
[1] "DEL PEAK  8(4P16.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE 
                          119                           357 
  DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE 
                          119                           357 
[1] "DEL PEAK  9(4Q34.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE 
                          172                           304 
  DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE 
                          172                           304 
[1] "DEL PEAK 10(5Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE 
                          169                           307 
  DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE 
                          169                           307 
[1] "DEL PEAK 11(5Q31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(5Q31.1) MUTATED DEL PEAK 11(5Q31.1) WILD-TYPE 
                          198                           278 
  DEL PEAK 11(5Q31.1) MUTATED DEL PEAK 11(5Q31.1) WILD-TYPE 
                          198                           278 
[1] "DEL PEAK 12(6Q11.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(6Q11.1) MUTATED DEL PEAK 12(6Q11.1) WILD-TYPE 
                          131                           345 
  DEL PEAK 12(6Q11.1) MUTATED DEL PEAK 12(6Q11.1) WILD-TYPE 
                          131                           345 
[1] "DEL PEAK 13(6Q22.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(6Q22.31) MUTATED DEL PEAK 13(6Q22.31) WILD-TYPE 
                           237                            239 
  DEL PEAK 13(6Q22.31) MUTATED DEL PEAK 13(6Q22.31) WILD-TYPE 
                           237                            239 
[1] "DEL PEAK 14(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE 
                        239                         237 
  DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE 
                        239                         237 
[1] "DEL PEAK 15(8P23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE 
                          236                           240 
  DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE 
                          236                           240 
[1] "DEL PEAK 16(8P11.21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE 
                           118                            358 
  DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE 
                           118                            358 
[1] "DEL PEAK 17(9P23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(9P23) MUTATED DEL PEAK 17(9P23) WILD-TYPE 
                        262                         214 
  DEL PEAK 17(9P23) MUTATED DEL PEAK 17(9P23) WILD-TYPE 
                        262                         214 
[1] "DEL PEAK 18(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE 
                          270                           206 
  DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE 
                          270                           206 
[1] "DEL PEAK 19(9Q21.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(9Q21.11) MUTATED DEL PEAK 19(9Q21.11) WILD-TYPE 
                           239                            237 
  DEL PEAK 19(9Q21.11) MUTATED DEL PEAK 19(9Q21.11) WILD-TYPE 
                           239                            237 
[1] "DEL PEAK 20(10P15.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(10P15.3) MUTATED DEL PEAK 20(10P15.3) WILD-TYPE 
                           117                            359 
  DEL PEAK 20(10P15.3) MUTATED DEL PEAK 20(10P15.3) WILD-TYPE 
                           117                            359 
[1] "DEL PEAK 21(10Q26.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(10Q26.3) MUTATED DEL PEAK 21(10Q26.3) WILD-TYPE 
                           140                            336 
  DEL PEAK 21(10Q26.3) MUTATED DEL PEAK 21(10Q26.3) WILD-TYPE 
                           140                            336 
[1] "DEL PEAK 22(11P15.5) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(11P15.5) MUTATED DEL PEAK 22(11P15.5) WILD-TYPE 
                           134                            342 
  DEL PEAK 22(11P15.5) MUTATED DEL PEAK 22(11P15.5) WILD-TYPE 
                           134                            342 
[1] "DEL PEAK 23(11Q23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(11Q23.2) MUTATED DEL PEAK 23(11Q23.2) WILD-TYPE 
                           111                            365 
  DEL PEAK 23(11Q23.2) MUTATED DEL PEAK 23(11Q23.2) WILD-TYPE 
                           111                            365 
[1] "DEL PEAK 24(11Q25) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(11Q25) MUTATED DEL PEAK 24(11Q25) WILD-TYPE 
                         107                          369 
  DEL PEAK 24(11Q25) MUTATED DEL PEAK 24(11Q25) WILD-TYPE 
                         107                          369 
[1] "DEL PEAK 25(12P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(12P13.2) MUTATED DEL PEAK 25(12P13.2) WILD-TYPE 
                           126                            350 
  DEL PEAK 25(12P13.2) MUTATED DEL PEAK 25(12P13.2) WILD-TYPE 
                           126                            350 
[1] "DEL PEAK 26(12Q12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(12Q12) MUTATED DEL PEAK 26(12Q12) WILD-TYPE 
                          91                          385 
  DEL PEAK 26(12Q12) MUTATED DEL PEAK 26(12Q12) WILD-TYPE 
                          91                          385 
[1] "DEL PEAK 27(12Q24.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(12Q24.33) MUTATED DEL PEAK 27(12Q24.33) WILD-TYPE 
                            120                             356 
  DEL PEAK 27(12Q24.33) MUTATED DEL PEAK 27(12Q24.33) WILD-TYPE 
                            120                             356 
[1] "DEL PEAK 28(13Q12.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(13Q12.11) MUTATED DEL PEAK 28(13Q12.11) WILD-TYPE 
                            271                             205 
  DEL PEAK 28(13Q12.11) MUTATED DEL PEAK 28(13Q12.11) WILD-TYPE 
                            271                             205 
[1] "DEL PEAK 29(13Q12.13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(13Q12.13) MUTATED DEL PEAK 29(13Q12.13) WILD-TYPE 
                            269                             207 
  DEL PEAK 29(13Q12.13) MUTATED DEL PEAK 29(13Q12.13) WILD-TYPE 
                            269                             207 
[1] "DEL PEAK 30(13Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(13Q14.2) MUTATED DEL PEAK 30(13Q14.2) WILD-TYPE 
                           259                            217 
  DEL PEAK 30(13Q14.2) MUTATED DEL PEAK 30(13Q14.2) WILD-TYPE 
                           259                            217 
[1] "DEL PEAK 31(13Q34) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(13Q34) MUTATED DEL PEAK 31(13Q34) WILD-TYPE 
                         221                          255 
  DEL PEAK 31(13Q34) MUTATED DEL PEAK 31(13Q34) WILD-TYPE 
                         221                          255 
[1] "DEL PEAK 32(14Q32.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(14Q32.33) MUTATED DEL PEAK 32(14Q32.33) WILD-TYPE 
                            142                             334 
  DEL PEAK 32(14Q32.33) MUTATED DEL PEAK 32(14Q32.33) WILD-TYPE 
                            142                             334 
[1] "DEL PEAK 33(15Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(15Q11.2) MUTATED DEL PEAK 33(15Q11.2) WILD-TYPE 
                           246                            230 
  DEL PEAK 33(15Q11.2) MUTATED DEL PEAK 33(15Q11.2) WILD-TYPE 
                           246                            230 
[1] "DEL PEAK 34(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(16Q23.1) MUTATED DEL PEAK 34(16Q23.1) WILD-TYPE 
                           159                            317 
  DEL PEAK 34(16Q23.1) MUTATED DEL PEAK 34(16Q23.1) WILD-TYPE 
                           159                            317 
[1] "DEL PEAK 35(17P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 35(17P13.3) MUTATED DEL PEAK 35(17P13.3) WILD-TYPE 
                           259                            217 
  DEL PEAK 35(17P13.3) MUTATED DEL PEAK 35(17P13.3) WILD-TYPE 
                           259                            217 
[1] "DEL PEAK 36(18Q21.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 36(18Q21.32) MUTATED DEL PEAK 36(18Q21.32) WILD-TYPE 
                            235                             241 
  DEL PEAK 36(18Q21.32) MUTATED DEL PEAK 36(18Q21.32) WILD-TYPE 
                            235                             241 
[1] "DEL PEAK 37(18Q23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 37(18Q23) MUTATED DEL PEAK 37(18Q23) WILD-TYPE 
                         231                          245 
  DEL PEAK 37(18Q23) MUTATED DEL PEAK 37(18Q23) WILD-TYPE 
                         231                          245 
[1] "DEL PEAK 38(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 38(19P13.3) MUTATED DEL PEAK 38(19P13.3) WILD-TYPE 
                           256                            220 
  DEL PEAK 38(19P13.3) MUTATED DEL PEAK 38(19P13.3) WILD-TYPE 
                           256                            220 
[1] "DEL PEAK 39(19P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 39(19P13.2) MUTATED DEL PEAK 39(19P13.2) WILD-TYPE 
                           248                            228 
  DEL PEAK 39(19P13.2) MUTATED DEL PEAK 39(19P13.2) WILD-TYPE 
                           248                            228 
[1] "DEL PEAK 40(19Q13.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 40(19Q13.33) MUTATED DEL PEAK 40(19Q13.33) WILD-TYPE 
                            179                             297 
  DEL PEAK 40(19Q13.33) MUTATED DEL PEAK 40(19Q13.33) WILD-TYPE 
                            179                             297 
[1] "DEL PEAK 41(20P13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 41(20P13) MUTATED DEL PEAK 41(20P13) WILD-TYPE 
                         124                          352 
  DEL PEAK 41(20P13) MUTATED DEL PEAK 41(20P13) WILD-TYPE 
                         124                          352 
[1] "DEL PEAK 42(20Q13.12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 42(20Q13.12) MUTATED DEL PEAK 42(20Q13.12) WILD-TYPE 
                             79                             397 
  DEL PEAK 42(20Q13.12) MUTATED DEL PEAK 42(20Q13.12) WILD-TYPE 
                             79                             397 
[1] "DEL PEAK 43(21Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 43(21Q11.2) MUTATED DEL PEAK 43(21Q11.2) WILD-TYPE 
                           164                            312 
  DEL PEAK 43(21Q11.2) MUTATED DEL PEAK 43(21Q11.2) WILD-TYPE 
                           164                            312 
[1] "DEL PEAK 44(22Q13.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE 
                            232                             244 
  DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE 
                            232                             244 
[1] "DEL PEAK 45(XP22.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 45(XP22.2) MUTATED DEL PEAK 45(XP22.2) WILD-TYPE 
                          134                           342 
  DEL PEAK 45(XP22.2) MUTATED DEL PEAK 45(XP22.2) WILD-TYPE 
                          134                           342 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDISEASE"                  
 [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 476 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-49-AARQ TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
        6443           NA         2174         2146          455          785 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
         944         1499          246          282          267         1091 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
        2370          653           NA           NA          567          883 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
         764          686           NA           NA           NA           NA 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8460 
          NA           NA         1015           NA          255          105 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 
          NA           NA          424          280          701         1178 
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-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
          NA         1239           NA           25         1475           NA 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
          NA           NA           67           NA           NA         1826 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 
          NA         1233         2151         1170           18           35 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
         121            6            4           95           40          705 
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-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
          16          197           21            3           31            5 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
          33          462          100            6          600           26 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8204 TCGA-55-8205 TCGA-55-8206 
           4           47           15           NA           33           46 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
          66          674          216           44           23           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-55-8513 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 
          NA            1           28            5           47          162 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
          NA         1216         1289           NA         2696         1445 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
          NA           NA           NA           NA         2067         2199 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
          NA           NA         1246          910         1728          628 
TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
        1189         1686         1126           NA         2676           62 
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-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 
         573          427          385           NA          174          141 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
         422          202          186          690          414          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-73-4662 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-73-A9RS TCGA-75-5122 TCGA-75-5125 
          38          621          519          305           NA           NA 
TCGA-75-5126 TCGA-75-5146 TCGA-75-5147 TCGA-75-6203 TCGA-75-6205 TCGA-75-6206 
          NA           NA           NA           NA           NA           NA 
TCGA-75-6207 TCGA-75-6211 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 
          NA           NA           NA           NA           NA           NA 
TCGA-75-7030 TCGA-75-7031 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
          NA           NA           NA           NA           NA           NA 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
          NA         1093           NA         1202          760           NA 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
          NA           NA           NA         1221          678          215 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
          NA         6812           NA           NA           NA           NA 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
          NA           NA          327          881           NA          994 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 
        6346           NA         2360           NA           NA           NA 
TCGA-80-5608 TCGA-80-5611 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
          NA           NA          824           NA           NA           11 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
         630          422           NA          591           NA          508 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
         745           10           NA           13           24          479 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8281 TCGA-86-8358 
         489          476          482           16           NA           19 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
          26           35           45           34           18           15 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 
         455          405           10           30           NA           14 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
          39          323           NA           60          310           79 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
         417          372          842          224           35          492 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
         505          174           36           44          218          297 
TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
         127          186           34            2           NA          568 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
         377          477          476          830           84          121 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
         553          605          964         1965         1932         1332 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
         775          181           NA           22          107          182 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
          NA           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-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A5IP 
         578          435          116            6          266           NA 
TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
         312          111          102          827         1175           84 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
          NA           NA           NA           NA           NA           NA 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
          NA           NA           NA           NA           NA           NA 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK 
          NA           NA          142           NA           NA           NA 
TCGA-MP-A5C7 TCGA-S2-AA1A 
        1490          121 
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=123,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=291,	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=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=23,	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=93,	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=26,	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 476 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 
147 267  42  18 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
147 267  42  18 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
147 267  42  18 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
147 267  42  18 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
301  91  72   2 
[1] "table(vv)"
vv
   N0    N1 N2+N3 
  301    91    74 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
 N0  N1  N2  N3 
301  91  72   2 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   N0    N1 N2+N3 
  301    91    74 
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=93, 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    88  28
  AMP PEAK  1(1P34.3) WILD-TYPE 241  59
  AMP PEAK  1(1P34.3) MUTATED AMP PEAK  1(1P34.3) WILD-TYPE 
                          116                           300 
  AMP PEAK  1(1P34.3) MUTATED AMP PEAK  1(1P34.3) WILD-TYPE 
                           28                            59 
$`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-49-AARQ 
         428          896          157          445          890         6443 
TCGA-50-5045 TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 TCGA-50-5941 TCGA-50-5944 
        2174         1499          246          267          567          764 
TCGA-50-5946 TCGA-50-6597 TCGA-53-7624 TCGA-55-1592 TCGA-55-6712 TCGA-55-6969 
         686         1015         1986          701           24         1239 
TCGA-55-6972 TCGA-55-6980 TCGA-55-6987 TCGA-55-7281 TCGA-55-7573 TCGA-55-7576 
        1475           67         1170           18            4           40 
TCGA-55-8091 TCGA-55-8096 TCGA-55-8206 TCGA-55-8507 TCGA-55-8508 TCGA-55-8514 
         600           47           46            8           15          202 
TCGA-55-A48X TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8399 TCGA-62-A46V TCGA-64-1676 
          33           47          162         2696         2199         1728 
TCGA-64-1681 TCGA-64-5779 TCGA-64-5781 TCGA-67-3770 TCGA-67-3772 TCGA-67-6217 
        1968          864         1559           31          573          422 
TCGA-69-7760 TCGA-69-7980 TCGA-69-8254 TCGA-69-A59K TCGA-71-6725 TCGA-73-4676 
         202          382           77          214           61          164 
TCGA-75-7025 TCGA-78-7145 TCGA-78-7147 TCGA-78-7149 TCGA-78-7155 TCGA-78-7161 
        1967         1973         1950         1093         1957          215 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7535 TCGA-78-7542 TCGA-78-8655 
        1940         1950         1937         1972         1952         1981 
TCGA-78-8662 TCGA-86-7713 TCGA-86-7953 TCGA-86-8055 TCGA-86-8074 TCGA-86-8075 
        1964          422          591           10           24          479 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8668 TCGA-86-A456 TCGA-86-A4P7 
         482           16           19           45           10           14 
TCGA-91-6831 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-7771 TCGA-91-8496 
         310          372          842          224          492          505 
TCGA-95-7039 TCGA-95-7562 TCGA-95-7944 TCGA-97-7546 TCGA-97-7553 TCGA-97-7937 
          34         1973          377          964         1332          181 
TCGA-97-8177 TCGA-97-8552 TCGA-99-7458 TCGA-J2-8192 TCGA-J2-A4AG TCGA-L9-A7SV 
         147          115          392          154          238          111 
TCGA-MN-A4N1 TCGA-MP-A4SW 
         827         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 
         705           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          462          100            6           26 
TCGA-55-8094 TCGA-55-8097 TCGA-55-8205 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
           4           15           33           66          674          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-55-8615 TCGA-55-8616 TCGA-55-8619 
           3          146          536           15           48           49 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
          66          106           42           29           48         1952 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
           1           28            5         1216         1289         1970 
TCGA-62-8402 TCGA-62-A46U TCGA-62-A471 TCGA-62-A472 TCGA-64-1677 TCGA-64-1678 
        1445         2067         1246          910          628         1189 
TCGA-64-1679 TCGA-64-1680 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5815 
        1686         1126         1959           62         1305          866 
TCGA-67-3771 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-69-7761 
         610          427          385          174          141          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-69-7979 TCGA-69-8253 TCGA-69-8255 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
          89          100          129         1600          711          912 
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-73-A9RS TCGA-75-6214 TCGA-75-7027 TCGA-75-7031 TCGA-78-7146 
         519          305         1970         1956         1965         1988 
TCGA-78-7148 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 
        1944         1963         1202          760         1948         1961 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7166 TCGA-78-7220 TCGA-78-7536 
        1963         1221          678         1934         1965         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-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8056 
         630         1968         1963          508          745         1963 
TCGA-86-8073 TCGA-86-8076 TCGA-86-8278 TCGA-86-8281 TCGA-86-8359 TCGA-86-8585 
          13          489          476         1955           26           35 
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-91-6836 
          39          323         1940           60           79          417 
TCGA-91-6849 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
          35          174           36           44          218          297 
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-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7547 
         830           84          121          553          605         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-L9-A50W TCGA-L9-A743 
         578          435          116            6          266          312 
TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4T2 TCGA-MP-A4T4 
         102         1175           84         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 TCGA-S2-AA1A 
        1970          142         1955         1971         1490          121 

  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 
                         6443                          2370 
  AMP PEAK  1(1P34.3) MUTATED AMP PEAK  1(1P34.3) WILD-TYPE 
                          536                           458 
[1] "4.0 - 6443.0 (536.0)" "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         3       29       40        17        19
  AMP PEAK  1(1P34.3) WILD-TYPE       2       87       92        32        51
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK  1(1P34.3) MUTATED           13          3        6
  AMP PEAK  1(1P34.3) WILD-TYPE         55          8       18
D1V3, multiclass
            clus
vv           AMP PEAK  1(1P34.3) MUTATED AMP PEAK  1(1P34.3) WILD-TYPE
  STAGE I                              3                             2
  STAGE IA                            29                            87
  STAGE IB                            40                            92
  STAGE IIA                           17                            32
  STAGE IIB                           19                            51
  STAGE IIIA                          13                            55
  STAGE IIIB                           3                             8
  STAGE IV                             6                            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  81   9   5
  AMP PEAK  1(1P34.3) WILD-TYPE 111 186  33  13
D1V4, multiclass
    clus
vv   AMP PEAK  1(1P34.3) MUTATED AMP PEAK  1(1P34.3) WILD-TYPE
  T1                          36                           111
  T2                          81                           186
  T3                           9                            33
  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    81  31    14
  AMP PEAK  1(1P34.3) WILD-TYPE 220  60    60
D1V5, multiclass
       clus
vv      AMP PEAK  1(1P34.3) MUTATED AMP PEAK  1(1P34.3) WILD-TYPE
  N0                             81                           220
  N1                             31                            60
  N2+N3                          14                            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  1(1P34.3) MUTATED    87   5   0   1  34
  AMP PEAK  1(1P34.3) WILD-TYPE 239  13   1   3  89
D1V6, multiclass
     clus
vv    AMP PEAK  1(1P34.3) MUTATED AMP PEAK  1(1P34.3) WILD-TYPE
  M0                           87                           239
  M1                            5                            13
  M1A                           0                             1
  M1B                           1                             3
  MX                           34                            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"
D1V7, binary
                               cls
clus                              0   1
  AMP PEAK  1(1P34.3) MUTATED    75  56
  AMP PEAK  1(1P34.3) WILD-TYPE 180 165
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P34.3) MUTATED     75   56
  AMP PEAK  1(1P34.3) WILD-TYPE  180  165
        clus
vv       AMP PEAK  1(1P34.3) MUTATED AMP PEAK  1(1P34.3) WILD-TYPE
  FEMALE                          75                           180
  MALE                            56                           165
[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                         11
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK  1(1P34.3) MUTATED                                  18
  AMP PEAK  1(1P34.3) WILD-TYPE                                76
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  1(1P34.3) MUTATED                                                   92
  AMP PEAK  1(1P34.3) WILD-TYPE                                                211
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK  1(1P34.3) MUTATED                                            1
  AMP PEAK  1(1P34.3) WILD-TYPE                                          4
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK  1(1P34.3) MUTATED                                               6
  AMP PEAK  1(1P34.3) WILD-TYPE                                            13
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK  1(1P34.3) MUTATED                                0
  AMP PEAK  1(1P34.3) WILD-TYPE                              2
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK  1(1P34.3) MUTATED                                    1
  AMP PEAK  1(1P34.3) WILD-TYPE                                  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                                             4
                               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)                          92
  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                                                    11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             76
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           211
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     4
  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                                  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"
D1V10, binary
                               cls
clus                              0   1
  AMP PEAK  1(1P34.3) MUTATED     4 127
  AMP PEAK  1(1P34.3) WILD-TYPE  17 328
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P34.3) MUTATED      4  127
  AMP PEAK  1(1P34.3) WILD-TYPE   17  328
     clus
vv    AMP PEAK  1(1P34.3) MUTATED AMP PEAK  1(1P34.3) WILD-TYPE
  NO                            4                            17
  YES                         127                           328
[1] 2 2
[1] FALSE
D1V11, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  1(1P34.3) MUTATED    80   6   1   5
  AMP PEAK  1(1P34.3) WILD-TYPE 247   6   3  16
D1V12, multiclass
    clus
vv   AMP PEAK  1(1P34.3) MUTATED AMP PEAK  1(1P34.3) WILD-TYPE
  R0                          80                           247
  R1                           6                             6
  R2                           1                             3
  RX                           5                            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  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                          14   102
  AMP PEAK  1(1P34.3) WILD-TYPE                        21   265
D1V13, multiclass
                                  clus
vv                                 AMP PEAK  1(1P34.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 14
  WHITE                                                    102
                                  clus
vv                                 AMP PEAK  1(1P34.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   21
  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"
D1V14, binary
                               cls
clus                              0   1
  AMP PEAK  1(1P34.3) MUTATED     2  93
  AMP PEAK  1(1P34.3) WILD-TYPE   5 252
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P34.3) MUTATED      2   93
  AMP PEAK  1(1P34.3) WILD-TYPE    5  252
                        clus
vv                       AMP PEAK  1(1P34.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          93
                        clus
vv                       AMP PEAK  1(1P34.3) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           252
[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    86  30
  AMP PEAK  2(1P22.3) WILD-TYPE 243  57
  AMP PEAK  2(1P22.3) MUTATED AMP PEAK  2(1P22.3) WILD-TYPE 
                          116                           300 
  AMP PEAK  2(1P22.3) MUTATED AMP PEAK  2(1P22.3) WILD-TYPE 
                           30                            57 
$`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-49-AARQ 
         428          268          157          445          890         6443 
TCGA-50-5045 TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 TCGA-50-5935 TCGA-50-5941 
        2174         1499          246          267          653          567 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6597 TCGA-55-1592 TCGA-55-6712 TCGA-55-6969 
         764          686         1015          701           24         1239 
TCGA-55-6980 TCGA-55-7281 TCGA-55-7283 TCGA-55-7573 TCGA-55-7576 TCGA-55-7910 
          67           18           35            4           40          197 
TCGA-55-8089 TCGA-55-8094 TCGA-55-8096 TCGA-55-8206 TCGA-55-8507 TCGA-55-8514 
         100            4           47           46            8          202 
TCGA-55-A48X TCGA-55-A48Z TCGA-55-A4DG TCGA-62-8399 TCGA-64-1676 TCGA-64-1679 
          33           29          162         2696         1728         1686 
TCGA-64-1681 TCGA-64-5775 TCGA-64-5781 TCGA-67-6215 TCGA-67-6217 TCGA-69-7979 
        1968           62         1559          174          422           89 
TCGA-69-8254 TCGA-69-A59K TCGA-73-4662 TCGA-73-4668 TCGA-73-4676 TCGA-73-7498 
          77          214          912          467          164          621 
TCGA-78-7145 TCGA-78-7147 TCGA-78-7149 TCGA-78-7155 TCGA-78-7158 TCGA-78-7161 
        1973         1950         1093         1957         1963          215 
TCGA-78-7162 TCGA-78-7167 TCGA-78-7535 TCGA-78-7542 TCGA-78-8640 TCGA-78-8655 
        1940         1937         1972         1952         1949         1981 
TCGA-86-7953 TCGA-86-8054 TCGA-86-8055 TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 
         591          745           10           24          479          482 
TCGA-86-8280 TCGA-86-8585 TCGA-86-A456 TCGA-86-A4P7 TCGA-91-6831 TCGA-91-6836 
          16           35           10           14          310          417 
TCGA-91-6840 TCGA-91-6847 TCGA-91-8499 TCGA-93-8067 TCGA-95-7562 TCGA-95-7944 
         372          842           36          186         1973          377 
TCGA-97-7546 TCGA-97-7553 TCGA-97-7937 TCGA-99-7458 TCGA-J2-8192 TCGA-J2-A4AG 
         964         1332          181          392          154          238 
TCGA-L9-A743 TCGA-L9-A7SV TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-MP-A4TE 
         312          111          827         1957         1944         1970 
TCGA-MP-A4TF TCGA-MP-A5C7 
        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          705           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          462            6          600           26 
TCGA-55-8097 TCGA-55-8205 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
          15           33           66          674          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-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
           3          146          536           15           48           49 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48Y TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
          66          106           42           48         1952            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-62-8402 TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 TCGA-64-1677 
        1445         2067         2199         1246          910          628 
TCGA-64-1678 TCGA-64-1680 TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 
        1189         1126         1959         1305          864          866 
TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6216 
          31          610          573          427          385          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-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8255 TCGA-71-6725 
         184           70          382          100          129           61 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4666 TCGA-73-4670 TCGA-73-4675 TCGA-73-4677 
        1600          711          800          131           40           38 
TCGA-73-7499 TCGA-73-A9RS TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 
         519          305         1970         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-78-7159 TCGA-78-7160 TCGA-78-7163 TCGA-78-7166 TCGA-78-7220 
        1961         1221          678         1950         1934         1965 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7633 TCGA-78-8648 
        1949         1944          327          881          994         1971 
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-86-7954 TCGA-86-7955 
          11          630          422         1968         1963          508 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8076 TCGA-86-8278 TCGA-86-8281 TCGA-86-8358 
        1963           13          489          476         1955           19 
TCGA-86-8359 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
          26           45           34           18           15          455 
TCGA-86-8674 TCGA-86-A4D0 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
         405           30           39          323         1940           60 
TCGA-91-6835 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
          79          224           35          492          505          174 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-95-7039 TCGA-95-7043 
          44          218          297          127           34            2 
TCGA-95-7567 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
         568          477          476          830           84          121 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7547 TCGA-97-7552 TCGA-97-7554 TCGA-97-7941 
         553          605         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-L9-A50W TCGA-L9-A8F4 TCGA-MN-A4N4 
         435          116            6          266          102         1175 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 
          84         1946         1967         1951         1954         1954 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-S2-AA1A 
        1980         1951          142         1955         1971          121 

  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 
                         6443                          2370 
  AMP PEAK  2(1P22.3) MUTATED AMP PEAK  2(1P22.3) WILD-TYPE 
                          473                           476 
[1] "4.0 - 6443.0 (473.0)" "1.0 - 2370.0 (476.0)"
[1] "hr=" "1.1"
D2V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK  2(1P22.3) MUTATED         1       31       34        20        17
  AMP PEAK  2(1P22.3) WILD-TYPE       4       85       98        29        53
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK  2(1P22.3) MUTATED           16          4        5
  AMP PEAK  2(1P22.3) WILD-TYPE         52          7       19
D2V3, multiclass
            clus
vv           AMP PEAK  2(1P22.3) MUTATED AMP PEAK  2(1P22.3) WILD-TYPE
  STAGE I                              1                             4
  STAGE IA                            31                            85
  STAGE IB                            34                            98
  STAGE IIA                           20                            29
  STAGE IIB                           17                            53
  STAGE IIIA                          16                            52
  STAGE IIIB                           4                             7
  STAGE IV                             5                            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  2(1P22.3) MUTATED    40  75   8   6
  AMP PEAK  2(1P22.3) WILD-TYPE 107 192  34  12
D2V4, multiclass
    clus
vv   AMP PEAK  2(1P22.3) MUTATED AMP PEAK  2(1P22.3) WILD-TYPE
  T1                          40                           107
  T2                          75                           192
  T3                           8                            34
  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    78  33    16
  AMP PEAK  2(1P22.3) WILD-TYPE 223  58    58
D2V5, multiclass
       clus
vv      AMP PEAK  2(1P22.3) MUTATED AMP PEAK  2(1P22.3) WILD-TYPE
  N0                             78                           223
  N1                             33                            58
  N2+N3                          16                            58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B  MX
  AMP PEAK  2(1P22.3) MUTATED    91   4   0   1  32
  AMP PEAK  2(1P22.3) WILD-TYPE 235  14   1   3  91
D2V6, multiclass
     clus
vv    AMP PEAK  2(1P22.3) MUTATED AMP PEAK  2(1P22.3) WILD-TYPE
  M0                           91                           235
  M1                            4                            14
  M1A                           0                             1
  M1B                           1                             3
  MX                           32                            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"
D2V7, binary
                               cls
clus                              0   1
  AMP PEAK  2(1P22.3) MUTATED    69  60
  AMP PEAK  2(1P22.3) WILD-TYPE 186 161
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1P22.3) MUTATED     69   60
  AMP PEAK  2(1P22.3) WILD-TYPE  186  161
        clus
vv       AMP PEAK  2(1P22.3) MUTATED AMP PEAK  2(1P22.3) WILD-TYPE
  FEMALE                          69                           186
  MALE                            60                           161
[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                         11
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK  2(1P22.3) MUTATED                                  22
  AMP PEAK  2(1P22.3) WILD-TYPE                                72
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  2(1P22.3) MUTATED                                                   88
  AMP PEAK  2(1P22.3) WILD-TYPE                                                215
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK  2(1P22.3) MUTATED                                            0
  AMP PEAK  2(1P22.3) WILD-TYPE                                          5
                               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                                             3
                               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)                          88
  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                                                    11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             72
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           215
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 12
  LUNG CLEAR CELL ADENOCARCINOMA                                                 2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             2
  LUNG MUCINOUS ADENOCARCINOMA                                                   2
  LUNG PAPILLARY ADENOCARCINOMA                                                 16
  LUNG SIGNET RING ADENOCARCINOMA                                                1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                  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"
D2V10, binary
                               cls
clus                              0   1
  AMP PEAK  2(1P22.3) MUTATED     5 124
  AMP PEAK  2(1P22.3) WILD-TYPE  16 331
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1P22.3) MUTATED      5  124
  AMP PEAK  2(1P22.3) WILD-TYPE   16  331
     clus
vv    AMP PEAK  2(1P22.3) MUTATED AMP PEAK  2(1P22.3) WILD-TYPE
  NO                            5                            16
  YES                         124                           331
[1] 2 2
[1] FALSE
D2V11, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  2(1P22.3) MUTATED    87   5   1   5
  AMP PEAK  2(1P22.3) WILD-TYPE 240   7   3  16
D2V12, multiclass
    clus
vv   AMP PEAK  2(1P22.3) MUTATED AMP PEAK  2(1P22.3) WILD-TYPE
  R0                          87                           240
  R1                           5                             7
  R2                           1                             3
  RX                           5                            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  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                          13    97
  AMP PEAK  2(1P22.3) WILD-TYPE                        22   270
D2V13, multiclass
                                  clus
vv                                 AMP PEAK  2(1P22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 13
  WHITE                                                     97
                                  clus
vv                                 AMP PEAK  2(1P22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   22
  WHITE                                                      270
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V14, binary
                               cls
clus                              0   1
  AMP PEAK  2(1P22.3) MUTATED     1  88
  AMP PEAK  2(1P22.3) WILD-TYPE   6 257
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1P22.3) MUTATED      1   88
  AMP PEAK  2(1P22.3) WILD-TYPE    6  257
                        clus
vv                       AMP PEAK  2(1P22.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          88
                        clus
vv                       AMP PEAK  2(1P22.3) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           257
[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   239  67
  AMP PEAK  3(1Q21.3) WILD-TYPE  90  20
  AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE 
                          306                           110 
  AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE 
                           67                            20 
$`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-49-AARQ TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
         890          354         6443         2174         2146          455 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
         944         1499          246          282          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-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
         255          105         1986         1971          424          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-55-6987 TCGA-55-7281 
          25         1475           67         1826         1170           18 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7725 
          35          121            4           95           40           39 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7914 TCGA-55-7995 
          54           19           16          197            3            5 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
          33          462          100           26            4           47 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8301 TCGA-55-8507 TCGA-55-8508 
          46           66          674           44            8           15 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8514 TCGA-55-8615 TCGA-55-8616 TCGA-55-A48X 
         228            9          202           15           48           33 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A492 TCGA-55-A494 TCGA-55-A4DF 
          42           29           48            1            5           47 
TCGA-55-A4DG TCGA-62-8398 TCGA-62-8399 TCGA-62-A46U TCGA-62-A46V TCGA-64-1676 
         162         1970         2696         2067         2199         1728 
TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 
        1686         1126         1968         1959         1305          864 
TCGA-64-5781 TCGA-67-3771 TCGA-67-3772 TCGA-67-3774 TCGA-67-6215 TCGA-67-6217 
        1559          610          573          385          174          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-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-A59K TCGA-71-6725 
          89          382          100           77          214           61 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
        1600          711          912          800          467          131 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS 
          40          164           38          621          519          305 
TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
        1967         1956         1965         1988         1950         1944 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 
        1093         1963         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-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        1934         1937         1965         1972         1949         1944 
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-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 
        1959           11          630          422          591         1963 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 TCGA-86-8075 
         508          745           10         1963           24          479 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8281 TCGA-86-8358 
         489          476          482           16         1955           19 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8669 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
          26           35           34           15          455          405 
TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-91-6828 TCGA-91-6829 TCGA-91-6831 
          10           30           14          323         1940          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-93-7348 TCGA-93-8067 TCGA-95-7039 
         505          174           36          127          186           34 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-8039 
           2         1973          568          377          477          830 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
          84          121          553          605          964         1965 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        1332          775          181          107          182         1965 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
          15          148          115          271          392          427 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L4-A4E5 
          44          170          114          287          238          578 
TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 TCGA-L9-A7SV TCGA-MN-A4N1 TCGA-MN-A4N4 
         116            6          312          111          827         1175 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4TC 
          84         1946         1967         1954         1957         1944 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-S2-AA1A 
        1970         1970          142         1971         1490          121 

$`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          705           39           34           24           21 
TCGA-55-7994 TCGA-55-8090 TCGA-55-8091 TCGA-55-8097 TCGA-55-8205 TCGA-55-8299 
          31            6          600           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-L9-A50W TCGA-L9-A8F4 TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T9 
         435          266          102         1951         1954         1980 
TCGA-MP-A4TA TCGA-MP-A4TI 
        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 
                         6443                          2151 
  AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE 
                        480.5                         431.0 
[1] "1.0 - 6443.0 (480.5)" "2.0 - 2151.0 (431.0)"
[1] "hr=" "1.1"
D3V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK  3(1Q21.3) MUTATED         5       84       95        37        46
  AMP PEAK  3(1Q21.3) WILD-TYPE       0       32       37        12        24
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK  3(1Q21.3) MUTATED           47         11       18
  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                              5                             0
  STAGE IA                            84                            32
  STAGE IB                            95                            37
  STAGE IIA                           37                            12
  STAGE IIB                           46                            24
  STAGE IIIA                          47                            21
  STAGE IIIB                          11                             0
  STAGE IV                            18                             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   102 196  29  15
  AMP PEAK  3(1Q21.3) WILD-TYPE  45  71  13   3
D3V4, multiclass
    clus
vv   AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE
  T1                         102                            45
  T2                         196                            71
  T3                          29                            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   214  67    54
  AMP PEAK  3(1Q21.3) WILD-TYPE  87  24    20
D3V5, multiclass
       clus
vv      AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE
  N0                            214                            87
  N1                             67                            24
  N2+N3                          54                            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   239  14   1   2  84
  AMP PEAK  3(1Q21.3) WILD-TYPE  87   4   0   2  39
D3V6, multiclass
     clus
vv    AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE
  M0                          239                            87
  M1                           14                             4
  M1A                           1                             0
  M1B                           2                             2
  MX                           84                            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"
D3V7, binary
                               cls
clus                              0   1
  AMP PEAK  3(1Q21.3) MUTATED   176 168
  AMP PEAK  3(1Q21.3) WILD-TYPE  79  53
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q21.3) MUTATED    176  168
  AMP PEAK  3(1Q21.3) WILD-TYPE   79   53
        clus
vv       AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE
  FEMALE                         176                            79
  MALE                           168                            53
[1] 2 2
[1] FALSE
D3V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  AMP PEAK  3(1Q21.3) MUTATED                           14
  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                                24
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  3(1Q21.3) MUTATED                                                  215
  AMP PEAK  3(1Q21.3) WILD-TYPE                                                 88
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK  3(1Q21.3) MUTATED                                            1
  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                                               3
  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                                                  14
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           70
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         215
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                   1
  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                                3
  MUCINOUS (COLLOID) CARCINOMA                                                 4
                                                    clus
vv                                                   AMP PEAK  3(1Q21.3) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             24
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            88
  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    17 327
  AMP PEAK  3(1Q21.3) WILD-TYPE   4 128
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q21.3) MUTATED     17  327
  AMP PEAK  3(1Q21.3) WILD-TYPE    4  128
     clus
vv    AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE
  NO                           17                             4
  YES                         327                           128
[1] 2 2
[1] FALSE
D3V11, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  3(1Q21.3) MUTATED   232   9   2  18
  AMP PEAK  3(1Q21.3) WILD-TYPE  95   3   2   3
D3V12, multiclass
    clus
vv   AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE
  R0                         232                            95
  R1                           9                             3
  R2                           2                             2
  RX                          18                             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                          26   265
  AMP PEAK  3(1Q21.3) WILD-TYPE                         9   102
D3V13, multiclass
                                  clus
vv                                 AMP PEAK  3(1Q21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      5
  BLACK OR AFRICAN AMERICAN                                 26
  WHITE                                                    265
                                  clus
vv                                 AMP PEAK  3(1Q21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                    9
  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     5 247
  AMP PEAK  3(1Q21.3) WILD-TYPE   2  98
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q21.3) MUTATED      5  247
  AMP PEAK  3(1Q21.3) WILD-TYPE    2   98
                        clus
vv                       AMP PEAK  3(1Q21.3) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         247
                        clus
vv                       AMP PEAK  3(1Q21.3) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            98
[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   108  29
  AMP PEAK  4(3Q26.2) WILD-TYPE 221  58
  AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE 
                          137                           279 
  AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE 
                           29                            58 
$`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-49-AARQ TCGA-50-5055 TCGA-50-5072 
         268          369          890         6443          785          246 
TCGA-50-5931 TCGA-50-5941 TCGA-50-5946 TCGA-53-7624 TCGA-53-A4EZ TCGA-55-1594 
         267          567          686         1986          280         1178 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6642 TCGA-55-6969 TCGA-55-6972 TCGA-55-6985 
        1375           87          993         1239         1475         1233 
TCGA-55-6987 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7726 TCGA-55-7815 
        1170          121            4          705           39           54 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8094 
          16          197           31            5           33            4 
TCGA-55-8205 TCGA-55-8208 TCGA-55-8507 TCGA-55-8508 TCGA-55-8614 TCGA-55-8620 
          33          674            8           15          536           66 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A493 TCGA-55-A4DF TCGA-64-1676 TCGA-64-1677 
          48         1952           28           47         1728          628 
TCGA-64-1679 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-69-7760 TCGA-69-7761 
        1686         1559          866          610          202          186 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 
          70           89          382          214           61          711 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4676 TCGA-73-7499 TCGA-73-A9RS TCGA-75-6214 
         800          467          164          519          305         1970 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7154 TCGA-78-7155 TCGA-78-7220 
        1973         1988         1950         1948         1957         1965 
TCGA-78-7539 TCGA-78-7540 TCGA-78-8662 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 
         327          881         1964          824         1959           11 
TCGA-86-7711 TCGA-86-7953 TCGA-86-8055 TCGA-86-8074 TCGA-86-8075 TCGA-86-8278 
         630          591           10           24          479          476 
TCGA-86-8358 TCGA-86-8669 TCGA-86-8673 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
          19           34          455          323         1940           60 
TCGA-91-6835 TCGA-91-6840 TCGA-91-6848 TCGA-91-7771 TCGA-91-8497 TCGA-91-8499 
          79          372          224          492          174           36 
TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7947 
         186           34            2         1973          568          477 
TCGA-95-8494 TCGA-97-7553 TCGA-J2-A4AD TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A8F4 
          84         1332          287          116            6          102 
TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4TF TCGA-MP-A4TK TCGA-S2-AA1A 
        1175         1946         1970         1971          121 

$`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          462          100            6 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8207 
         600           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          505           44          218          297 
TCGA-93-7348 TCGA-95-7944 TCGA-95-7948 TCGA-95-8039 TCGA-95-A4VK TCGA-95-A4VN 
         127          377          476          830          121          553 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7554 TCGA-97-7937 
         605          964         1965         1932          775          181 
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-97-8547 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-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A743 
         282          238          578          435          266          312 
TCGA-L9-A7SV TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 
         111          827           84         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 
                         6443                          2696 
  AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE 
                          492                           459 
[1] "2.0 - 6443.0 (492.0)" "1.0 - 2696.0 (459.0)"
[1] "hr=" "1.1"
D4V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK  4(3Q26.2) MUTATED         2       38       42        21        25
  AMP PEAK  4(3Q26.2) WILD-TYPE       3       78       90        28        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         49          8       14
D4V3, multiclass
            clus
vv           AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE
  STAGE I                              2                             3
  STAGE IA                            38                            78
  STAGE IB                            42                            90
  STAGE IIA                           21                            28
  STAGE IIB                           25                            45
  STAGE IIIA                          19                            49
  STAGE IIIB                           3                             8
  STAGE IV                            10                            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  4(3Q26.2) MUTATED    49  92  13   5
  AMP PEAK  4(3Q26.2) WILD-TYPE  98 175  29  13
D4V4, multiclass
    clus
vv   AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE
  T1                          49                            98
  T2                          92                           175
  T3                          13                            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
  AMP PEAK  4(3Q26.2) MUTATED   101  37    20
  AMP PEAK  4(3Q26.2) WILD-TYPE 200  54    54
D4V5, multiclass
       clus
vv      AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE
  N0                            101                           200
  N1                             37                            54
  N2+N3                          20                            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  4(3Q26.2) MUTATED   107   8   0   2  43
  AMP PEAK  4(3Q26.2) WILD-TYPE 219  10   1   2  80
D4V6, multiclass
     clus
vv    AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE
  M0                          107                           219
  M1                            8                            10
  M1A                           0                             1
  M1B                           2                             2
  MX                           43                            80
[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    88  72
  AMP PEAK  4(3Q26.2) WILD-TYPE 167 149
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(3Q26.2) MUTATED     88   72
  AMP PEAK  4(3Q26.2) WILD-TYPE  167  149
        clus
vv       AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE
  FEMALE                          88                           167
  MALE                            72                           149
[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                         10
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK  4(3Q26.2) MUTATED                                  32
  AMP PEAK  4(3Q26.2) WILD-TYPE                                62
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  4(3Q26.2) MUTATED                                                  107
  AMP PEAK  4(3Q26.2) WILD-TYPE                                                196
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK  4(3Q26.2) MUTATED                                            2
  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                                             4
                               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)                         107
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                   2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                5
  LUNG CLEAR CELL ADENOCARCINOMA                                               1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                           1
  LUNG MUCINOUS ADENOCARCINOMA                                                 0
  LUNG PAPILLARY ADENOCARCINOMA                                                4
  LUNG SIGNET RING ADENOCARCINOMA                                              1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                1
  MUCINOUS (COLLOID) CARCINOMA                                                 1
                                                    clus
vv                                                   AMP PEAK  4(3Q26.2) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                    10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             62
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           196
  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                                  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"
D4V10, binary
                               cls
clus                              0   1
  AMP PEAK  4(3Q26.2) MUTATED     6 154
  AMP PEAK  4(3Q26.2) WILD-TYPE  15 301
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(3Q26.2) MUTATED      6  154
  AMP PEAK  4(3Q26.2) WILD-TYPE   15  301
     clus
vv    AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE
  NO                            6                            15
  YES                         154                           301
[1] 2 2
[1] FALSE
D4V11, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  4(3Q26.2) MUTATED   110   3   3   7
  AMP PEAK  4(3Q26.2) WILD-TYPE 217   9   1  14
D4V12, multiclass
    clus
vv   AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE
  R0                         110                           217
  R1                           3                             9
  R2                           3                             1
  RX                           7                            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  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                          11   119
  AMP PEAK  4(3Q26.2) WILD-TYPE                        24   248
D4V13, multiclass
                                  clus
vv                                 AMP PEAK  4(3Q26.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 11
  WHITE                                                    119
                                  clus
vv                                 AMP PEAK  4(3Q26.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        3
  BLACK OR AFRICAN AMERICAN                                   24
  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"
D4V14, binary
                               cls
clus                              0   1
  AMP PEAK  4(3Q26.2) MUTATED     4 112
  AMP PEAK  4(3Q26.2) WILD-TYPE   3 233
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(3Q26.2) MUTATED      4  112
  AMP PEAK  4(3Q26.2) WILD-TYPE    3  233
                        clus
vv                       AMP PEAK  4(3Q26.2) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         112
                        clus
vv                       AMP PEAK  4(3Q26.2) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           233
[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    62  17
  AMP PEAK  5(4Q12) WILD-TYPE 267  70
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                         79                         337 
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                         17                          70 
$`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-49-AARQ TCGA-53-7624 TCGA-53-7813 TCGA-55-1592 TCGA-55-1594 
         268         6443         1986          424          701         1178 
TCGA-55-1595 TCGA-55-1596 TCGA-55-6712 TCGA-55-7283 TCGA-55-7573 TCGA-55-7576 
        1479         1375           24           35            4           40 
TCGA-55-7995 TCGA-55-8089 TCGA-55-8091 TCGA-55-8092 TCGA-55-8620 TCGA-55-A490 
           5          100          600           26           66           48 
TCGA-55-A493 TCGA-55-A4DF TCGA-62-8402 TCGA-62-A471 TCGA-64-1676 TCGA-64-1680 
          28           47         1445         1246         1728         1126 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-73-4662 TCGA-73-A9RS TCGA-75-6214 
          89          382          100          912          305         1970 
TCGA-78-7145 TCGA-78-7150 TCGA-78-7154 TCGA-78-7161 TCGA-78-7163 TCGA-78-7535 
        1973         1963         1948          215         1950         1972 
TCGA-78-7542 TCGA-78-8662 TCGA-86-7953 TCGA-86-7955 TCGA-86-8054 TCGA-86-8074 
        1952         1964          591          508          745           24 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8669 TCGA-86-8673 TCGA-86-A456 TCGA-91-6848 
         476          482           34          455           10          224 
TCGA-91-8499 TCGA-95-7039 TCGA-95-7567 TCGA-95-7948 TCGA-95-8494 TCGA-97-7937 
          36           34          568          476           84          181 
TCGA-97-8179 TCGA-J2-8194 TCGA-L4-A4E5 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4TF 
          15          114          578           84         1967         1970 
TCGA-MP-A4TK 
        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 
         705           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          462            6            4           47           15 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
          33           46           66          674          216           44 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
          23           29           11            8           15          228 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
           9            3          146          202          536           15 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
          48           49          106           33           42           29 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 
        1952            1            5          162         1216         1289 
TCGA-62-8398 TCGA-62-8399 TCGA-62-A46U TCGA-62-A46V TCGA-62-A472 TCGA-64-1677 
        1970         2696         2067         2199          910          628 
TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
        1189         1686         1968         1959           62         1305 
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-67-3773 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-69-7764 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-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
         711          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-78-7152 TCGA-78-7153 
        1988         1950         1944         1093         1202          760 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7162 
        1957         1961         1963         1221          678         1940 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
        1934         1937         1965         1949         1944          327 
TCGA-78-7540 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
         881          994         1949         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-86-7713 TCGA-86-7714 TCGA-86-7954 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
         422         1968         1963           10         1963           13 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8280 TCGA-86-8281 TCGA-86-8358 TCGA-86-8359 
         479          489           16         1955           19           26 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 TCGA-86-A4D0 
          35           45           18           15          405           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-91-6847 TCGA-91-6849 TCGA-91-7771 
          79          417          372          842           35          492 
TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
         505          174           44          218          297          127 
TCGA-93-8067 TCGA-95-7043 TCGA-95-7562 TCGA-95-7944 TCGA-95-7947 TCGA-95-8039 
         186            2         1973          377          477          830 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
         121          553          605          964         1965         1932 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        1332          775           22          107          182         1965 
TCGA-97-8175 TCGA-97-8177 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 
          87          147          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-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
         287          282          238          435          116            6 
TCGA-L9-A50W TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 
         266          312          111          102          827         1175 
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-A4TH TCGA-MP-A4TI TCGA-MP-A5C7 
        1951         1944         1970          142         1955         1490 
TCGA-S2-AA1A 
         121 

  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                          4                           1 
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                       6443                        2696 
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                        508                         462 
[1] "4.0 - 6443.0 (508.0)" "1.0 - 2696.0 (462.0)"
[1] "hr=" "1"  
D5V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK  5(4Q12) MUTATED         3       17       28         7        22
  AMP PEAK  5(4Q12) WILD-TYPE       2       99      104        42        48
                             vv
clus                          STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK  5(4Q12) MUTATED           10          1        5
  AMP PEAK  5(4Q12) WILD-TYPE         58         10       19
D5V3, multiclass
            clus
vv           AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  STAGE I                            3                           2
  STAGE IA                          17                          99
  STAGE IB                          28                         104
  STAGE IIA                          7                          42
  STAGE IIB                         22                          48
  STAGE IIIA                        10                          58
  STAGE IIIB                         1                          10
  STAGE IV                           5                          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  5(4Q12) MUTATED    24  56  11   2
  AMP PEAK  5(4Q12) WILD-TYPE 123 211  31  16
D5V4, multiclass
    clus
vv   AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  T1                        24                         123
  T2                        56                         211
  T3                        11                          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
  AMP PEAK  5(4Q12) MUTATED    59  23    10
  AMP PEAK  5(4Q12) WILD-TYPE 242  68    64
D5V5, multiclass
       clus
vv      AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  N0                           59                         242
  N1                           23                          68
  N2+N3                        10                          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
  AMP PEAK  5(4Q12) MUTATED    66   4   0   1  20
  AMP PEAK  5(4Q12) WILD-TYPE 260  14   1   3 103
D5V6, multiclass
     clus
vv    AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  M0                         66                         260
  M1                          4                          14
  M1A                         0                           1
  M1B                         1                           3
  MX                         20                         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"
D5V7, binary
                             cls
clus                            0   1
  AMP PEAK  5(4Q12) MUTATED    47  46
  AMP PEAK  5(4Q12) WILD-TYPE 208 175
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(4Q12) MUTATED     47   46
  AMP PEAK  5(4Q12) WILD-TYPE  208  175
        clus
vv       AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  FEMALE                        47                         208
  MALE                          46                         175
[1] 2 2
[1] FALSE
D5V8, continuous
                             vv
clus                          LUNG ACINAR ADENOCARCINOMA
  AMP PEAK  5(4Q12) MUTATED                            3
  AMP PEAK  5(4Q12) WILD-TYPE                         12
                             vv
clus                          LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK  5(4Q12) MUTATED                                  12
  AMP PEAK  5(4Q12) WILD-TYPE                                82
                             vv
clus                          LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  5(4Q12) MUTATED                                                   70
  AMP PEAK  5(4Q12) WILD-TYPE                                                233
                             vv
clus                          LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK  5(4Q12) MUTATED                                            0
  AMP PEAK  5(4Q12) WILD-TYPE                                          5
                             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                                             4
                             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)                        70
  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                                                  12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           82
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         233
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                   5
  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                                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"
D5V10, binary
                             cls
clus                            0   1
  AMP PEAK  5(4Q12) MUTATED     2  91
  AMP PEAK  5(4Q12) WILD-TYPE  19 364
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(4Q12) MUTATED      2   91
  AMP PEAK  5(4Q12) WILD-TYPE   19  364
     clus
vv    AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  NO                          2                          19
  YES                        91                         364
[1] 2 2
[1] FALSE
D5V11, continuous
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK  5(4Q12) MUTATED    61   3   0   3
  AMP PEAK  5(4Q12) WILD-TYPE 266   9   4  18
D5V12, multiclass
    clus
vv   AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  R0                        61                         266
  R1                         3                           9
  R2                         0                           4
  RX                         3                          18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  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                           7    69
  AMP PEAK  5(4Q12) WILD-TYPE                        28   298
D5V13, multiclass
                                  clus
vv                                 AMP PEAK  5(4Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    3
  BLACK OR AFRICAN AMERICAN                                7
  WHITE                                                   69
                                  clus
vv                                 AMP PEAK  5(4Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 28
  WHITE                                                    298
[1] 4 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  65
  AMP PEAK  5(4Q12) WILD-TYPE   4 280
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(4Q12) MUTATED      3   65
  AMP PEAK  5(4Q12) WILD-TYPE    4  280
                        clus
vv                       AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  HISPANIC OR LATINO                             3                           4
  NOT HISPANIC OR LATINO                        65                         280
[1] 2 2
[1] FALSE

Clustering(6) Variable = AMP PEAK  6(5P15.33) MUTATION ANALYSIS
D6V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  6(5P15.33) MUTATED   217  58
  AMP PEAK  6(5P15.33) WILD-TYPE 112  29
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                           275                            141 
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                            58                             29 
$`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-49-AARQ TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5066 
         354         6443         2174         2146          455          944 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5935 
        1499          246          282          267         2370          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-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 
        1971          424          701         1178         1479         1375 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6712 TCGA-55-6969 TCGA-55-6972 TCGA-55-6980 
          87            2           24         1239         1475           67 
TCGA-55-6983 TCGA-55-6985 TCGA-55-6987 TCGA-55-7281 TCGA-55-7570 TCGA-55-7573 
        1826         1233         1170           18            6            4 
TCGA-55-7574 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7903 
          95          705           39           39           34           19 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7994 TCGA-55-8091 TCGA-55-8094 TCGA-55-8096 
         197           21           31          600            4           47 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 
          46           66          674           44           23           11 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8514 TCGA-55-8614 
           8           15          228            9          202          536 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A490 
          15           48           66           33           42           48 
TCGA-55-A491 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 
        1952           28            5           47          162         1216 
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-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 TCGA-64-5781 
        1686         1126         1968         1959         1305         1559 
TCGA-67-3770 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7763 
          31          174          141          422          202          690 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 TCGA-69-7980 
         414          165          230          184           89          382 
TCGA-69-8253 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4662 
         100          129          214           61         1600          912 
TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 TCGA-73-7499 TCGA-75-6214 TCGA-75-7031 
         467           40          164          519         1970         1965 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 TCGA-78-7153 TCGA-78-7154 
        1973         1988         1950         1093          760         1948 
TCGA-78-7155 TCGA-78-7159 TCGA-78-7160 TCGA-78-7163 TCGA-78-7166 TCGA-78-7220 
        1957         1221          678         1950         1934         1965 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 TCGA-78-7633 TCGA-78-8640 TCGA-78-8655 
        1972         1949          327          994         1949         1981 
TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 
        1964         1972          824         1959          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-86-8358 TCGA-86-8359 
          24          479          482           16           19           26 
TCGA-86-8585 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-A4D0 TCGA-91-6828 
          35           18           15          455           30          323 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6836 TCGA-91-6840 TCGA-91-6848 TCGA-91-8499 
        1940           60          417          372          224           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-95-7562 TCGA-95-7567 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
           2         1973          568          477          476          830 
TCGA-95-8494 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 TCGA-97-7553 TCGA-97-7554 
          84          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-99-8028 TCGA-99-8033 
         115          271          392          427          459          170 
TCGA-J2-8192 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L9-A444 TCGA-L9-A743 
         154          287          282          578            6          312 
TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SW 
         111          102          827         1175           84         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-A4TF TCGA-MP-A4TH TCGA-MP-A4TK TCGA-S2-AA1A 
        1944         1970          142         1971          121 

$`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          462 
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-73-A9RS TCGA-75-7025 TCGA-75-7027 
         131           38          621          305         1967         1956 
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-86-8674 TCGA-86-A456 
         476         1955           45           34          405           10 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6831 TCGA-91-6835 TCGA-91-6847 TCGA-91-6849 
          14           39          310           79          842           35 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-95-7944 TCGA-95-A4VN TCGA-95-A4VP 
         492          505          174          377          553          605 
TCGA-97-7552 TCGA-97-7941 TCGA-97-8175 TCGA-97-8177 TCGA-97-A4M2 TCGA-99-8032 
        1932           22           87          147          197           44 
TCGA-J2-8194 TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A50W TCGA-MP-A4SV 
         114          238          435          116          266         1946 
TCGA-MP-A4TE TCGA-MP-A4TI TCGA-MP-A5C7 
        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 
                          6443                           2199 
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                           508                            445 
[1] "2.0 - 6443.0 (508.0)" "1.0 - 2199.0 (445.0)"
[1] "hr=" "1.3"
D6V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK  6(5P15.33) MUTATED         5       78       84        37        40
  AMP PEAK  6(5P15.33) WILD-TYPE       0       38       48        12        30
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK  6(5P15.33) MUTATED           45          8       15
  AMP PEAK  6(5P15.33) WILD-TYPE         23          3        9
D6V3, multiclass
            clus
vv           AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE
  STAGE I                               5                              0
  STAGE IA                             78                             38
  STAGE IB                             84                             48
  STAGE IIA                            37                             12
  STAGE IIB                            40                             30
  STAGE IIIA                           45                             23
  STAGE IIIB                            8                              3
  STAGE IV                             15                              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   100 176  22  12
  AMP PEAK  6(5P15.33) WILD-TYPE  47  91  20   6
D6V4, multiclass
    clus
vv   AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE
  T1                          100                             47
  T2                          176                             91
  T3                           22                             20
  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   192  60    53
  AMP PEAK  6(5P15.33) WILD-TYPE 109  31    21
D6V5, multiclass
       clus
vv      AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE
  N0                             192                            109
  N1                              60                             31
  N2+N3                           53                             21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  AMP PEAK  6(5P15.33) MUTATED   212  10   1   3  83
  AMP PEAK  6(5P15.33) WILD-TYPE 114   8   0   1  40
D6V6, multiclass
     clus
vv    AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE
  M0                           212                            114
  M1                            10                              8
  M1A                            1                              0
  M1B                            3                              1
  MX                            83                             40
[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   174 138
  AMP PEAK  6(5P15.33) WILD-TYPE  81  83
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(5P15.33) MUTATED    174  138
  AMP PEAK  6(5P15.33) WILD-TYPE   81   83
        clus
vv       AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE
  FEMALE                          174                             81
  MALE                            138                             83
[1] 2 2
[1] FALSE
D6V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  AMP PEAK  6(5P15.33) MUTATED                           10
  AMP PEAK  6(5P15.33) WILD-TYPE                          5
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK  6(5P15.33) MUTATED                                  56
  AMP PEAK  6(5P15.33) WILD-TYPE                                38
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  6(5P15.33) MUTATED                                                  209
  AMP PEAK  6(5P15.33) WILD-TYPE                                                 94
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK  6(5P15.33) MUTATED                                            2
  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                                             2
                                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                                                   10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            56
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          209
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    2
  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                                                      5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              38
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             94
  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                                   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"
D6V10, binary
                                cls
clus                               0   1
  AMP PEAK  6(5P15.33) MUTATED    16 296
  AMP PEAK  6(5P15.33) WILD-TYPE   5 159
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(5P15.33) MUTATED     16  296
  AMP PEAK  6(5P15.33) WILD-TYPE    5  159
     clus
vv    AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE
  NO                            16                              5
  YES                          296                            159
[1] 2 2
[1] FALSE
D6V11, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK  6(5P15.33) MUTATED   212   8   2  16
  AMP PEAK  6(5P15.33) WILD-TYPE 115   4   2   5
D6V12, multiclass
    clus
vv   AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE
  R0                          212                            115
  R1                            8                              4
  R2                            2                              2
  RX                           16                              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                          25   242
  AMP PEAK  6(5P15.33) WILD-TYPE                        10   125
D6V13, multiclass
                                  clus
vv                                 AMP PEAK  6(5P15.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  25
  WHITE                                                     242
                                  clus
vv                                 AMP PEAK  6(5P15.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         1
  BLACK OR AFRICAN AMERICAN                                    10
  WHITE                                                       125
[1] 4 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     5 229
  AMP PEAK  6(5P15.33) WILD-TYPE   2 116
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(5P15.33) MUTATED      5  229
  AMP PEAK  6(5P15.33) WILD-TYPE    2  116
                        clus
vv                       AMP PEAK  6(5P15.33) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          229
                        clus
vv                       AMP PEAK  6(5P15.33) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            116
[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   206  47
  AMP PEAK  7(5P13.1) WILD-TYPE 123  40
  AMP PEAK  7(5P13.1) MUTATED AMP PEAK  7(5P13.1) WILD-TYPE 
                          253                           163 
  AMP PEAK  7(5P13.1) MUTATED AMP PEAK  7(5P13.1) WILD-TYPE 
                           47                            40 
$`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-49-AARQ TCGA-50-5045 TCGA-50-5049 
         369          890          354         6443         2174         2146 
TCGA-50-5051 TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 TCGA-50-5935 
         455          944         1499          282          267          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-55-1592 TCGA-55-1594 TCGA-55-1595 
        1971          424          280          701         1178         1479 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6969 TCGA-55-6972 TCGA-55-6980 TCGA-55-6983 
          87            2         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 
         705           39           39           34           19          197 
TCGA-55-7911 TCGA-55-7994 TCGA-55-7995 TCGA-55-8091 TCGA-55-8094 TCGA-55-8096 
          21           31            5          600            4           47 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8302 TCGA-55-8506 TCGA-55-8507 
          46           66          674           23           11            8 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
          15          228            9          202          536           15 
TCGA-55-8616 TCGA-55-8620 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
          48           66           33           42           29           48 
TCGA-55-A491 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 
        1952           28            5           47          162         1216 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46U TCGA-62-A471 TCGA-64-1678 TCGA-64-1679 
        2696         1445         2067         1246         1189         1686 
TCGA-64-1680 TCGA-64-5774 TCGA-64-5778 TCGA-64-5781 TCGA-67-3773 TCGA-67-6215 
        1126         1959         1305         1559          427          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-69-7980 TCGA-69-8253 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
         230          382          100          129          214           61 
TCGA-73-4658 TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 TCGA-73-7499 TCGA-75-6214 
        1600          467           40          164          519         1970 
TCGA-75-7031 TCGA-78-7147 TCGA-78-7149 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
        1965         1950         1093          760         1948         1957 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7163 TCGA-78-7166 TCGA-78-7220 TCGA-78-7535 
        1221          678         1950         1934         1965         1972 
TCGA-78-7536 TCGA-78-7539 TCGA-78-7633 TCGA-78-8640 TCGA-78-8655 TCGA-78-8662 
        1949          327          994         1949         1981         1964 
TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 
        1972          824         1959          630          422          591 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8073 TCGA-86-8074 
        1963          508          745           10           13           24 
TCGA-86-8075 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
         479          482           16           19           26           35 
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-91-6831 TCGA-91-6836 TCGA-91-6840 TCGA-91-6848 TCGA-91-8499 TCGA-91-A4BC 
         310          417          372          224           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-95-8039 TCGA-95-8494 TCGA-97-7546 TCGA-97-7547 TCGA-97-7553 
         476          830           84          964         1965         1332 
TCGA-97-7554 TCGA-97-7937 TCGA-97-8172 TCGA-97-8174 TCGA-97-8179 TCGA-97-8547 
         775          181          182         1965           15          148 
TCGA-97-8552 TCGA-97-A4M7 TCGA-99-8025 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE 
         115          271          427          170          287          282 
TCGA-L4-A4E5 TCGA-L9-A444 TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 
         578            6          312          111          102          827 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 
        1175           84         1967         1951         1954         1954 
TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TK 
        1957         1951         1944         1970          142         1971 
TCGA-S2-AA1A 
         121 

$`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          462 
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-73-A9RS TCGA-75-7025 TCGA-75-7027 TCGA-78-7145 
          38          621          305         1967         1956         1973 
TCGA-78-7146 TCGA-78-7148 TCGA-78-7150 TCGA-78-7152 TCGA-78-7156 TCGA-78-7158 
        1988         1944         1963         1202         1961         1963 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7167 TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 
         215         1940         1937         1944          881         1952 
TCGA-78-8648 TCGA-78-8660 TCGA-80-5607 TCGA-86-7701 TCGA-86-7714 TCGA-86-8056 
        1971         1954         1965           11         1968         1963 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8281 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
         489          476         1955           45           34           18 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6835 TCGA-91-6847 
         405           10           14           39           79          842 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-93-8067 TCGA-95-7562 
          35          492          505          174          186         1973 
TCGA-95-7567 TCGA-95-7944 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7552 
         568          377          121          553          605         1932 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8175 TCGA-97-8177 TCGA-97-A4M2 TCGA-99-7458 
          22          107           87          147          197          392 
TCGA-99-8028 TCGA-99-8032 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AG TCGA-L4-A4E6 
         459           44          154          114          238          435 
TCGA-L9-A443 TCGA-L9-A50W TCGA-MP-A4SV TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TI 
         116          266         1946         1980         1970         1955 
TCGA-MP-A5C7 
        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 
                         6443                          2370 
  AMP PEAK  7(5P13.1) MUTATED AMP PEAK  7(5P13.1) WILD-TYPE 
                          477                           462 
[1] "2.0 - 6443.0 (477.0)" "1.0 - 2370.0 (462.0)"
[1] "hr=" "1.2"
D7V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK  7(5P13.1) MUTATED         5       73       83        36        33
  AMP PEAK  7(5P13.1) WILD-TYPE       0       43       49        13        37
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK  7(5P13.1) MUTATED           37          7       13
  AMP PEAK  7(5P13.1) WILD-TYPE         31          4       11
D7V3, multiclass
            clus
vv           AMP PEAK  7(5P13.1) MUTATED AMP PEAK  7(5P13.1) WILD-TYPE
  STAGE I                              5                             0
  STAGE IA                            73                            43
  STAGE IB                            83                            49
  STAGE IIA                           36                            13
  STAGE IIB                           33                            37
  STAGE IIIA                          37                            31
  STAGE IIIB                           7                             4
  STAGE IV                            13                            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    97 160  20   8
  AMP PEAK  7(5P13.1) WILD-TYPE  50 107  22  10
D7V4, multiclass
    clus
vv   AMP PEAK  7(5P13.1) MUTATED AMP PEAK  7(5P13.1) WILD-TYPE
  T1                          97                            50
  T2                         160                           107
  T3                          20                            22
  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   185  52    44
  AMP PEAK  7(5P13.1) WILD-TYPE 116  39    30
D7V5, multiclass
       clus
vv      AMP PEAK  7(5P13.1) MUTATED AMP PEAK  7(5P13.1) WILD-TYPE
  N0                            185                           116
  N1                             52                            39
  N2+N3                          44                            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
  AMP PEAK  7(5P13.1) MUTATED   194   9   0   3  78
  AMP PEAK  7(5P13.1) WILD-TYPE 132   9   1   1  45
D7V6, multiclass
     clus
vv    AMP PEAK  7(5P13.1) MUTATED AMP PEAK  7(5P13.1) WILD-TYPE
  M0                          194                           132
  M1                            9                             9
  M1A                           0                             1
  M1B                           3                             1
  MX                           78                            45
[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   161 126
  AMP PEAK  7(5P13.1) WILD-TYPE  94  95
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(5P13.1) MUTATED    161  126
  AMP PEAK  7(5P13.1) WILD-TYPE   94   95
        clus
vv       AMP PEAK  7(5P13.1) MUTATED AMP PEAK  7(5P13.1) WILD-TYPE
  FEMALE                         161                            94
  MALE                           126                            95
[1] 2 2
[1] FALSE
D7V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  AMP PEAK  7(5P13.1) MUTATED                           10
  AMP PEAK  7(5P13.1) WILD-TYPE                          5
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK  7(5P13.1) MUTATED                                  50
  AMP PEAK  7(5P13.1) WILD-TYPE                                44
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  7(5P13.1) MUTATED                                                  193
  AMP PEAK  7(5P13.1) WILD-TYPE                                                110
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK  7(5P13.1) MUTATED                                            2
  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                                             2
                               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                                                  10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           50
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         193
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                   2
  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                                                     5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             44
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           110
  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                                  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"
D7V10, binary
                               cls
clus                              0   1
  AMP PEAK  7(5P13.1) MUTATED    13 274
  AMP PEAK  7(5P13.1) WILD-TYPE   8 181
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(5P13.1) MUTATED     13  274
  AMP PEAK  7(5P13.1) WILD-TYPE    8  181
     clus
vv    AMP PEAK  7(5P13.1) MUTATED AMP PEAK  7(5P13.1) WILD-TYPE
  NO                           13                             8
  YES                         274                           181
[1] 2 2
[1] FALSE
D7V11, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  7(5P13.1) MUTATED   200   6   1  13
  AMP PEAK  7(5P13.1) WILD-TYPE 127   6   3   8
D7V12, multiclass
    clus
vv   AMP PEAK  7(5P13.1) MUTATED AMP PEAK  7(5P13.1) WILD-TYPE
  R0                         200                           127
  R1                           6                             6
  R2                           1                             3
  RX                          13                             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  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                          23   227
  AMP PEAK  7(5P13.1) WILD-TYPE                        12   140
D7V13, multiclass
                                  clus
vv                                 AMP PEAK  7(5P13.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 23
  WHITE                                                    227
                                  clus
vv                                 AMP PEAK  7(5P13.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   12
  WHITE                                                      140
[1] 4 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     6 213
  AMP PEAK  7(5P13.1) WILD-TYPE   1 132
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(5P13.1) MUTATED      6  213
  AMP PEAK  7(5P13.1) WILD-TYPE    1  132
                        clus
vv                       AMP PEAK  7(5P13.1) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                         213
                        clus
vv                       AMP PEAK  7(5P13.1) WILD-TYPE
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                           132
[1] 2 2
[1] FALSE

Clustering(8) Variable = AMP PEAK  8(6P21.1) MUTATION ANALYSIS
D8V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  8(6P21.1) MUTATED   131  28
  AMP PEAK  8(6P21.1) WILD-TYPE 198  59
  AMP PEAK  8(6P21.1) MUTATED AMP PEAK  8(6P21.1) WILD-TYPE 
                          159                           257 
  AMP PEAK  8(6P21.1) MUTATED AMP PEAK  8(6P21.1) WILD-TYPE 
                           28                            59 
$`AMP PEAK  8(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-55-8208 TCGA-55-8507 TCGA-55-8511 TCGA-55-8512 TCGA-55-8514 TCGA-55-8614 
         674            8            9            3          202          536 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A490 
          15           48           66           33           42           48 
TCGA-55-A494 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46U TCGA-62-A46V 
           5         1970         2696         1445         2067         2199 
TCGA-62-A471 TCGA-64-1677 TCGA-64-1680 TCGA-64-5774 TCGA-64-5779 TCGA-67-3773 
        1246          628         1126         1959          864          427 
TCGA-67-6215 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7979 TCGA-69-7980 
         174          690          414          165           89          382 
TCGA-69-8255 TCGA-71-6725 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
         129           61          912          800          467          131 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-75-6214 TCGA-78-7145 TCGA-78-7147 
          38          621          519         1970         1973         1950 
TCGA-78-7149 TCGA-78-7155 TCGA-78-7158 TCGA-78-7159 TCGA-78-7161 TCGA-78-7162 
        1093         1957         1963         1221          215         1940 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7539 TCGA-78-7542 TCGA-78-7633 TCGA-78-8655 
        1937         1965          327         1952          994         1981 
TCGA-78-8662 TCGA-80-5608 TCGA-86-6851 TCGA-86-7713 TCGA-86-7954 TCGA-86-8074 
        1964         1972         1959          422         1963           24 
TCGA-86-8075 TCGA-86-8279 TCGA-86-8280 TCGA-86-8281 TCGA-86-8358 TCGA-86-8359 
         479          482           16         1955           19           26 
TCGA-86-8672 TCGA-86-8674 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 
          15          405          310           79          372          842 
TCGA-91-6848 TCGA-91-8499 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7948 
         224           36         1973          568          377          476 
TCGA-97-7546 TCGA-97-7553 TCGA-97-7554 TCGA-97-8171 TCGA-97-8174 TCGA-97-8177 
         964         1332          775          107         1965          147 
TCGA-97-8179 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-8033 TCGA-J2-8194 TCGA-J2-A4AD 
          15          197          271          170          114          287 
TCGA-J2-A4AE TCGA-L9-A444 TCGA-L9-A7SV TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
         282            6          111         1175           84         1946 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A5C7 
        1970         1970         1490 

$`AMP PEAK  8(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-49-AARQ TCGA-50-5045 TCGA-50-5049 
         369          890          522         6443         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-50-5942 TCGA-50-8460 TCGA-53-7626 TCGA-55-1594 TCGA-55-6543 TCGA-55-6712 
         883          105         1971         1178            2           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-55-7570 TCGA-55-7574 TCGA-55-7724 TCGA-55-7725 
          18          121            6           95          705           39 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
          39           34           24           16          197           21 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
         462          100            6          600           26            4 
TCGA-55-8096 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
          47          216           44           23           29           11 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8513 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48Z 
          15          228          146           49          106           29 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 
        1952            1           28           47          162         1216 
TCGA-62-8397 TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 
        1289          910         1728         1189         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-67-3774 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
         573          385          141          422          202          186 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-8253 TCGA-69-8254 TCGA-69-A59K 
         230          184           70          100           77          214 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4675 TCGA-73-4676 TCGA-73-A9RS TCGA-75-7025 
        1600          711           40          164          305         1967 
TCGA-75-7027 TCGA-75-7031 TCGA-78-7146 TCGA-78-7148 TCGA-78-7150 TCGA-78-7152 
        1956         1965         1988         1944         1963         1202 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7160 TCGA-78-7163 TCGA-78-7166 
         760         1948         1961          678         1950         1934 
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-78-8660 TCGA-80-5607 TCGA-83-5908 TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 
        1954         1965          824           11          630         1968 
TCGA-86-7953 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
         591          508          745           10         1963           13 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
         489          476           35           45           34           18 
TCGA-86-8673 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
         455           10           30           14           39          323 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6836 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
        1940           60          417           35          492          505 
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-95-7043 TCGA-95-7947 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
          34            2          477          830           84          121 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7547 TCGA-97-7552 TCGA-97-7937 TCGA-97-7941 
         553          605         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-L9-A50W TCGA-L9-A743 TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MP-A4SW 
         116          266          312          102          827         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-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-S2-AA1A 
        1944          142         1955         1971          121 

  AMP PEAK  8(6P21.1) MUTATED AMP PEAK  8(6P21.1) WILD-TYPE 
                            3                             1 
  AMP PEAK  8(6P21.1) MUTATED AMP PEAK  8(6P21.1) WILD-TYPE 
                         2696                          6443 
  AMP PEAK  8(6P21.1) MUTATED AMP PEAK  8(6P21.1) WILD-TYPE 
                          482                           462 
[1] "3.0 - 2696.0 (482.0)" "1.0 - 6443.0 (462.0)"
[1] "hr=" "1.5"
D8V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK  8(6P21.1) MUTATED         2       48       49        18        22
  AMP PEAK  8(6P21.1) WILD-TYPE       3       68       83        31        48
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK  8(6P21.1) MUTATED           22          5       12
  AMP PEAK  8(6P21.1) WILD-TYPE         46          6       12
D8V3, multiclass
            clus
vv           AMP PEAK  8(6P21.1) MUTATED AMP PEAK  8(6P21.1) WILD-TYPE
  STAGE I                              2                             3
  STAGE IA                            48                            68
  STAGE IB                            49                            83
  STAGE IIA                           18                            31
  STAGE IIB                           22                            48
  STAGE IIIA                          22                            46
  STAGE IIIB                           5                             6
  STAGE IV                            12                            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  8(6P21.1) MUTATED    59  99  12   7
  AMP PEAK  8(6P21.1) WILD-TYPE  88 168  30  11
D8V4, multiclass
    clus
vv   AMP PEAK  8(6P21.1) MUTATED AMP PEAK  8(6P21.1) WILD-TYPE
  T1                          59                            88
  T2                          99                           168
  T3                          12                            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  8(6P21.1) MUTATED   119  28    27
  AMP PEAK  8(6P21.1) WILD-TYPE 182  63    47
D8V5, multiclass
       clus
vv      AMP PEAK  8(6P21.1) MUTATED AMP PEAK  8(6P21.1) WILD-TYPE
  N0                            119                           182
  N1                             28                            63
  N2+N3                          27                            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  8(6P21.1) MUTATED   122   8   1   2  44
  AMP PEAK  8(6P21.1) WILD-TYPE 204  10   0   2  79
D8V6, multiclass
     clus
vv    AMP PEAK  8(6P21.1) MUTATED AMP PEAK  8(6P21.1) WILD-TYPE
  M0                          122                           204
  M1                            8                            10
  M1A                           1                             0
  M1B                           2                             2
  MX                           44                            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"
D8V7, binary
                               cls
clus                              0   1
  AMP PEAK  8(6P21.1) MUTATED    95  83
  AMP PEAK  8(6P21.1) WILD-TYPE 160 138
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(6P21.1) MUTATED     95   83
  AMP PEAK  8(6P21.1) WILD-TYPE  160  138
        clus
vv       AMP PEAK  8(6P21.1) MUTATED AMP PEAK  8(6P21.1) WILD-TYPE
  FEMALE                          95                           160
  MALE                            83                           138
[1] 2 2
[1] FALSE
D8V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  AMP PEAK  8(6P21.1) MUTATED                            8
  AMP PEAK  8(6P21.1) WILD-TYPE                          7
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK  8(6P21.1) MUTATED                                  35
  AMP PEAK  8(6P21.1) WILD-TYPE                                59
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  8(6P21.1) MUTATED                                                  112
  AMP PEAK  8(6P21.1) WILD-TYPE                                                191
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK  8(6P21.1) MUTATED                                            0
  AMP PEAK  8(6P21.1) WILD-TYPE                                          5
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK  8(6P21.1) MUTATED                                               8
  AMP PEAK  8(6P21.1) WILD-TYPE                                            11
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK  8(6P21.1) MUTATED                                1
  AMP PEAK  8(6P21.1) WILD-TYPE                              1
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK  8(6P21.1) MUTATED                                    1
  AMP PEAK  8(6P21.1) WILD-TYPE                                  3
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK  8(6P21.1) MUTATED                              0
  AMP PEAK  8(6P21.1) WILD-TYPE                            2
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK  8(6P21.1) MUTATED                              11
  AMP PEAK  8(6P21.1) WILD-TYPE                             8
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK  8(6P21.1) MUTATED                                 0
  AMP PEAK  8(6P21.1) WILD-TYPE                               1
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK  8(6P21.1) MUTATED                                               1
  AMP PEAK  8(6P21.1) WILD-TYPE                                             4
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK  8(6P21.1) MUTATED                              1
  AMP PEAK  8(6P21.1) WILD-TYPE                            6
D8V9, multiclass
                                                    clus
vv                                                   AMP PEAK  8(6P21.1) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           35
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         112
  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  8(6P21.1) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             59
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           191
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     5
  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                                  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"
D8V10, binary
                               cls
clus                              0   1
  AMP PEAK  8(6P21.1) MUTATED     7 171
  AMP PEAK  8(6P21.1) WILD-TYPE  14 284
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(6P21.1) MUTATED      7  171
  AMP PEAK  8(6P21.1) WILD-TYPE   14  284
     clus
vv    AMP PEAK  8(6P21.1) MUTATED AMP PEAK  8(6P21.1) WILD-TYPE
  NO                            7                            14
  YES                         171                           284
[1] 2 2
[1] FALSE
D8V11, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  8(6P21.1) MUTATED   123   6   0   7
  AMP PEAK  8(6P21.1) WILD-TYPE 204   6   4  14
D8V12, multiclass
    clus
vv   AMP PEAK  8(6P21.1) MUTATED AMP PEAK  8(6P21.1) WILD-TYPE
  R0                         123                           204
  R1                           6                             6
  R2                           0                             4
  RX                           7                            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(6P21.1) MUTATED                                  1     4
  AMP PEAK  8(6P21.1) WILD-TYPE                                0     2
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  8(6P21.1) MUTATED                           7   151
  AMP PEAK  8(6P21.1) WILD-TYPE                        28   216
D8V13, multiclass
                                  clus
vv                                 AMP PEAK  8(6P21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                  7
  WHITE                                                    151
                                  clus
vv                                 AMP PEAK  8(6P21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   28
  WHITE                                                      216
[1] 4 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(6P21.1) MUTATED     4 137
  AMP PEAK  8(6P21.1) WILD-TYPE   3 208
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(6P21.1) MUTATED      4  137
  AMP PEAK  8(6P21.1) WILD-TYPE    3  208
                        clus
vv                       AMP PEAK  8(6P21.1) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         137
                        clus
vv                       AMP PEAK  8(6P21.1) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           208
[1] 2 2
[1] FALSE

Clustering(9) Variable = AMP PEAK  9(7P11.2) MUTATION ANALYSIS
D9V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  9(7P11.2) MUTATED   174  46
  AMP PEAK  9(7P11.2) WILD-TYPE 155  41
  AMP PEAK  9(7P11.2) MUTATED AMP PEAK  9(7P11.2) WILD-TYPE 
                          220                           196 
  AMP PEAK  9(7P11.2) MUTATED AMP PEAK  9(7P11.2) WILD-TYPE 
                           46                            41 
$`AMP PEAK  9(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-49-AARQ TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 
         354         6443         2174         2146          785          944 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5933 TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 
         246          282         2370          567          764          686 
TCGA-53-7624 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 
        1986          280         1178         1375           87            2 
TCGA-55-6712 TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 TCGA-55-6985 TCGA-55-6987 
          24           25         1475           67         1233         1170 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7576 TCGA-55-7724 TCGA-55-7726 TCGA-55-7727 
          35          121           40          705           39           34 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7994 TCGA-55-8085 TCGA-55-8089 TCGA-55-8091 
          16          197           31           33          100          600 
TCGA-55-8092 TCGA-55-8096 TCGA-55-8205 TCGA-55-8206 TCGA-55-8301 TCGA-55-8302 
          26           47           33           46           44           23 
TCGA-55-8505 TCGA-55-8510 TCGA-55-8511 TCGA-55-8514 TCGA-55-8615 TCGA-55-8616 
          29          228            9          202           15           48 
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-A472 TCGA-64-1676 
         162         1289         1970         2696          910         1728 
TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5779 TCGA-64-5781 TCGA-67-3770 
        1686         1126         1968          864         1559           31 
TCGA-67-3771 TCGA-67-3772 TCGA-67-6217 TCGA-69-7760 TCGA-69-7764 TCGA-69-7765 
         610          573          422          202          414          165 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8255 TCGA-69-A59K 
         184           70           89          382          129          214 
TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4668 TCGA-73-4670 
          61         1600          711          912          467          131 
TCGA-73-4675 TCGA-73-4676 TCGA-73-7499 TCGA-73-A9RS TCGA-75-6214 TCGA-75-7025 
          40          164          519          305         1970         1967 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7150 TCGA-78-7154 TCGA-78-7155 
        1973         1988         1950         1963         1948         1957 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7163 TCGA-78-7535 TCGA-78-7540 TCGA-78-8655 
         678          215         1950         1972          881         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-86-8359 TCGA-86-8668 TCGA-86-8673 TCGA-86-A456 TCGA-86-A4P7 
          16           26           45          455           10           14 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6847 TCGA-91-6848 TCGA-91-8496 TCGA-91-A4BC 
         310           79          842          224          505           44 
TCGA-93-7348 TCGA-95-7039 TCGA-95-7562 TCGA-95-7944 TCGA-95-7947 TCGA-95-8494 
         127           34         1973          377          477           84 
TCGA-95-A4VN TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-8171 TCGA-97-8175 
         553         1332          775          181          107           87 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M7 TCGA-99-8025 
         147           15          148          115          271          427 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E5 
         170          154          114          287          282          578 
TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A7SV TCGA-MN-A4N1 TCGA-MN-A4N4 
         116            6          266          111          827         1175 
TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
          84         1967         1951         1957         1980         1951 
TCGA-MP-A4TC TCGA-MP-A4TF TCGA-MP-A4TK TCGA-S2-AA1A 
        1944         1970         1971          121 

$`AMP PEAK  9(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          462            6 
TCGA-55-8094 TCGA-55-8097 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8506 
           4           15           66          674          216           11 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-8619 
           8           15            3          146          536           49 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A4DF TCGA-62-8395 
          66          106           33           42           47         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-64-5815 TCGA-67-3773 TCGA-67-3774 
        1959           62         1305          866          427          385 
TCGA-67-6215 TCGA-67-6216 TCGA-69-7761 TCGA-69-7763 TCGA-69-7973 TCGA-69-8253 
         174          141          186          690          230          100 
TCGA-69-8254 TCGA-73-4666 TCGA-73-4677 TCGA-73-7498 TCGA-75-7027 TCGA-75-7031 
          77          800           38          621         1956         1965 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7156 TCGA-78-7158 
        1944         1093         1202          760         1961         1963 
TCGA-78-7159 TCGA-78-7162 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 
        1221         1940         1934         1937         1965         1949 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
        1944          327         1952          994         1949         1971 
TCGA-78-8660 TCGA-80-5607 TCGA-80-5608 TCGA-86-6851 TCGA-86-7711 TCGA-86-7714 
        1954         1965         1972         1959          630         1968 
TCGA-86-7954 TCGA-86-8054 TCGA-86-8056 TCGA-86-8076 TCGA-86-8281 TCGA-86-8358 
        1963          745         1963          489         1955           19 
TCGA-86-8585 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 TCGA-86-A4D0 
          35           34           18           15          405           30 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6836 TCGA-91-6840 
          39          323         1940           60          417          372 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 
          35          492          174           36          218          297 
TCGA-93-8067 TCGA-95-7043 TCGA-95-7567 TCGA-95-7948 TCGA-95-8039 TCGA-95-A4VK 
         186            2          568          476          830          121 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7941 TCGA-97-8172 
         605          964         1965         1932           22          182 
TCGA-97-8174 TCGA-97-A4M2 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 TCGA-J2-A4AG 
        1965          197          392          459           44          238 
TCGA-L4-A4E6 TCGA-L9-A743 TCGA-L9-A8F4 TCGA-MP-A4SV TCGA-MP-A4T4 TCGA-MP-A4T7 
         435          312          102         1946         1954         1954 
TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A5C7 
        1970          142         1955         1490 

  AMP PEAK  9(7P11.2) MUTATED AMP PEAK  9(7P11.2) WILD-TYPE 
                            1                             2 
  AMP PEAK  9(7P11.2) MUTATED AMP PEAK  9(7P11.2) WILD-TYPE 
                         6443                          2199 
  AMP PEAK  9(7P11.2) MUTATED AMP PEAK  9(7P11.2) WILD-TYPE 
                        451.5                         535.5 
[1] "1.0 - 6443.0 (451.5)" "2.0 - 2199.0 (535.5)"
[1] "hr=" "1.2"
D9V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK  9(7P11.2) MUTATED         4       55       70        27        38
  AMP PEAK  9(7P11.2) WILD-TYPE       1       61       62        22        32
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK  9(7P11.2) MUTATED           46          6       13
  AMP PEAK  9(7P11.2) WILD-TYPE         22          5       11
D9V3, multiclass
            clus
vv           AMP PEAK  9(7P11.2) MUTATED AMP PEAK  9(7P11.2) WILD-TYPE
  STAGE I                              4                             1
  STAGE IA                            55                            61
  STAGE IB                            70                            62
  STAGE IIA                           27                            22
  STAGE IIB                           38                            32
  STAGE IIIA                          46                            22
  STAGE IIIB                           6                             5
  STAGE IV                            13                            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(7P11.2) MUTATED    72 151  27   8
  AMP PEAK  9(7P11.2) WILD-TYPE  75 116  15  10
D9V4, multiclass
    clus
vv   AMP PEAK  9(7P11.2) MUTATED AMP PEAK  9(7P11.2) WILD-TYPE
  T1                          72                            75
  T2                         151                           116
  T3                          27                            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  9(7P11.2) MUTATED   149  49    54
  AMP PEAK  9(7P11.2) WILD-TYPE 152  42    20
D9V5, multiclass
       clus
vv      AMP PEAK  9(7P11.2) MUTATED AMP PEAK  9(7P11.2) WILD-TYPE
  N0                            149                           152
  N1                             49                            42
  N2+N3                          54                            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  9(7P11.2) MUTATED   175  10   1   1  69
  AMP PEAK  9(7P11.2) WILD-TYPE 151   8   0   3  54
D9V6, multiclass
     clus
vv    AMP PEAK  9(7P11.2) MUTATED AMP PEAK  9(7P11.2) WILD-TYPE
  M0                          175                           151
  M1                           10                             8
  M1A                           1                             0
  M1B                           1                             3
  MX                           69                            54
[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(7P11.2) MUTATED   143 116
  AMP PEAK  9(7P11.2) WILD-TYPE 112 105
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(7P11.2) MUTATED    143  116
  AMP PEAK  9(7P11.2) WILD-TYPE  112  105
        clus
vv       AMP PEAK  9(7P11.2) MUTATED AMP PEAK  9(7P11.2) WILD-TYPE
  FEMALE                         143                           112
  MALE                           116                           105
[1] 2 2
[1] FALSE
D9V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  AMP PEAK  9(7P11.2) MUTATED                            6
  AMP PEAK  9(7P11.2) WILD-TYPE                          9
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK  9(7P11.2) MUTATED                                  46
  AMP PEAK  9(7P11.2) WILD-TYPE                                48
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  9(7P11.2) MUTATED                                                  176
  AMP PEAK  9(7P11.2) WILD-TYPE                                                127
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK  9(7P11.2) MUTATED                                            4
  AMP PEAK  9(7P11.2) WILD-TYPE                                          1
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK  9(7P11.2) MUTATED                                              10
  AMP PEAK  9(7P11.2) WILD-TYPE                                             9
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK  9(7P11.2) MUTATED                                0
  AMP PEAK  9(7P11.2) WILD-TYPE                              2
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK  9(7P11.2) MUTATED                                    3
  AMP PEAK  9(7P11.2) WILD-TYPE                                  1
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK  9(7P11.2) MUTATED                              0
  AMP PEAK  9(7P11.2) WILD-TYPE                            2
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK  9(7P11.2) MUTATED                               8
  AMP PEAK  9(7P11.2) WILD-TYPE                            11
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK  9(7P11.2) MUTATED                                 0
  AMP PEAK  9(7P11.2) WILD-TYPE                               1
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK  9(7P11.2) MUTATED                                               4
  AMP PEAK  9(7P11.2) WILD-TYPE                                             1
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK  9(7P11.2) MUTATED                              2
  AMP PEAK  9(7P11.2) WILD-TYPE                            5
D9V9, multiclass
                                                    clus
vv                                                   AMP PEAK  9(7P11.2) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           46
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         176
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                   4
  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                                4
  MUCINOUS (COLLOID) CARCINOMA                                                 2
                                                    clus
vv                                                   AMP PEAK  9(7P11.2) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             48
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           127
  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"
D9V10, binary
                               cls
clus                              0   1
  AMP PEAK  9(7P11.2) MUTATED    10 249
  AMP PEAK  9(7P11.2) WILD-TYPE  11 206
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(7P11.2) MUTATED     10  249
  AMP PEAK  9(7P11.2) WILD-TYPE   11  206
     clus
vv    AMP PEAK  9(7P11.2) MUTATED AMP PEAK  9(7P11.2) WILD-TYPE
  NO                           10                            11
  YES                         249                           206
[1] 2 2
[1] FALSE
D9V11, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  9(7P11.2) MUTATED   172   6   3  12
  AMP PEAK  9(7P11.2) WILD-TYPE 155   6   1   9
D9V12, multiclass
    clus
vv   AMP PEAK  9(7P11.2) MUTATED AMP PEAK  9(7P11.2) WILD-TYPE
  R0                         172                           155
  R1                           6                             6
  R2                           3                             1
  RX                          12                             9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  9(7P11.2) MUTATED                                  1     4
  AMP PEAK  9(7P11.2) WILD-TYPE                                0     2
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  9(7P11.2) MUTATED                          24   200
  AMP PEAK  9(7P11.2) WILD-TYPE                        11   167
D9V13, multiclass
                                  clus
vv                                 AMP PEAK  9(7P11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 24
  WHITE                                                    200
                                  clus
vv                                 AMP PEAK  9(7P11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   11
  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"
D9V14, binary
                               cls
clus                              0   1
  AMP PEAK  9(7P11.2) MUTATED     4 195
  AMP PEAK  9(7P11.2) WILD-TYPE   3 150
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(7P11.2) MUTATED      4  195
  AMP PEAK  9(7P11.2) WILD-TYPE    3  150
                        clus
vv                       AMP PEAK  9(7P11.2) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         195
                        clus
vv                       AMP PEAK  9(7P11.2) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           150
[1] 2 2
[1] FALSE

Clustering(10) Variable = AMP PEAK 10(7Q31.2) MUTATION ANALYSIS
D10V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 10(7Q31.2) MUTATED   142  37
  AMP PEAK 10(7Q31.2) WILD-TYPE 187  50
  AMP PEAK 10(7Q31.2) MUTATED AMP PEAK 10(7Q31.2) WILD-TYPE 
                          179                           237 
  AMP PEAK 10(7Q31.2) MUTATED AMP PEAK 10(7Q31.2) WILD-TYPE 
                           37                            50 
$`AMP PEAK 10(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-49-AARQ TCGA-50-5045 TCGA-50-5049 TCGA-50-5066 TCGA-50-5930 
         522         6443         2174         2146          944          282 
TCGA-50-5935 TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 TCGA-53-A4EZ TCGA-55-1592 
         653          567          764          686          280          701 
TCGA-55-1596 TCGA-55-6543 TCGA-55-6712 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 
        1375            2           24         1239           25         1475 
TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 TCGA-55-6987 TCGA-55-7283 TCGA-55-7284 
          67         1826         1233         1170           35          121 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7726 TCGA-55-7907 TCGA-55-7910 TCGA-55-7994 
          40          705           39           16          197           31 
TCGA-55-7995 TCGA-55-8091 TCGA-55-8092 TCGA-55-8205 TCGA-55-8206 TCGA-55-8301 
           5          600           26           33           46           44 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8510 TCGA-55-8511 TCGA-55-8514 
          23           29            8          228            9          202 
TCGA-55-8616 TCGA-55-8620 TCGA-55-A490 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
          48           66           48            1           28            5 
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-64-5781 TCGA-67-3772 TCGA-69-7764 TCGA-69-7765 
        1126         1968         1559          573          414          165 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 
         184           70           89          214           61         1600 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
         711          912          800          131           40          164 
TCGA-73-7499 TCGA-78-7145 TCGA-78-7147 TCGA-78-7154 TCGA-78-7160 TCGA-78-7163 
         519         1973         1950         1948          678         1950 
TCGA-78-7220 TCGA-78-7536 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8655 
        1965         1949          881         1952         1949         1981 
TCGA-83-5908 TCGA-86-7701 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
         824           11          422          591         1963          508 
TCGA-86-8055 TCGA-86-8073 TCGA-86-8075 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
          10           13          479           16           19           26 
TCGA-86-8672 TCGA-86-8673 TCGA-86-A4P7 TCGA-91-6835 TCGA-91-6836 TCGA-91-6847 
          15          455           14           79          417          842 
TCGA-91-6848 TCGA-91-8496 TCGA-91-A4BC TCGA-93-7348 TCGA-95-7039 TCGA-95-7043 
         224          505           44          127           34            2 
TCGA-95-7562 TCGA-95-7944 TCGA-95-7947 TCGA-95-8494 TCGA-97-7553 TCGA-97-7554 
        1973          377          477           84         1332          775 
TCGA-97-7937 TCGA-97-8171 TCGA-97-8175 TCGA-97-8179 TCGA-97-8552 TCGA-99-8025 
         181          107           87           15          115          427 
TCGA-99-8033 TCGA-J2-8192 TCGA-L4-A4E5 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A7SV 
         170          154          578            6          266          111 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T8 
         827         1175         1946         1951         1954         1957 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TK TCGA-S2-AA1A 
        1980         1951         1944         1971          121 

$`AMP PEAK 10(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          462          100            6            4           47 
TCGA-55-8097 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8506 TCGA-55-8508 
          15           66          674          216           11           15 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-8615 TCGA-55-8619 TCGA-55-8621 
           3          146          536           15           49          106 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 TCGA-55-A4DF TCGA-55-A4DG 
          33           42           29         1952           47          162 
TCGA-62-8395 TCGA-62-8402 TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 TCGA-64-1677 
        1216         1445         2067         2199         1246          628 
TCGA-64-1678 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 
        1189         1959           62         1305          864          866 
TCGA-67-3770 TCGA-67-3771 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 
          31          610          427          385          174          141 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7973 TCGA-69-7980 
         422          202          186          690          230          382 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-73-4668 TCGA-73-4677 TCGA-73-7498 
         100           77          129          467           38          621 
TCGA-73-A9RS TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 TCGA-78-7146 
         305         1970         1967         1956         1965         1988 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7155 
        1944         1093         1963         1202          760         1957 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7161 TCGA-78-7162 TCGA-78-7166 
        1961         1963         1221          215         1940         1934 
TCGA-78-7167 TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 TCGA-78-7633 TCGA-78-8648 
        1937         1972         1944          327          994         1971 
TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 TCGA-86-6851 TCGA-86-7711 
        1954         1964         1965         1972         1959          630 
TCGA-86-7714 TCGA-86-8054 TCGA-86-8056 TCGA-86-8074 TCGA-86-8076 TCGA-86-8278 
        1968          745         1963           24          489          476 
TCGA-86-8279 TCGA-86-8281 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
         482         1955           35           45           34           18 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
         405           10           30           39          323         1940 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6840 TCGA-91-6849 TCGA-91-7771 TCGA-91-8497 
          60          310          372           35          492          174 
TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-8067 TCGA-95-7567 TCGA-95-7948 
          36          218          297          186          568          476 
TCGA-95-8039 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
         830          121          553          605          964         1965 
TCGA-97-7552 TCGA-97-7941 TCGA-97-8172 TCGA-97-8174 TCGA-97-8177 TCGA-97-8547 
        1932           22          182         1965          147          148 
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-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A743 
         287          282          238          435          116          312 
TCGA-L9-A8F4 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T7 TCGA-MP-A4TE TCGA-MP-A4TF 
         102           84         1967         1954         1970         1970 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A5C7 
         142         1955         1490 

  AMP PEAK 10(7Q31.2) MUTATED AMP PEAK 10(7Q31.2) WILD-TYPE 
                            1                             3 
  AMP PEAK 10(7Q31.2) MUTATED AMP PEAK 10(7Q31.2) WILD-TYPE 
                         6443                          2370 
  AMP PEAK 10(7Q31.2) MUTATED AMP PEAK 10(7Q31.2) WILD-TYPE 
                          477                           476 
[1] "1.0 - 6443.0 (477.0)" "3.0 - 2370.0 (476.0)"
[1] "hr=" "1.1"
D10V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 10(7Q31.2) MUTATED         3       45       56        22        28
  AMP PEAK 10(7Q31.2) WILD-TYPE       2       71       76        27        42
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 10(7Q31.2) MUTATED           37          2       12
  AMP PEAK 10(7Q31.2) WILD-TYPE         31          9       12
D10V3, multiclass
            clus
vv           AMP PEAK 10(7Q31.2) MUTATED AMP PEAK 10(7Q31.2) WILD-TYPE
  STAGE I                              3                             2
  STAGE IA                            45                            71
  STAGE IB                            56                            76
  STAGE IIA                           22                            27
  STAGE IIB                           28                            42
  STAGE IIIA                          37                            31
  STAGE IIIB                           2                             9
  STAGE IV                            12                            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 10(7Q31.2) MUTATED    56 122  20   5
  AMP PEAK 10(7Q31.2) WILD-TYPE  91 145  22  13
D10V4, multiclass
    clus
vv   AMP PEAK 10(7Q31.2) MUTATED AMP PEAK 10(7Q31.2) WILD-TYPE
  T1                          56                            91
  T2                         122                           145
  T3                          20                            22
  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 10(7Q31.2) MUTATED   119  39    40
  AMP PEAK 10(7Q31.2) WILD-TYPE 182  52    34
D10V5, multiclass
       clus
vv      AMP PEAK 10(7Q31.2) MUTATED AMP PEAK 10(7Q31.2) WILD-TYPE
  N0                            119                           182
  N1                             39                            52
  N2+N3                          40                            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 10(7Q31.2) MUTATED   135   9   1   1  57
  AMP PEAK 10(7Q31.2) WILD-TYPE 191   9   0   3  66
D10V6, multiclass
     clus
vv    AMP PEAK 10(7Q31.2) MUTATED AMP PEAK 10(7Q31.2) WILD-TYPE
  M0                          135                           191
  M1                            9                             9
  M1A                           1                             0
  M1B                           1                             3
  MX                           57                            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"
D10V7, binary
                               cls
clus                              0   1
  AMP PEAK 10(7Q31.2) MUTATED   107  98
  AMP PEAK 10(7Q31.2) WILD-TYPE 148 123
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7Q31.2) MUTATED    107   98
  AMP PEAK 10(7Q31.2) WILD-TYPE  148  123
        clus
vv       AMP PEAK 10(7Q31.2) MUTATED AMP PEAK 10(7Q31.2) WILD-TYPE
  FEMALE                         107                           148
  MALE                            98                           123
[1] 2 2
[1] FALSE
D10V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 10(7Q31.2) MUTATED                            4
  AMP PEAK 10(7Q31.2) WILD-TYPE                         11
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 10(7Q31.2) MUTATED                                  35
  AMP PEAK 10(7Q31.2) WILD-TYPE                                59
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 10(7Q31.2) MUTATED                                                  142
  AMP PEAK 10(7Q31.2) WILD-TYPE                                                161
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 10(7Q31.2) MUTATED                                            3
  AMP PEAK 10(7Q31.2) WILD-TYPE                                          2
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 10(7Q31.2) MUTATED                                              11
  AMP PEAK 10(7Q31.2) WILD-TYPE                                             8
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 10(7Q31.2) MUTATED                                0
  AMP PEAK 10(7Q31.2) WILD-TYPE                              2
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 10(7Q31.2) MUTATED                                    1
  AMP PEAK 10(7Q31.2) WILD-TYPE                                  3
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 10(7Q31.2) MUTATED                              0
  AMP PEAK 10(7Q31.2) WILD-TYPE                            2
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 10(7Q31.2) MUTATED                               7
  AMP PEAK 10(7Q31.2) WILD-TYPE                            12
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 10(7Q31.2) MUTATED                                 0
  AMP PEAK 10(7Q31.2) WILD-TYPE                               1
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 10(7Q31.2) MUTATED                                               1
  AMP PEAK 10(7Q31.2) WILD-TYPE                                             4
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 10(7Q31.2) MUTATED                              1
  AMP PEAK 10(7Q31.2) WILD-TYPE                            6
D10V9, multiclass
                                                    clus
vv                                                   AMP PEAK 10(7Q31.2) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           35
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         142
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                   3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                               11
  LUNG CLEAR CELL ADENOCARCINOMA                                               0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                           1
  LUNG MUCINOUS ADENOCARCINOMA                                                 0
  LUNG PAPILLARY ADENOCARCINOMA                                                7
  LUNG SIGNET RING ADENOCARCINOMA                                              0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                1
  MUCINOUS (COLLOID) CARCINOMA                                                 1
                                                    clus
vv                                                   AMP PEAK 10(7Q31.2) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                    11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             59
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           161
  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                                  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"
D10V10, binary
                               cls
clus                              0   1
  AMP PEAK 10(7Q31.2) MUTATED    11 194
  AMP PEAK 10(7Q31.2) WILD-TYPE  10 261
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7Q31.2) MUTATED     11  194
  AMP PEAK 10(7Q31.2) WILD-TYPE   10  261
     clus
vv    AMP PEAK 10(7Q31.2) MUTATED AMP PEAK 10(7Q31.2) WILD-TYPE
  NO                           11                            10
  YES                         194                           261
[1] 2 2
[1] FALSE
D10V11, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 10(7Q31.2) MUTATED   136   4   3  10
  AMP PEAK 10(7Q31.2) WILD-TYPE 191   8   1  11
D10V12, multiclass
    clus
vv   AMP PEAK 10(7Q31.2) MUTATED AMP PEAK 10(7Q31.2) WILD-TYPE
  R0                         136                           191
  R1                           4                             8
  R2                           3                             1
  RX                          10                            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 10(7Q31.2) MUTATED                                  0     3
  AMP PEAK 10(7Q31.2) WILD-TYPE                                1     3
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 10(7Q31.2) MUTATED                          18   163
  AMP PEAK 10(7Q31.2) WILD-TYPE                        17   204
D10V13, multiclass
                                  clus
vv                                 AMP PEAK 10(7Q31.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 18
  WHITE                                                    163
                                  clus
vv                                 AMP PEAK 10(7Q31.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        3
  BLACK OR AFRICAN AMERICAN                                   17
  WHITE                                                      204
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V14, binary
                               cls
clus                              0   1
  AMP PEAK 10(7Q31.2) MUTATED     1 155
  AMP PEAK 10(7Q31.2) WILD-TYPE   6 190
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7Q31.2) MUTATED      1  155
  AMP PEAK 10(7Q31.2) WILD-TYPE    6  190
                        clus
vv                       AMP PEAK 10(7Q31.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                         155
                        clus
vv                       AMP PEAK 10(7Q31.2) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           190
[1] 2 2
[1] FALSE

Clustering(11) Variable = AMP PEAK 11(8P11.23) MUTATION ANALYSIS
D11V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 11(8P11.23) MUTATED    91  22
  AMP PEAK 11(8P11.23) WILD-TYPE 238  65
  AMP PEAK 11(8P11.23) MUTATED AMP PEAK 11(8P11.23) WILD-TYPE 
                           113                            303 
  AMP PEAK 11(8P11.23) MUTATED AMP PEAK 11(8P11.23) WILD-TYPE 
                            22                             65 
$`AMP PEAK 11(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          705           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-95-A4VN TCGA-95-A4VP TCGA-97-7547 
         297            2          476          553          605         1965 
TCGA-97-7553 TCGA-97-8172 TCGA-97-8552 TCGA-97-A4M2 TCGA-99-8032 TCGA-99-8033 
        1332          182          115          197           44          170 
TCGA-L9-A444 TCGA-MP-A4T2 TCGA-MP-A4TA TCGA-MP-A4TE TCGA-MP-A4TH 
           6         1951         1951         1970          142 

$`AMP PEAK 11(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-49-AARQ TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 
         354         6443         2174         2146          785          944 
TCGA-50-5068 TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5942 
        1499          282         1091         2370          653          883 
TCGA-50-6597 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 
        1015          105         1971          424          280         1178 
TCGA-55-1595 TCGA-55-1596 TCGA-55-6543 TCGA-55-6712 TCGA-55-6972 TCGA-55-6980 
        1479         1375            2           24         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-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7725 TCGA-55-7726 
         121            4           95           40           39           39 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
          34           24           54          197           21            3 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
          31            5           33          462          100            6 
TCGA-55-8091 TCGA-55-8094 TCGA-55-8097 TCGA-55-8205 TCGA-55-8207 TCGA-55-8208 
         600            4           15           33           66          674 
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-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8615 TCGA-55-8616 
         228            9            3          146           15           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-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 
        1952            1           28           47          162         1216 
TCGA-62-8397 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46U TCGA-62-A46V TCGA-62-A472 
        1289         2696         1445         2067         2199          910 
TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
         628         1189         1686         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-69-7765 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
         186          165           70          382          100           77 
TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4670 
         214           61          711          912          800          131 
TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS TCGA-75-7025 TCGA-78-7146 TCGA-78-7147 
         621          519          305         1967         1988         1950 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7160 
        1963         1202          760         1948         1961          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-78-7540 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
        1944          327          881          994         1949         1971 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-7711 
        1981         1954         1964         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-86-8669 TCGA-86-8671 
        1955           19           26           45           34           18 
TCGA-86-8672 TCGA-86-8673 TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
          15          455           10           14           39          323 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 TCGA-91-6836 TCGA-91-6847 TCGA-91-6848 
        1940           60           79          417          842          224 
TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7348 
          35          505          174           44          218          127 
TCGA-93-8067 TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
         186           34         1973          568          377          477 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7552 TCGA-97-7554 
         830           84          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-L9-A50W TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 
         435          116          266          312          111          102 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T4 
         827         1175           84         1946         1967         1954 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TC TCGA-MP-A4TF TCGA-MP-A4TI 
        1954         1957         1980         1944         1970         1955 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-S2-AA1A 
        1971         1490          121 

  AMP PEAK 11(8P11.23) MUTATED AMP PEAK 11(8P11.23) WILD-TYPE 
                             2                              1 
  AMP PEAK 11(8P11.23) MUTATED AMP PEAK 11(8P11.23) WILD-TYPE 
                          1986                           6443 
  AMP PEAK 11(8P11.23) MUTATED AMP PEAK 11(8P11.23) WILD-TYPE 
                           553                            448 
[1] "2.0 - 1986.0 (553.0)" "1.0 - 6443.0 (448.0)"
[1] "hr=" "1"  
D11V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 11(8P11.23) MUTATED         2       33       40        12        14
  AMP PEAK 11(8P11.23) WILD-TYPE       3       83       92        37        56
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 11(8P11.23) MUTATED           17          3        6
  AMP PEAK 11(8P11.23) WILD-TYPE         51          8       18
D11V3, multiclass
            clus
vv           AMP PEAK 11(8P11.23) MUTATED AMP PEAK 11(8P11.23) WILD-TYPE
  STAGE I                               2                              3
  STAGE IA                             33                             83
  STAGE IB                             40                             92
  STAGE IIA                            12                             37
  STAGE IIB                            14                             56
  STAGE IIIA                           17                             51
  STAGE IIIB                            3                              8
  STAGE IV                              6                             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 11(8P11.23) MUTATED    39  75   7   4
  AMP PEAK 11(8P11.23) WILD-TYPE 108 192  35  14
D11V4, multiclass
    clus
vv   AMP PEAK 11(8P11.23) MUTATED AMP PEAK 11(8P11.23) WILD-TYPE
  T1                           39                            108
  T2                           75                            192
  T3                            7                             35
  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 11(8P11.23) MUTATED    82  24    18
  AMP PEAK 11(8P11.23) WILD-TYPE 219  67    56
D11V5, multiclass
       clus
vv      AMP PEAK 11(8P11.23) MUTATED AMP PEAK 11(8P11.23) WILD-TYPE
  N0                              82                            219
  N1                              24                             67
  N2+N3                           18                             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 11(8P11.23) MUTATED    87   5   0   1  34
  AMP PEAK 11(8P11.23) WILD-TYPE 239  13   1   3  89
D11V6, multiclass
     clus
vv    AMP PEAK 11(8P11.23) MUTATED AMP PEAK 11(8P11.23) WILD-TYPE
  M0                            87                            239
  M1                             5                             13
  M1A                            0                              1
  M1B                            1                              3
  MX                            34                             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"
D11V7, binary
                                cls
clus                               0   1
  AMP PEAK 11(8P11.23) MUTATED    60  67
  AMP PEAK 11(8P11.23) WILD-TYPE 195 154
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(8P11.23) MUTATED     60   67
  AMP PEAK 11(8P11.23) WILD-TYPE  195  154
        clus
vv       AMP PEAK 11(8P11.23) MUTATED AMP PEAK 11(8P11.23) WILD-TYPE
  FEMALE                           60                            195
  MALE                             67                            154
[1] 2 2
[1] FALSE
D11V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 11(8P11.23) MUTATED                            6
  AMP PEAK 11(8P11.23) WILD-TYPE                          9
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 11(8P11.23) MUTATED                                  31
  AMP PEAK 11(8P11.23) WILD-TYPE                                63
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 11(8P11.23) MUTATED                                                   76
  AMP PEAK 11(8P11.23) WILD-TYPE                                                227
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 11(8P11.23) MUTATED                                            0
  AMP PEAK 11(8P11.23) WILD-TYPE                                          5
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 11(8P11.23) MUTATED                                               4
  AMP PEAK 11(8P11.23) WILD-TYPE                                            15
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 11(8P11.23) MUTATED                                0
  AMP PEAK 11(8P11.23) WILD-TYPE                              2
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 11(8P11.23) MUTATED                                    1
  AMP PEAK 11(8P11.23) WILD-TYPE                                  3
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 11(8P11.23) MUTATED                              0
  AMP PEAK 11(8P11.23) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 11(8P11.23) MUTATED                               5
  AMP PEAK 11(8P11.23) WILD-TYPE                            14
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 11(8P11.23) MUTATED                                 0
  AMP PEAK 11(8P11.23) WILD-TYPE                               1
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 11(8P11.23) MUTATED                                               3
  AMP PEAK 11(8P11.23) WILD-TYPE                                             2
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 11(8P11.23) MUTATED                              1
  AMP PEAK 11(8P11.23) WILD-TYPE                            6
D11V9, multiclass
                                                    clus
vv                                                   AMP PEAK 11(8P11.23) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    6
  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                                 3
  MUCINOUS (COLLOID) CARCINOMA                                                  1
                                                    clus
vv                                                   AMP PEAK 11(8P11.23) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              63
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            227
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      5
  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"
D11V10, binary
                                cls
clus                               0   1
  AMP PEAK 11(8P11.23) MUTATED     7 120
  AMP PEAK 11(8P11.23) WILD-TYPE  14 335
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(8P11.23) MUTATED      7  120
  AMP PEAK 11(8P11.23) WILD-TYPE   14  335
     clus
vv    AMP PEAK 11(8P11.23) MUTATED AMP PEAK 11(8P11.23) WILD-TYPE
  NO                             7                             14
  YES                          120                            335
[1] 2 2
[1] FALSE
D11V11, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 11(8P11.23) MUTATED    85   5   1   3
  AMP PEAK 11(8P11.23) WILD-TYPE 242   7   3  18
D11V12, multiclass
    clus
vv   AMP PEAK 11(8P11.23) MUTATED AMP PEAK 11(8P11.23) WILD-TYPE
  R0                           85                            242
  R1                            5                              7
  R2                            1                              3
  RX                            3                             18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 11(8P11.23) MUTATED                                  1     0
  AMP PEAK 11(8P11.23) WILD-TYPE                                0     6
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 11(8P11.23) MUTATED                           5   104
  AMP PEAK 11(8P11.23) WILD-TYPE                        30   263
D11V13, multiclass
                                  clus
vv                                 AMP PEAK 11(8P11.23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   5
  WHITE                                                     104
                                  clus
vv                                 AMP PEAK 11(8P11.23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         6
  BLACK OR AFRICAN AMERICAN                                    30
  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"
D11V14, binary
                                cls
clus                               0   1
  AMP PEAK 11(8P11.23) MUTATED     3  87
  AMP PEAK 11(8P11.23) WILD-TYPE   4 258
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(8P11.23) MUTATED      3   87
  AMP PEAK 11(8P11.23) WILD-TYPE    4  258
                        clus
vv                       AMP PEAK 11(8P11.23) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           87
                        clus
vv                       AMP PEAK 11(8P11.23) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            258
[1] 2 2
[1] FALSE

Clustering(12) Variable = AMP PEAK 12(8P11.21) MUTATION ANALYSIS
D12V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 12(8P11.21) MUTATED   111  30
  AMP PEAK 12(8P11.21) WILD-TYPE 218  57
  AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE 
                           141                            275 
  AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE 
                            30                             57 
$`AMP PEAK 12(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          705           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-95-A4VN TCGA-95-A4VP TCGA-97-7547 TCGA-97-7553 TCGA-97-7554 
         476          553          605         1965         1332          775 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M2 TCGA-99-8032 
         107          182           15          115          197           44 
TCGA-99-8033 TCGA-L9-A444 TCGA-MN-A4N5 TCGA-MP-A4T2 TCGA-MP-A4TA TCGA-MP-A4TE 
         170            6           84         1951         1951         1970 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TK 
        1970          142         1971 

$`AMP PEAK 12(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-49-AARQ TCGA-50-5045 TCGA-50-5049 
         890          522          354         6443         2174         2146 
TCGA-50-5055 TCGA-50-5068 TCGA-50-5930 TCGA-50-5932 TCGA-50-5935 TCGA-50-5942 
         785         1499          282         1091          653          883 
TCGA-50-6597 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-55-1594 
        1015          105         1986         1971          424         1178 
TCGA-55-1595 TCGA-55-1596 TCGA-55-6543 TCGA-55-6712 TCGA-55-6972 TCGA-55-6980 
        1479         1375            2           24         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-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7725 TCGA-55-7726 
         121            4           95           40           39           39 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
          34           24           54          197           21            3 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
          31            5           33          462          100            6 
TCGA-55-8091 TCGA-55-8097 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8302 
         600           15           66          674          216           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-55-8615 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Z 
         146           15           49          106           33           29 
TCGA-55-A490 TCGA-55-A492 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8397 TCGA-62-8399 
          48            1           47          162         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-64-5778 TCGA-64-5781 TCGA-64-5815 
        1686         1968         1959         1305         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-69-7761 TCGA-69-7765 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 
         422          186          165           70          382          100 
TCGA-69-8254 TCGA-69-A59K TCGA-71-6725 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
          77          214           61          912          800          467 
TCGA-73-4670 TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS TCGA-75-7025 TCGA-78-7146 
         131          621          519          305         1967         1988 
TCGA-78-7147 TCGA-78-7150 TCGA-78-7152 TCGA-78-7154 TCGA-78-7156 TCGA-78-7160 
        1950         1963         1202         1948         1961          678 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7537 
         215         1940         1950         1934         1937         1944 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
         327          881          994         1949         1971         1981 
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-86-8671 TCGA-86-8672 TCGA-86-A456 TCGA-86-A4P8 TCGA-91-6829 
          45           18           15           10           39         1940 
TCGA-91-6830 TCGA-91-6835 TCGA-91-6847 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
          60           79          842           35          492          505 
TCGA-91-8497 TCGA-91-A4BD TCGA-93-7348 TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 
         174          218          127           34         1973          568 
TCGA-95-7944 TCGA-95-7947 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-97-7546 
         377          477          830           84          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-L9-A50W TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 
         116          266          312          111          102          827 
TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 
        1175         1946         1967         1954         1954         1957 
TCGA-MP-A4T9 TCGA-MP-A4TC TCGA-MP-A4TI TCGA-MP-A5C7 TCGA-S2-AA1A 
        1980         1944         1955         1490          121 

  AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE 
                             2                              1 
  AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE 
                          2370                           6443 
  AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE 
                           508                            466 
[1] "2.0 - 2370.0 (508.0)" "1.0 - 6443.0 (466.0)"
[1] "hr=" "1.1"
D12V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 12(8P11.21) MUTATED         2       38       53        16        18
  AMP PEAK 12(8P11.21) WILD-TYPE       3       78       79        33        52
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 12(8P11.21) MUTATED           23          5        8
  AMP PEAK 12(8P11.21) WILD-TYPE         45          6       16
D12V3, multiclass
            clus
vv           AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE
  STAGE I                               2                              3
  STAGE IA                             38                             78
  STAGE IB                             53                             79
  STAGE IIA                            16                             33
  STAGE IIB                            18                             52
  STAGE IIIA                           23                             45
  STAGE IIIB                            5                              6
  STAGE IV                              8                             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 12(8P11.21) MUTATED    44 100  10   7
  AMP PEAK 12(8P11.21) WILD-TYPE 103 167  32  11
D12V4, multiclass
    clus
vv   AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE
  T1                           44                            103
  T2                          100                            167
  T3                           10                             32
  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 12(8P11.21) MUTATED   108  25    27
  AMP PEAK 12(8P11.21) WILD-TYPE 193  66    47
D12V5, multiclass
       clus
vv      AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE
  N0                             108                            193
  N1                              25                             66
  N2+N3                           27                             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 12(8P11.21) MUTATED   112   5   1   2  43
  AMP PEAK 12(8P11.21) WILD-TYPE 214  13   0   2  80
D12V6, multiclass
     clus
vv    AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE
  M0                           112                            214
  M1                             5                             13
  M1A                            1                              0
  M1B                            2                              2
  MX                            43                             80
[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(8P11.21) MUTATED    73  90
  AMP PEAK 12(8P11.21) WILD-TYPE 182 131
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8P11.21) MUTATED     73   90
  AMP PEAK 12(8P11.21) WILD-TYPE  182  131
        clus
vv       AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE
  FEMALE                           73                            182
  MALE                             90                            131
[1] 2 2
[1] FALSE
D12V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 12(8P11.21) MUTATED                            9
  AMP PEAK 12(8P11.21) WILD-TYPE                          6
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 12(8P11.21) MUTATED                                  34
  AMP PEAK 12(8P11.21) WILD-TYPE                                60
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 12(8P11.21) MUTATED                                                  104
  AMP PEAK 12(8P11.21) WILD-TYPE                                                199
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 12(8P11.21) MUTATED                                            0
  AMP PEAK 12(8P11.21) WILD-TYPE                                          5
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 12(8P11.21) MUTATED                                               5
  AMP PEAK 12(8P11.21) WILD-TYPE                                            14
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 12(8P11.21) MUTATED                                0
  AMP PEAK 12(8P11.21) WILD-TYPE                              2
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 12(8P11.21) MUTATED                                    0
  AMP PEAK 12(8P11.21) WILD-TYPE                                  4
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 12(8P11.21) MUTATED                              0
  AMP PEAK 12(8P11.21) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 12(8P11.21) MUTATED                               6
  AMP PEAK 12(8P11.21) WILD-TYPE                            13
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 12(8P11.21) MUTATED                                 1
  AMP PEAK 12(8P11.21) WILD-TYPE                               0
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 12(8P11.21) MUTATED                                               4
  AMP PEAK 12(8P11.21) WILD-TYPE                                             1
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 12(8P11.21) MUTATED                              0
  AMP PEAK 12(8P11.21) WILD-TYPE                            7
D12V9, multiclass
                                                    clus
vv                                                   AMP PEAK 12(8P11.21) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    9
  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                                 4
  MUCINOUS (COLLOID) CARCINOMA                                                  0
                                                    clus
vv                                                   AMP PEAK 12(8P11.21) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              60
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            199
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  14
  LUNG CLEAR CELL ADENOCARCINOMA                                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              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"
D12V10, binary
                                cls
clus                               0   1
  AMP PEAK 12(8P11.21) MUTATED     9 154
  AMP PEAK 12(8P11.21) WILD-TYPE  12 301
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8P11.21) MUTATED      9  154
  AMP PEAK 12(8P11.21) WILD-TYPE   12  301
     clus
vv    AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE
  NO                             9                             12
  YES                          154                            301
[1] 2 2
[1] FALSE
D12V11, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 12(8P11.21) MUTATED   110   5   1   6
  AMP PEAK 12(8P11.21) WILD-TYPE 217   7   3  15
D12V12, multiclass
    clus
vv   AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE
  R0                          110                            217
  R1                            5                              7
  R2                            1                              3
  RX                            6                             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 12(8P11.21) MUTATED                                  0     2
  AMP PEAK 12(8P11.21) WILD-TYPE                                1     4
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 12(8P11.21) MUTATED                           8   128
  AMP PEAK 12(8P11.21) WILD-TYPE                        27   239
D12V13, multiclass
                                  clus
vv                                 AMP PEAK 12(8P11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   8
  WHITE                                                     128
                                  clus
vv                                 AMP PEAK 12(8P11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    27
  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"
D12V14, binary
                                cls
clus                               0   1
  AMP PEAK 12(8P11.21) MUTATED     3 113
  AMP PEAK 12(8P11.21) WILD-TYPE   4 232
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8P11.21) MUTATED      3  113
  AMP PEAK 12(8P11.21) WILD-TYPE    4  232
                        clus
vv                       AMP PEAK 12(8P11.21) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          113
                        clus
vv                       AMP PEAK 12(8P11.21) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            232
[1] 2 2
[1] FALSE

Clustering(13) Variable = AMP PEAK 13(8Q11.1) MUTATION ANALYSIS
D13V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 13(8Q11.1) MUTATED   151  42
  AMP PEAK 13(8Q11.1) WILD-TYPE 178  45
  AMP PEAK 13(8Q11.1) MUTATED AMP PEAK 13(8Q11.1) WILD-TYPE 
                          193                           223 
  AMP PEAK 13(8Q11.1) MUTATED AMP PEAK 13(8Q11.1) WILD-TYPE 
                           42                            45 
$`AMP PEAK 13(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 
         705           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-95-8494 TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7547 TCGA-97-7553 
         476           84          553          605         1965         1332 
TCGA-97-7554 TCGA-97-8171 TCGA-97-8172 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M2 
         775          107          182           15          115          197 
TCGA-99-8025 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8194 TCGA-L4-A4E5 TCGA-L9-A443 
         427           44          170          114          578          116 
TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A743 TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MN-A4N5 
           6          266          312          102         1175           84 
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 13(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-49-AARQ TCGA-50-5045 TCGA-50-5055 TCGA-50-5930 TCGA-50-5932 TCGA-50-5935 
        6443         2174          785          282         1091          653 
TCGA-50-5942 TCGA-50-6597 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-55-1594 
         883         1015          105         1986         1971         1178 
TCGA-55-6543 TCGA-55-6980 TCGA-55-6983 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 
           2           67         1826         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-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7910 
          39           39           34           24           54          197 
TCGA-55-7911 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
          21            5           33          462          100            6 
TCGA-55-8091 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8302 TCGA-55-8505 
         600           66          674          216           23           29 
TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8619 
          11           15          228            3          146           49 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A492 TCGA-55-A4DF TCGA-62-8395 TCGA-62-8397 
         106           33            1           47         1216         1289 
TCGA-62-8399 TCGA-62-A46U TCGA-62-A46V TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 
        2696         2067         2199         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-69-7760 TCGA-69-7761 
         427          385          174          141          202          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-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-A9RS TCGA-75-7025 TCGA-78-7145 
         912          800          467          305         1967         1973 
TCGA-78-7147 TCGA-78-7152 TCGA-78-7154 TCGA-78-7156 TCGA-78-7160 TCGA-78-7161 
        1950         1202         1948         1961          678          215 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7537 TCGA-78-7540 
        1940         1950         1934         1937         1944          881 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-83-5908 TCGA-86-7711 
         994         1949         1971         1981          824          630 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
         422         1968          591           10         1963           13 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8281 TCGA-86-8358 TCGA-86-8668 
         479          489          476         1955           19           45 
TCGA-86-8671 TCGA-86-8672 TCGA-86-A456 TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 
          18           15           10           39         1940           60 
TCGA-91-6835 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
          79          224           35          492          505          174 
TCGA-91-8499 TCGA-91-A4BD TCGA-93-7348 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
          36          218          127            2         1973          568 
TCGA-95-7944 TCGA-95-7947 TCGA-95-8039 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7552 
         377          477          830          121          964         1932 
TCGA-97-7937 TCGA-97-7941 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 TCGA-97-8547 
         181           22         1965           87          147          148 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8028 TCGA-J2-8192 TCGA-J2-A4AD TCGA-J2-A4AE 
         271          392          459          154          287          282 
TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A7SV TCGA-MN-A4N1 TCGA-MP-A4SV TCGA-MP-A4SW 
         238          435          111          827         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 
TCGA-S2-AA1A 
         121 

  AMP PEAK 13(8Q11.1) MUTATED AMP PEAK 13(8Q11.1) WILD-TYPE 
                            3                             1 
  AMP PEAK 13(8Q11.1) MUTATED AMP PEAK 13(8Q11.1) WILD-TYPE 
                         2370                          6443 
  AMP PEAK 13(8Q11.1) MUTATED AMP PEAK 13(8Q11.1) WILD-TYPE 
                          476                           476 
[1] "3.0 - 2370.0 (476.0)" "1.0 - 6443.0 (476.0)"
[1] "hr=" "1.3"
D13V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 13(8Q11.1) MUTATED         3       48       67        26        24
  AMP PEAK 13(8Q11.1) WILD-TYPE       2       68       65        23        46
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 13(8Q11.1) MUTATED           32          7       12
  AMP PEAK 13(8Q11.1) WILD-TYPE         36          4       12
D13V3, multiclass
            clus
vv           AMP PEAK 13(8Q11.1) MUTATED AMP PEAK 13(8Q11.1) WILD-TYPE
  STAGE I                              3                             2
  STAGE IA                            48                            68
  STAGE IB                            67                            65
  STAGE IIA                           26                            23
  STAGE IIB                           24                            46
  STAGE IIIA                          32                            36
  STAGE IIIB                           7                             4
  STAGE IV                            12                            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 13(8Q11.1) MUTATED    62 134  15   7
  AMP PEAK 13(8Q11.1) WILD-TYPE  85 133  27  11
D13V4, multiclass
    clus
vv   AMP PEAK 13(8Q11.1) MUTATED AMP PEAK 13(8Q11.1) WILD-TYPE
  T1                          62                            85
  T2                         134                           133
  T3                          15                            27
  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 13(8Q11.1) MUTATED   140  37    38
  AMP PEAK 13(8Q11.1) WILD-TYPE 161  54    36
D13V5, multiclass
       clus
vv      AMP PEAK 13(8Q11.1) MUTATED AMP PEAK 13(8Q11.1) WILD-TYPE
  N0                            140                           161
  N1                             37                            54
  N2+N3                          38                            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 13(8Q11.1) MUTATED   147   8   1   3  58
  AMP PEAK 13(8Q11.1) WILD-TYPE 179  10   0   1  65
D13V6, multiclass
     clus
vv    AMP PEAK 13(8Q11.1) MUTATED AMP PEAK 13(8Q11.1) WILD-TYPE
  M0                          147                           179
  M1                            8                            10
  M1A                           1                             0
  M1B                           3                             1
  MX                           58                            65
[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(8Q11.1) MUTATED   111 108
  AMP PEAK 13(8Q11.1) WILD-TYPE 144 113
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(8Q11.1) MUTATED    111  108
  AMP PEAK 13(8Q11.1) WILD-TYPE  144  113
        clus
vv       AMP PEAK 13(8Q11.1) MUTATED AMP PEAK 13(8Q11.1) WILD-TYPE
  FEMALE                         111                           144
  MALE                           108                           113
[1] 2 2
[1] FALSE
D13V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 13(8Q11.1) MUTATED                            9
  AMP PEAK 13(8Q11.1) WILD-TYPE                          6
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 13(8Q11.1) MUTATED                                  42
  AMP PEAK 13(8Q11.1) WILD-TYPE                                52
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 13(8Q11.1) MUTATED                                                  147
  AMP PEAK 13(8Q11.1) WILD-TYPE                                                156
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 13(8Q11.1) MUTATED                                            0
  AMP PEAK 13(8Q11.1) WILD-TYPE                                          5
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 13(8Q11.1) MUTATED                                               8
  AMP PEAK 13(8Q11.1) WILD-TYPE                                            11
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 13(8Q11.1) MUTATED                                1
  AMP PEAK 13(8Q11.1) WILD-TYPE                              1
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 13(8Q11.1) MUTATED                                    0
  AMP PEAK 13(8Q11.1) WILD-TYPE                                  4
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 13(8Q11.1) MUTATED                              0
  AMP PEAK 13(8Q11.1) WILD-TYPE                            2
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 13(8Q11.1) MUTATED                               7
  AMP PEAK 13(8Q11.1) WILD-TYPE                            12
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 13(8Q11.1) MUTATED                                 1
  AMP PEAK 13(8Q11.1) WILD-TYPE                               0
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 13(8Q11.1) MUTATED                                               4
  AMP PEAK 13(8Q11.1) WILD-TYPE                                             1
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 13(8Q11.1) MUTATED                              0
  AMP PEAK 13(8Q11.1) WILD-TYPE                            7
D13V9, multiclass
                                                    clus
vv                                                   AMP PEAK 13(8Q11.1) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           42
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         147
  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                                4
  MUCINOUS (COLLOID) CARCINOMA                                                 0
                                                    clus
vv                                                   AMP PEAK 13(8Q11.1) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             52
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           156
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     5
  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"
D13V10, binary
                               cls
clus                              0   1
  AMP PEAK 13(8Q11.1) MUTATED    11 208
  AMP PEAK 13(8Q11.1) WILD-TYPE  10 247
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(8Q11.1) MUTATED     11  208
  AMP PEAK 13(8Q11.1) WILD-TYPE   10  247
     clus
vv    AMP PEAK 13(8Q11.1) MUTATED AMP PEAK 13(8Q11.1) WILD-TYPE
  NO                           11                            10
  YES                         208                           247
[1] 2 2
[1] FALSE
D13V11, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 13(8Q11.1) MUTATED   153   7   1   7
  AMP PEAK 13(8Q11.1) WILD-TYPE 174   5   3  14
D13V12, multiclass
    clus
vv   AMP PEAK 13(8Q11.1) MUTATED AMP PEAK 13(8Q11.1) WILD-TYPE
  R0                         153                           174
  R1                           7                             5
  R2                           1                             3
  RX                           7                            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 13(8Q11.1) MUTATED                                  0     5
  AMP PEAK 13(8Q11.1) WILD-TYPE                                1     1
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 13(8Q11.1) MUTATED                          14   172
  AMP PEAK 13(8Q11.1) WILD-TYPE                        21   195
D13V13, multiclass
                                  clus
vv                                 AMP PEAK 13(8Q11.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      5
  BLACK OR AFRICAN AMERICAN                                 14
  WHITE                                                    172
                                  clus
vv                                 AMP PEAK 13(8Q11.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                   21
  WHITE                                                      195
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V14, binary
                               cls
clus                              0   1
  AMP PEAK 13(8Q11.1) MUTATED     3 160
  AMP PEAK 13(8Q11.1) WILD-TYPE   4 185
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(8Q11.1) MUTATED      3  160
  AMP PEAK 13(8Q11.1) WILD-TYPE    4  185
                        clus
vv                       AMP PEAK 13(8Q11.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                         160
                        clus
vv                       AMP PEAK 13(8Q11.1) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           185
[1] 2 2
[1] FALSE

Clustering(14) Variable = AMP PEAK 14(8Q24.21) MUTATION ANALYSIS
D14V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 14(8Q24.21) MUTATED   199  62
  AMP PEAK 14(8Q24.21) WILD-TYPE 130  25
  AMP PEAK 14(8Q24.21) MUTATED AMP PEAK 14(8Q24.21) WILD-TYPE 
                           261                            155 
  AMP PEAK 14(8Q24.21) MUTATED AMP PEAK 14(8Q24.21) WILD-TYPE 
                            62                             25 
$`AMP PEAK 14(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          705 
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-95-7562 TCGA-95-7567 TCGA-95-7948 TCGA-95-8494 TCGA-95-A4VN TCGA-95-A4VP 
        1973          568          476           84          553          605 
TCGA-97-7547 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-8171 TCGA-97-8172 
        1965         1332          775          181          107          182 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 TCGA-99-8025 TCGA-99-8028 
          15          148          115          197          427          459 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L9-A443 
          44          170          114          287          282          116 
TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 
           6          266          312          111          102          827 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 
        1175           84         1946         1967         1951         1954 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TF 
        1954         1957         1951         1944         1970         1970 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
         142         1955         1971 

$`AMP PEAK 14(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-49-AARQ TCGA-50-5045 TCGA-50-5055 TCGA-50-5930 TCGA-50-5935 
         890         6443         2174          785          282          653 
TCGA-50-5942 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-55-1594 TCGA-55-6980 
         883          105         1986         1971         1178           67 
TCGA-55-6983 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
        1826         1170           18           35          121            6 
TCGA-55-7573 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7910 TCGA-55-7995 
           4           34           24           54          197            5 
TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
         462            6          600           66          674          216 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 
          29           11           15          228            3          146 
TCGA-55-8619 TCGA-55-A48X TCGA-55-A492 TCGA-55-A4DF TCGA-62-8397 TCGA-62-8399 
          49           33            1           47         1289         2696 
TCGA-62-A46U TCGA-62-A46V TCGA-64-1679 TCGA-64-1681 TCGA-64-5778 TCGA-64-5781 
        2067         2199         1686         1968         1305         1559 
TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 
         866          573          427          385          174          141 
TCGA-69-7761 TCGA-69-7765 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
         186          165           70          382          100           77 
TCGA-73-4666 TCGA-73-A9RS TCGA-75-7025 TCGA-78-7150 TCGA-78-7156 TCGA-78-7160 
         800          305         1967         1963         1961          678 
TCGA-78-7163 TCGA-78-7537 TCGA-78-7540 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
        1950         1944          881          994         1949         1971 
TCGA-78-8655 TCGA-86-7953 TCGA-86-8055 TCGA-86-8056 TCGA-86-8075 TCGA-86-8076 
        1981          591           10         1963          479          489 
TCGA-86-8278 TCGA-86-8281 TCGA-86-8668 TCGA-86-8671 TCGA-86-A4P8 TCGA-91-6829 
         476         1955           45           18           39         1940 
TCGA-91-6830 TCGA-91-6835 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 
          60           79          224           35          505          174 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7348 TCGA-95-7039 TCGA-95-7944 TCGA-95-7947 
          44          218          127           34          377          477 
TCGA-95-8039 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7552 TCGA-97-7941 TCGA-97-8174 
         830          121          964         1932           22         1965 
TCGA-97-8175 TCGA-97-8177 TCGA-97-A4M7 TCGA-99-7458 TCGA-J2-8192 TCGA-J2-A4AG 
          87          147          271          392          154          238 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MP-A4T9 TCGA-MP-A5C7 TCGA-S2-AA1A 
         578          435         1980         1490          121 

  AMP PEAK 14(8Q24.21) MUTATED AMP PEAK 14(8Q24.21) WILD-TYPE 
                             2                              1 
  AMP PEAK 14(8Q24.21) MUTATED AMP PEAK 14(8Q24.21) WILD-TYPE 
                          2370                           6443 
  AMP PEAK 14(8Q24.21) MUTATED AMP PEAK 14(8Q24.21) WILD-TYPE 
                           492                            462 
[1] "2.0 - 2370.0 (492.0)" "1.0 - 6443.0 (462.0)"
[1] "hr=" "1.8"
D14V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 14(8Q24.21) MUTATED         2       67       90        32        43
  AMP PEAK 14(8Q24.21) WILD-TYPE       3       49       42        17        27
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 14(8Q24.21) MUTATED           44          8       17
  AMP PEAK 14(8Q24.21) WILD-TYPE         24          3        7
D14V3, multiclass
            clus
vv           AMP PEAK 14(8Q24.21) MUTATED AMP PEAK 14(8Q24.21) WILD-TYPE
  STAGE I                               2                              3
  STAGE IA                             67                             49
  STAGE IB                             90                             42
  STAGE IIA                            32                             17
  STAGE IIB                            43                             27
  STAGE IIIA                           44                             24
  STAGE IIIB                            8                              3
  STAGE IV                             17                              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 14(8Q24.21) MUTATED    80 185  26  10
  AMP PEAK 14(8Q24.21) WILD-TYPE  67  82  16   8
D14V4, multiclass
    clus
vv   AMP PEAK 14(8Q24.21) MUTATED AMP PEAK 14(8Q24.21) WILD-TYPE
  T1                           80                             67
  T2                          185                             82
  T3                           26                             16
  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 14(8Q24.21) MUTATED   190  57    50
  AMP PEAK 14(8Q24.21) WILD-TYPE 111  34    24
D14V5, multiclass
       clus
vv      AMP PEAK 14(8Q24.21) MUTATED AMP PEAK 14(8Q24.21) WILD-TYPE
  N0                             190                            111
  N1                              57                             34
  N2+N3                           50                             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 14(8Q24.21) MUTATED   211  13   1   3  73
  AMP PEAK 14(8Q24.21) WILD-TYPE 115   5   0   1  50
D14V6, multiclass
     clus
vv    AMP PEAK 14(8Q24.21) MUTATED AMP PEAK 14(8Q24.21) WILD-TYPE
  M0                           211                            115
  M1                            13                              5
  M1A                            1                              0
  M1B                            3                              1
  MX                            73                             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"
D14V7, binary
                                cls
clus                               0   1
  AMP PEAK 14(8Q24.21) MUTATED   159 144
  AMP PEAK 14(8Q24.21) WILD-TYPE  96  77
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(8Q24.21) MUTATED    159  144
  AMP PEAK 14(8Q24.21) WILD-TYPE   96   77
        clus
vv       AMP PEAK 14(8Q24.21) MUTATED AMP PEAK 14(8Q24.21) WILD-TYPE
  FEMALE                          159                             96
  MALE                            144                             77
[1] 2 2
[1] FALSE
D14V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 14(8Q24.21) MUTATED                           10
  AMP PEAK 14(8Q24.21) WILD-TYPE                          5
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 14(8Q24.21) MUTATED                                  55
  AMP PEAK 14(8Q24.21) WILD-TYPE                                39
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 14(8Q24.21) MUTATED                                                  205
  AMP PEAK 14(8Q24.21) WILD-TYPE                                                 98
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 14(8Q24.21) MUTATED                                            1
  AMP PEAK 14(8Q24.21) WILD-TYPE                                          4
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 14(8Q24.21) MUTATED                                              11
  AMP PEAK 14(8Q24.21) WILD-TYPE                                             8
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 14(8Q24.21) MUTATED                                1
  AMP PEAK 14(8Q24.21) WILD-TYPE                              1
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 14(8Q24.21) MUTATED                                    3
  AMP PEAK 14(8Q24.21) WILD-TYPE                                  1
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 14(8Q24.21) MUTATED                              0
  AMP PEAK 14(8Q24.21) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 14(8Q24.21) MUTATED                              12
  AMP PEAK 14(8Q24.21) WILD-TYPE                             7
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 14(8Q24.21) MUTATED                                 1
  AMP PEAK 14(8Q24.21) WILD-TYPE                               0
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 14(8Q24.21) MUTATED                                               4
  AMP PEAK 14(8Q24.21) WILD-TYPE                                             1
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 14(8Q24.21) MUTATED                              0
  AMP PEAK 14(8Q24.21) WILD-TYPE                            7
D14V9, multiclass
                                                    clus
vv                                                   AMP PEAK 14(8Q24.21) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            55
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          205
  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                                 4
  MUCINOUS (COLLOID) CARCINOMA                                                  0
                                                    clus
vv                                                   AMP PEAK 14(8Q24.21) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              39
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             98
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                   8
  LUNG CLEAR CELL ADENOCARCINOMA                                                  1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              1
  LUNG MUCINOUS ADENOCARCINOMA                                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                                   7
  LUNG SIGNET RING ADENOCARCINOMA                                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                   1
  MUCINOUS (COLLOID) CARCINOMA                                                    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(8Q24.21) MUTATED    14 289
  AMP PEAK 14(8Q24.21) WILD-TYPE   7 166
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(8Q24.21) MUTATED     14  289
  AMP PEAK 14(8Q24.21) WILD-TYPE    7  166
     clus
vv    AMP PEAK 14(8Q24.21) MUTATED AMP PEAK 14(8Q24.21) WILD-TYPE
  NO                            14                              7
  YES                          289                            166
[1] 2 2
[1] FALSE
D14V11, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 14(8Q24.21) MUTATED   208  10   4  13
  AMP PEAK 14(8Q24.21) WILD-TYPE 119   2   0   8
D14V12, multiclass
    clus
vv   AMP PEAK 14(8Q24.21) MUTATED AMP PEAK 14(8Q24.21) WILD-TYPE
  R0                          208                            119
  R1                           10                              2
  R2                            4                              0
  RX                           13                              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 14(8Q24.21) MUTATED                                  1     6
  AMP PEAK 14(8Q24.21) WILD-TYPE                                0     0
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 14(8Q24.21) MUTATED                          21   232
  AMP PEAK 14(8Q24.21) WILD-TYPE                        14   135
D14V13, multiclass
                                  clus
vv                                 AMP PEAK 14(8Q24.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       6
  BLACK OR AFRICAN AMERICAN                                  21
  WHITE                                                     232
                                  clus
vv                                 AMP PEAK 14(8Q24.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         0
  BLACK OR AFRICAN AMERICAN                                    14
  WHITE                                                       135
[1] 4 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(8Q24.21) MUTATED     5 210
  AMP PEAK 14(8Q24.21) WILD-TYPE   2 135
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(8Q24.21) MUTATED      5  210
  AMP PEAK 14(8Q24.21) WILD-TYPE    2  135
                        clus
vv                       AMP PEAK 14(8Q24.21) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          210
                        clus
vv                       AMP PEAK 14(8Q24.21) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            135
[1] 2 2
[1] FALSE

Clustering(15) Variable = AMP PEAK 15(10P15.1) MUTATION ANALYSIS
D15V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 15(10P15.1) MUTATED    97  22
  AMP PEAK 15(10P15.1) WILD-TYPE 232  65
  AMP PEAK 15(10P15.1) MUTATED AMP PEAK 15(10P15.1) WILD-TYPE 
                           119                            297 
  AMP PEAK 15(10P15.1) MUTATED AMP PEAK 15(10P15.1) WILD-TYPE 
                            22                             65 
$`AMP PEAK 15(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-73-A9RS TCGA-75-6214 
         912          467          131           38          305         1970 
TCGA-75-7027 TCGA-78-7149 TCGA-78-7154 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
        1956         1093         1948         1221          678          215 
TCGA-78-7539 TCGA-78-7542 TCGA-78-7633 TCGA-78-8660 TCGA-78-8662 TCGA-80-5608 
         327         1952          994         1954         1964         1972 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7955 TCGA-86-8585 TCGA-86-8672 
          11          630          422          508           35           15 
TCGA-86-8673 TCGA-86-A456 TCGA-86-A4D0 TCGA-91-6829 TCGA-91-6836 TCGA-91-7771 
         455           10           30         1940          417          492 
TCGA-93-8067 TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 TCGA-95-A4VN TCGA-95-A4VP 
         186            2          568          377          553          605 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-8179 TCGA-99-8025 TCGA-J2-8194 
        1332          775          181           15          427          114 
TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A7SV TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
         116            6          111          827         1175           84 
TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4TE TCGA-MP-A4TF 
        1954         1954         1957         1970         1970 

$`AMP PEAK 15(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-49-AARQ 
         445          369          890          522          354         6443 
TCGA-50-5045 TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
        2174          785          944          246          282          267 
TCGA-50-5932 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 TCGA-50-6597 TCGA-50-8460 
        1091          653          567          883         1015          105 
TCGA-53-7626 TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
        1971          701         1178         1479           87            2 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6971 TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 
         993           24           25           67         1826         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-55-7725 TCGA-55-7726 TCGA-55-7728 
           4           40          705           39           39           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-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8094 
           5          462          100            6          600            4 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
          47           15           33           46           66          674 
TCGA-55-8299 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 
         216           29            8           15          228            3 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 TCGA-55-8621 
         146          202          536           48           49          106 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A492 TCGA-55-A493 
          33           42           29           48            1           28 
TCGA-55-A494 TCGA-55-A4DF TCGA-62-8395 TCGA-62-8397 TCGA-62-8402 TCGA-62-A46U 
           5           47         1216         1289         1445         2067 
TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
        2199         1246          910         1728          628         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-67-3772 TCGA-67-3773 TCGA-67-3774 
        1559          866           31          573          427          385 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 
         174          141          422          202          186          414 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 
         165          230          184           70          382          100 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-73-4659 TCGA-73-4666 TCGA-73-4675 
          77          129          214          711          800           40 
TCGA-73-4676 TCGA-73-7498 TCGA-73-7499 TCGA-75-7025 TCGA-75-7031 TCGA-78-7145 
         164          621          519         1967         1965         1973 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
        1988         1950         1944         1963         1202          760 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
        1957         1961         1963         1940         1950         1934 
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-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-80-5607 TCGA-83-5908 TCGA-86-6851 
        1949         1971         1981         1965          824         1959 
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-86-8074 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-86-8668 TCGA-86-8669 
          16         1955           19           26           45           34 
TCGA-86-8671 TCGA-86-8674 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 
          18          405           14           39          323           60 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
         310           79          372          842          224           35 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
         505          174           36           44          218          297 
TCGA-93-7348 TCGA-95-7039 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
         127           34         1973          477          476          830 
TCGA-95-8494 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7941 
          84          121          964         1965         1932           22 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 TCGA-97-8547 
         107          182         1965           87          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-99-8033 TCGA-J2-8192 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
         170          154          287          282          238          578 
TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A743 TCGA-L9-A8F4 TCGA-MP-A4SV TCGA-MP-A4SW 
         435          266          312          102         1946         1967 
TCGA-MP-A4T2 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TH TCGA-MP-A4TI 
        1951         1980         1951         1944          142         1955 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-S2-AA1A 
        1971         1490          121 

  AMP PEAK 15(10P15.1) MUTATED AMP PEAK 15(10P15.1) WILD-TYPE 
                             2                              1 
  AMP PEAK 15(10P15.1) MUTATED AMP PEAK 15(10P15.1) WILD-TYPE 
                          2696                           6443 
  AMP PEAK 15(10P15.1) MUTATED AMP PEAK 15(10P15.1) WILD-TYPE 
                           607                            435 
[1] "2.0 - 2696.0 (607.0)" "1.0 - 6443.0 (435.0)"
[1] "hr=" "1.4"
D15V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 15(10P15.1) MUTATED         1       31       40        13        20
  AMP PEAK 15(10P15.1) WILD-TYPE       4       85       92        36        50
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 15(10P15.1) MUTATED           16          5        8
  AMP PEAK 15(10P15.1) WILD-TYPE         52          6       16
D15V3, multiclass
            clus
vv           AMP PEAK 15(10P15.1) MUTATED AMP PEAK 15(10P15.1) WILD-TYPE
  STAGE I                               1                              4
  STAGE IA                             31                             85
  STAGE IB                             40                             92
  STAGE IIA                            13                             36
  STAGE IIB                            20                             50
  STAGE IIIA                           16                             52
  STAGE IIIB                            5                              6
  STAGE IV                              8                             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 15(10P15.1) MUTATED    31  83  13   6
  AMP PEAK 15(10P15.1) WILD-TYPE 116 184  29  12
D15V4, multiclass
    clus
vv   AMP PEAK 15(10P15.1) MUTATED AMP PEAK 15(10P15.1) WILD-TYPE
  T1                           31                            116
  T2                           83                            184
  T3                           13                             29
  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 15(10P15.1) MUTATED    96  17    20
  AMP PEAK 15(10P15.1) WILD-TYPE 205  74    54
D15V5, multiclass
       clus
vv      AMP PEAK 15(10P15.1) MUTATED AMP PEAK 15(10P15.1) WILD-TYPE
  N0                              96                            205
  N1                              17                             74
  N2+N3                           20                             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 15(10P15.1) MUTATED    96   7   0   1  30
  AMP PEAK 15(10P15.1) WILD-TYPE 230  11   1   3  93
D15V6, multiclass
     clus
vv    AMP PEAK 15(10P15.1) MUTATED AMP PEAK 15(10P15.1) WILD-TYPE
  M0                            96                            230
  M1                             7                             11
  M1A                            0                              1
  M1B                            1                              3
  MX                            30                             93
[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(10P15.1) MUTATED    55  79
  AMP PEAK 15(10P15.1) WILD-TYPE 200 142
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(10P15.1) MUTATED     55   79
  AMP PEAK 15(10P15.1) WILD-TYPE  200  142
        clus
vv       AMP PEAK 15(10P15.1) MUTATED AMP PEAK 15(10P15.1) WILD-TYPE
  FEMALE                           55                            200
  MALE                             79                            142
[1] 2 2
[1] FALSE
D15V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 15(10P15.1) MUTATED                            6
  AMP PEAK 15(10P15.1) WILD-TYPE                          9
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 15(10P15.1) MUTATED                                  28
  AMP PEAK 15(10P15.1) WILD-TYPE                                66
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 15(10P15.1) MUTATED                                                   81
  AMP PEAK 15(10P15.1) WILD-TYPE                                                222
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 15(10P15.1) MUTATED                                            0
  AMP PEAK 15(10P15.1) WILD-TYPE                                          5
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 15(10P15.1) MUTATED                                               4
  AMP PEAK 15(10P15.1) WILD-TYPE                                            15
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 15(10P15.1) MUTATED                                0
  AMP PEAK 15(10P15.1) WILD-TYPE                              2
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 15(10P15.1) MUTATED                                    2
  AMP PEAK 15(10P15.1) WILD-TYPE                                  2
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 15(10P15.1) MUTATED                              0
  AMP PEAK 15(10P15.1) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 15(10P15.1) MUTATED                               9
  AMP PEAK 15(10P15.1) WILD-TYPE                            10
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 15(10P15.1) MUTATED                                 0
  AMP PEAK 15(10P15.1) WILD-TYPE                               1
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 15(10P15.1) MUTATED                                               3
  AMP PEAK 15(10P15.1) WILD-TYPE                                             2
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 15(10P15.1) MUTATED                              1
  AMP PEAK 15(10P15.1) WILD-TYPE                            6
D15V9, multiclass
                                                    clus
vv                                                   AMP PEAK 15(10P15.1) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            28
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           81
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 4
  LUNG CLEAR CELL ADENOCARCINOMA                                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            2
  LUNG MUCINOUS ADENOCARCINOMA                                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                                 9
  LUNG SIGNET RING ADENOCARCINOMA                                               0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 3
  MUCINOUS (COLLOID) CARCINOMA                                                  1
                                                    clus
vv                                                   AMP PEAK 15(10P15.1) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              66
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            222
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  15
  LUNG CLEAR CELL ADENOCARCINOMA                                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              2
  LUNG MUCINOUS ADENOCARCINOMA                                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                                  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"
D15V10, binary
                                cls
clus                               0   1
  AMP PEAK 15(10P15.1) MUTATED     3 131
  AMP PEAK 15(10P15.1) WILD-TYPE  18 324
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(10P15.1) MUTATED      3  131
  AMP PEAK 15(10P15.1) WILD-TYPE   18  324
     clus
vv    AMP PEAK 15(10P15.1) MUTATED AMP PEAK 15(10P15.1) WILD-TYPE
  NO                             3                             18
  YES                          131                            324
[1] 2 2
[1] FALSE
D15V11, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 15(10P15.1) MUTATED    92   4   0   8
  AMP PEAK 15(10P15.1) WILD-TYPE 235   8   4  13
D15V12, multiclass
    clus
vv   AMP PEAK 15(10P15.1) MUTATED AMP PEAK 15(10P15.1) WILD-TYPE
  R0                           92                            235
  R1                            4                              8
  R2                            0                              4
  RX                            8                             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 15(10P15.1) MUTATED                                  1     4
  AMP PEAK 15(10P15.1) WILD-TYPE                                0     2
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 15(10P15.1) MUTATED                          10    92
  AMP PEAK 15(10P15.1) WILD-TYPE                        25   275
D15V13, multiclass
                                  clus
vv                                 AMP PEAK 15(10P15.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  10
  WHITE                                                      92
                                  clus
vv                                 AMP PEAK 15(10P15.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         2
  BLACK OR AFRICAN AMERICAN                                    25
  WHITE                                                       275
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V14, binary
                                cls
clus                               0   1
  AMP PEAK 15(10P15.1) MUTATED     3  86
  AMP PEAK 15(10P15.1) WILD-TYPE   4 259
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(10P15.1) MUTATED      3   86
  AMP PEAK 15(10P15.1) WILD-TYPE    4  259
                        clus
vv                       AMP PEAK 15(10P15.1) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           86
                        clus
vv                       AMP PEAK 15(10P15.1) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            259
[1] 2 2
[1] FALSE

Clustering(16) Variable = AMP PEAK 16(11Q13.3) MUTATION ANALYSIS
D16V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 16(11Q13.3) MUTATED   116  34
  AMP PEAK 16(11Q13.3) WILD-TYPE 213  53
  AMP PEAK 16(11Q13.3) MUTATED AMP PEAK 16(11Q13.3) WILD-TYPE 
                           150                            266 
  AMP PEAK 16(11Q13.3) MUTATED AMP PEAK 16(11Q13.3) WILD-TYPE 
                            34                             53 
$`AMP PEAK 16(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-73-A9RS TCGA-78-7147 TCGA-78-7148 
         800          467          164          305         1950         1944 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7159 TCGA-78-7161 TCGA-78-7163 TCGA-78-7167 
        1948         1957         1221          215         1950         1937 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 TCGA-78-7542 TCGA-78-8655 
        1965         1972         1949          327         1952         1981 
TCGA-78-8662 TCGA-80-5608 TCGA-86-6851 TCGA-86-7701 TCGA-86-7953 TCGA-86-7955 
        1964         1972         1959           11          591          508 
TCGA-86-8054 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
         745          476          482           16           19           26 
TCGA-86-A4D0 TCGA-91-6829 TCGA-91-6831 TCGA-91-6836 TCGA-91-6840 TCGA-91-6848 
          30         1940          310          417          372          224 
TCGA-91-A4BC TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
          44          127          186           34            2         1973 
TCGA-95-8494 TCGA-97-7553 TCGA-97-7937 TCGA-97-8174 TCGA-97-8177 TCGA-99-8032 
          84         1332          181         1965          147           44 
TCGA-99-8033 TCGA-J2-A4AD TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A7SV TCGA-L9-A8F4 
         170          287          116            6          111          102 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TI TCGA-S2-AA1A 
         827         1175         1951         1944         1955          121 

$`AMP PEAK 16(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-49-AARQ TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
         522          354         6443         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-50-5935 TCGA-50-5942 TCGA-50-5944 TCGA-50-7109 TCGA-50-8460 TCGA-53-7626 
         653          883          764          255          105         1971 
TCGA-53-A4EZ TCGA-55-6969 TCGA-55-6972 TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 
         280         1239         1475           67         1826         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-55-7574 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
           4           95          705           39           39           34 
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-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8097 
          33          462          100            6          600           15 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
          46           66          674          216           44           23 
TCGA-55-8505 TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-8619 
          29           15            3          146          536           49 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 
          66          106           33           42           29         1952 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A4DF TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
           1           28           47         1216         1289         1970 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 TCGA-64-1679 TCGA-64-1680 
        2067         2199         1246          910         1686         1126 
TCGA-64-5778 TCGA-64-5781 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6216 
        1305         1559          573          427          385          141 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
         422          202          186          690          414          165 
TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-73-4659 TCGA-73-4670 
          70          382          100           77          711          131 
TCGA-73-4675 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-75-6214 TCGA-75-7025 
          40           38          621          519         1970         1967 
TCGA-75-7027 TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 TCGA-78-7149 TCGA-78-7150 
        1956         1965         1973         1988         1093         1963 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 TCGA-78-7162 
        1202          760         1961         1963          678         1940 
TCGA-78-7166 TCGA-78-7537 TCGA-78-7540 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
        1934         1944          881          994         1949         1971 
TCGA-78-8660 TCGA-80-5607 TCGA-83-5908 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
        1954         1965          824          630          422         1968 
TCGA-86-7954 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
        1963           10         1963           13           24          479 
TCGA-86-8076 TCGA-86-8281 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
         489         1955           35           45           34           18 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 
          15          455          405           10           14           39 
TCGA-91-6828 TCGA-91-6830 TCGA-91-6835 TCGA-91-6847 TCGA-91-6849 TCGA-91-7771 
         323           60           79          842           35          492 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-95-7567 
         505          174           36          218          297          568 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-A4VK TCGA-95-A4VN 
         377          477          476          830          121          553 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7554 TCGA-97-7941 
         605          964         1965         1932          775           22 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
         107          182           87           15          148          115 
TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-J2-8192 
         197          271          392          427          459          154 
TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A50W 
         114          282          238          578          435          266 
TCGA-L9-A743 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 
         312           84         1946         1967         1951         1954 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
        1954         1957         1980         1970         1970          142 
TCGA-MP-A4TK TCGA-MP-A5C7 
        1971         1490 

  AMP PEAK 16(11Q13.3) MUTATED AMP PEAK 16(11Q13.3) WILD-TYPE 
                             2                              1 
  AMP PEAK 16(11Q13.3) MUTATED AMP PEAK 16(11Q13.3) WILD-TYPE 
                          2696                           6443 
  AMP PEAK 16(11Q13.3) MUTATED AMP PEAK 16(11Q13.3) WILD-TYPE 
                           479                            469 
[1] "2.0 - 2696.0 (479.0)" "1.0 - 6443.0 (469.0)"
[1] "hr=" "1"  
D16V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 16(11Q13.3) MUTATED         0       34       47        18        27
  AMP PEAK 16(11Q13.3) WILD-TYPE       5       82       85        31        43
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 16(11Q13.3) MUTATED           24          4       11
  AMP PEAK 16(11Q13.3) WILD-TYPE         44          7       13
D16V3, multiclass
            clus
vv           AMP PEAK 16(11Q13.3) MUTATED AMP PEAK 16(11Q13.3) WILD-TYPE
  STAGE I                               0                              5
  STAGE IA                             34                             82
  STAGE IB                             47                             85
  STAGE IIA                            18                             31
  STAGE IIB                            27                             43
  STAGE IIIA                           24                             44
  STAGE IIIB                            4                              7
  STAGE IV                             11                             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 16(11Q13.3) MUTATED    41 101  16   5
  AMP PEAK 16(11Q13.3) WILD-TYPE 106 166  26  13
D16V4, multiclass
    clus
vv   AMP PEAK 16(11Q13.3) MUTATED AMP PEAK 16(11Q13.3) WILD-TYPE
  T1                           41                            106
  T2                          101                            166
  T3                           16                             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 16(11Q13.3) MUTATED   105  28    28
  AMP PEAK 16(11Q13.3) WILD-TYPE 196  63    46
D16V5, multiclass
       clus
vv      AMP PEAK 16(11Q13.3) MUTATED AMP PEAK 16(11Q13.3) WILD-TYPE
  N0                             105                            196
  N1                              28                             63
  N2+N3                           28                             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 16(11Q13.3) MUTATED   107   9   0   2  45
  AMP PEAK 16(11Q13.3) WILD-TYPE 219   9   1   2  78
D16V6, multiclass
     clus
vv    AMP PEAK 16(11Q13.3) MUTATED AMP PEAK 16(11Q13.3) WILD-TYPE
  M0                           107                            219
  M1                             9                              9
  M1A                            0                              1
  M1B                            2                              2
  MX                            45                             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"
D16V7, binary
                                cls
clus                               0   1
  AMP PEAK 16(11Q13.3) MUTATED    85  80
  AMP PEAK 16(11Q13.3) WILD-TYPE 170 141
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(11Q13.3) MUTATED     85   80
  AMP PEAK 16(11Q13.3) WILD-TYPE  170  141
        clus
vv       AMP PEAK 16(11Q13.3) MUTATED AMP PEAK 16(11Q13.3) WILD-TYPE
  FEMALE                           85                            170
  MALE                             80                            141
[1] 2 2
[1] FALSE
D16V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 16(11Q13.3) MUTATED                            4
  AMP PEAK 16(11Q13.3) WILD-TYPE                         11
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 16(11Q13.3) MUTATED                                  29
  AMP PEAK 16(11Q13.3) WILD-TYPE                                65
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 16(11Q13.3) MUTATED                                                  117
  AMP PEAK 16(11Q13.3) WILD-TYPE                                                186
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 16(11Q13.3) MUTATED                                            2
  AMP PEAK 16(11Q13.3) WILD-TYPE                                          3
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 16(11Q13.3) MUTATED                                               4
  AMP PEAK 16(11Q13.3) WILD-TYPE                                            15
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 16(11Q13.3) MUTATED                                1
  AMP PEAK 16(11Q13.3) WILD-TYPE                              1
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 16(11Q13.3) MUTATED                                    2
  AMP PEAK 16(11Q13.3) WILD-TYPE                                  2
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 16(11Q13.3) MUTATED                              0
  AMP PEAK 16(11Q13.3) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 16(11Q13.3) MUTATED                               4
  AMP PEAK 16(11Q13.3) WILD-TYPE                            15
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 16(11Q13.3) MUTATED                                 1
  AMP PEAK 16(11Q13.3) WILD-TYPE                               0
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 16(11Q13.3) MUTATED                                               1
  AMP PEAK 16(11Q13.3) WILD-TYPE                                             4
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 16(11Q13.3) MUTATED                              0
  AMP PEAK 16(11Q13.3) WILD-TYPE                            7
D16V9, multiclass
                                                    clus
vv                                                   AMP PEAK 16(11Q13.3) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            29
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          117
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 4
  LUNG CLEAR CELL ADENOCARCINOMA                                                1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            2
  LUNG MUCINOUS ADENOCARCINOMA                                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                                 4
  LUNG SIGNET RING ADENOCARCINOMA                                               1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 1
  MUCINOUS (COLLOID) CARCINOMA                                                  0
                                                    clus
vv                                                   AMP PEAK 16(11Q13.3) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              65
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            186
  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                                   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"
D16V10, binary
                                cls
clus                               0   1
  AMP PEAK 16(11Q13.3) MUTATED     8 157
  AMP PEAK 16(11Q13.3) WILD-TYPE  13 298
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(11Q13.3) MUTATED      8  157
  AMP PEAK 16(11Q13.3) WILD-TYPE   13  298
     clus
vv    AMP PEAK 16(11Q13.3) MUTATED AMP PEAK 16(11Q13.3) WILD-TYPE
  NO                             8                             13
  YES                          157                            298
[1] 2 2
[1] FALSE
D16V11, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 16(11Q13.3) MUTATED   111   4   1   9
  AMP PEAK 16(11Q13.3) WILD-TYPE 216   8   3  12
D16V12, multiclass
    clus
vv   AMP PEAK 16(11Q13.3) MUTATED AMP PEAK 16(11Q13.3) WILD-TYPE
  R0                          111                            216
  R1                            4                              8
  R2                            1                              3
  RX                            9                             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 16(11Q13.3) MUTATED                                  1     4
  AMP PEAK 16(11Q13.3) WILD-TYPE                                0     2
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 16(11Q13.3) MUTATED                          17   124
  AMP PEAK 16(11Q13.3) WILD-TYPE                        18   243
D16V13, multiclass
                                  clus
vv                                 AMP PEAK 16(11Q13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  17
  WHITE                                                     124
                                  clus
vv                                 AMP PEAK 16(11Q13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         2
  BLACK OR AFRICAN AMERICAN                                    18
  WHITE                                                       243
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V14, binary
                                cls
clus                               0   1
  AMP PEAK 16(11Q13.3) MUTATED     3 120
  AMP PEAK 16(11Q13.3) WILD-TYPE   4 225
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(11Q13.3) MUTATED      3  120
  AMP PEAK 16(11Q13.3) WILD-TYPE    4  225
                        clus
vv                       AMP PEAK 16(11Q13.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          120
                        clus
vv                       AMP PEAK 16(11Q13.3) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            225
[1] 2 2
[1] FALSE

Clustering(17) Variable = AMP PEAK 17(12P12.1) MUTATION ANALYSIS
D17V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 17(12P12.1) MUTATED   116  32
  AMP PEAK 17(12P12.1) WILD-TYPE 213  55
  AMP PEAK 17(12P12.1) MUTATED AMP PEAK 17(12P12.1) WILD-TYPE 
                           148                            268 
  AMP PEAK 17(12P12.1) MUTATED AMP PEAK 17(12P12.1) WILD-TYPE 
                            32                             55 
$`AMP PEAK 17(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-49-AARQ 
         268          896          157          445          522         6443 
TCGA-50-5045 TCGA-50-5072 TCGA-50-5931 TCGA-50-5935 TCGA-50-5941 TCGA-50-5944 
        2174          246          267          653          567          764 
TCGA-50-6597 TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-6642 
        1015          701         1178         1479         1375          993 
TCGA-55-6712 TCGA-55-6971 TCGA-55-6980 TCGA-55-6985 TCGA-55-6987 TCGA-55-7283 
          24           25           67         1233         1170           35 
TCGA-55-7284 TCGA-55-7576 TCGA-55-7726 TCGA-55-7728 TCGA-55-7815 TCGA-55-7907 
         121           40           39           24           54           16 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7995 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 
         197           21            5          100           26            4 
TCGA-55-8096 TCGA-55-8208 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 
          47          674           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-A471 TCGA-64-1678 TCGA-64-1681 TCGA-64-5775 TCGA-67-3774 
        1445         1246         1189         1968           62          385 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 TCGA-69-7980 TCGA-69-8255 TCGA-69-A59K 
         230          184           89          382          129          214 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-75-7027 
         912          800          467          131           40         1956 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 TCGA-78-7154 TCGA-78-7155 TCGA-78-7159 
        1973         1988         1944         1948         1957         1221 
TCGA-78-7161 TCGA-78-7167 TCGA-78-7220 TCGA-78-8655 TCGA-83-5908 TCGA-86-6851 
         215         1937         1965         1981          824         1959 
TCGA-86-7701 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-8278 TCGA-86-8280 
          11          422          591         1963          476           16 
TCGA-86-8669 TCGA-86-8673 TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6829 TCGA-91-6835 
          34          455           30          323         1940           79 
TCGA-91-6836 TCGA-91-6847 TCGA-91-6848 TCGA-91-7771 TCGA-91-8499 TCGA-93-8067 
         417          842          224          492           36          186 
TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7554 
         568          377          830           84          605          775 
TCGA-97-8552 TCGA-97-A4M7 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-L9-A443 
         115          271          459           44          170          116 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4T7 TCGA-MP-A4TE 
         827         1175           84         1946         1954         1970 
TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TK TCGA-S2-AA1A 
        1970         1955         1971          121 

$`AMP PEAK 17(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          705           39 
TCGA-55-7727 TCGA-55-7903 TCGA-55-7914 TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 
          34           19            3           31           33          462 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
           6          600           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-73-A9RS TCGA-75-6214 TCGA-75-7025 TCGA-75-7031 
         621          519          305         1970         1967         1965 
TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7156 
        1950         1093         1963         1202          760         1961 
TCGA-78-7158 TCGA-78-7160 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7535 
        1963          678         1940         1950         1934         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-78-8640 TCGA-78-8648 TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 
        1949         1971         1954         1964         1965         1972 
TCGA-86-7711 TCGA-86-7714 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
         630         1968          508          745           10         1963 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8279 TCGA-86-8281 
          13           24          479          489          482         1955 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 
          19           26           35           45           18           15 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6830 TCGA-91-6831 
         405           10           14           39           60          310 
TCGA-91-6840 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD 
         372           35          505          174           44          218 
TCGA-93-7347 TCGA-93-7348 TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 
         297          127           34            2         1973          477 
TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
         476          121          553          964         1965         1932 
TCGA-97-7553 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        1332          181           22          107          182         1965 
TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-A4M2 TCGA-99-7458 
          87          147           15          148          197          392 
TCGA-99-8025 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
         427          154          114          287          282          238 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A743 TCGA-L9-A7SV 
         578          435            6          266          312          111 
TCGA-L9-A8F4 TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4T9 
         102         1967         1951         1954         1957         1980 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TH TCGA-MP-A5C7 
        1951         1944          142         1490 

  AMP PEAK 17(12P12.1) MUTATED AMP PEAK 17(12P12.1) WILD-TYPE 
                             4                              1 
  AMP PEAK 17(12P12.1) MUTATED AMP PEAK 17(12P12.1) WILD-TYPE 
                          6443                           2696 
  AMP PEAK 17(12P12.1) MUTATED AMP PEAK 17(12P12.1) WILD-TYPE 
                         466.5                          478.0 
[1] "4.0 - 6443.0 (466.5)" "1.0 - 2696.0 (478.0)"
[1] "hr=" "1"  
D17V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 17(12P12.1) MUTATED         3       39       43        20        22
  AMP PEAK 17(12P12.1) WILD-TYPE       2       77       89        29        48
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 17(12P12.1) MUTATED           30          2       12
  AMP PEAK 17(12P12.1) WILD-TYPE         38          9       12
D17V3, multiclass
            clus
vv           AMP PEAK 17(12P12.1) MUTATED AMP PEAK 17(12P12.1) WILD-TYPE
  STAGE I                               3                              2
  STAGE IA                             39                             77
  STAGE IB                             43                             89
  STAGE IIA                            20                             29
  STAGE IIB                            22                             48
  STAGE IIIA                           30                             38
  STAGE IIIB                            2                              9
  STAGE IV                             12                             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 17(12P12.1) MUTATED    46 103  16   5
  AMP PEAK 17(12P12.1) WILD-TYPE 101 164  26  13
D17V4, multiclass
    clus
vv   AMP PEAK 17(12P12.1) MUTATED AMP PEAK 17(12P12.1) WILD-TYPE
  T1                           46                            101
  T2                          103                            164
  T3                           16                             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 17(12P12.1) MUTATED   105  33    29
  AMP PEAK 17(12P12.1) WILD-TYPE 196  58    45
D17V5, multiclass
       clus
vv      AMP PEAK 17(12P12.1) MUTATED AMP PEAK 17(12P12.1) WILD-TYPE
  N0                             105                            196
  N1                              33                             58
  N2+N3                           29                             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 17(12P12.1) MUTATED   111  10   0   2  47
  AMP PEAK 17(12P12.1) WILD-TYPE 215   8   1   2  76
D17V6, multiclass
     clus
vv    AMP PEAK 17(12P12.1) MUTATED AMP PEAK 17(12P12.1) WILD-TYPE
  M0                           111                            215
  M1                            10                              8
  M1A                            0                              1
  M1B                            2                              2
  MX                            47                             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"
D17V7, binary
                                cls
clus                               0   1
  AMP PEAK 17(12P12.1) MUTATED    90  81
  AMP PEAK 17(12P12.1) WILD-TYPE 165 140
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(12P12.1) MUTATED     90   81
  AMP PEAK 17(12P12.1) WILD-TYPE  165  140
        clus
vv       AMP PEAK 17(12P12.1) MUTATED AMP PEAK 17(12P12.1) WILD-TYPE
  FEMALE                           90                            165
  MALE                             81                            140
[1] 2 2
[1] FALSE
D17V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 17(12P12.1) MUTATED                            5
  AMP PEAK 17(12P12.1) WILD-TYPE                         10
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 17(12P12.1) MUTATED                                  28
  AMP PEAK 17(12P12.1) WILD-TYPE                                66
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 17(12P12.1) MUTATED                                                  120
  AMP PEAK 17(12P12.1) WILD-TYPE                                                183
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 17(12P12.1) MUTATED                                            1
  AMP PEAK 17(12P12.1) WILD-TYPE                                          4
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 17(12P12.1) MUTATED                                               8
  AMP PEAK 17(12P12.1) WILD-TYPE                                            11
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 17(12P12.1) MUTATED                                1
  AMP PEAK 17(12P12.1) WILD-TYPE                              1
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 17(12P12.1) MUTATED                                    1
  AMP PEAK 17(12P12.1) WILD-TYPE                                  3
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 17(12P12.1) MUTATED                              0
  AMP PEAK 17(12P12.1) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 17(12P12.1) MUTATED                               3
  AMP PEAK 17(12P12.1) WILD-TYPE                            16
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 17(12P12.1) MUTATED                                 0
  AMP PEAK 17(12P12.1) WILD-TYPE                               1
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 17(12P12.1) MUTATED                                               1
  AMP PEAK 17(12P12.1) WILD-TYPE                                             4
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 17(12P12.1) MUTATED                              3
  AMP PEAK 17(12P12.1) WILD-TYPE                            4
D17V9, multiclass
                                                    clus
vv                                                   AMP PEAK 17(12P12.1) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            28
  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                                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                                 3
  LUNG SIGNET RING ADENOCARCINOMA                                               0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 1
  MUCINOUS (COLLOID) CARCINOMA                                                  3
                                                    clus
vv                                                   AMP PEAK 17(12P12.1) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              66
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            183
  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                                   4
  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"
D17V10, binary
                                cls
clus                               0   1
  AMP PEAK 17(12P12.1) MUTATED     8 163
  AMP PEAK 17(12P12.1) WILD-TYPE  13 292
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(12P12.1) MUTATED      8  163
  AMP PEAK 17(12P12.1) WILD-TYPE   13  292
     clus
vv    AMP PEAK 17(12P12.1) MUTATED AMP PEAK 17(12P12.1) WILD-TYPE
  NO                             8                             13
  YES                          163                            292
[1] 2 2
[1] FALSE
D17V11, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 17(12P12.1) MUTATED   117   4   4   7
  AMP PEAK 17(12P12.1) WILD-TYPE 210   8   0  14
D17V12, multiclass
    clus
vv   AMP PEAK 17(12P12.1) MUTATED AMP PEAK 17(12P12.1) WILD-TYPE
  R0                          117                            210
  R1                            4                              8
  R2                            4                              0
  RX                            7                             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 17(12P12.1) MUTATED                                  1     3
  AMP PEAK 17(12P12.1) WILD-TYPE                                0     3
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 17(12P12.1) MUTATED                          15   126
  AMP PEAK 17(12P12.1) WILD-TYPE                        20   241
D17V13, multiclass
                                  clus
vv                                 AMP PEAK 17(12P12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  15
  WHITE                                                     126
                                  clus
vv                                 AMP PEAK 17(12P12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         3
  BLACK OR AFRICAN AMERICAN                                    20
  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"
D17V14, binary
                                cls
clus                               0   1
  AMP PEAK 17(12P12.1) MUTATED     2 120
  AMP PEAK 17(12P12.1) WILD-TYPE   5 225
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(12P12.1) MUTATED      2  120
  AMP PEAK 17(12P12.1) WILD-TYPE    5  225
                        clus
vv                       AMP PEAK 17(12P12.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          120
                        clus
vv                       AMP PEAK 17(12P12.1) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            225
[1] 2 2
[1] FALSE

Clustering(18) Variable = AMP PEAK 18(12Q14.1) MUTATION ANALYSIS
D18V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 18(12Q14.1) MUTATED   110  28
  AMP PEAK 18(12Q14.1) WILD-TYPE 219  59
  AMP PEAK 18(12Q14.1) MUTATED AMP PEAK 18(12Q14.1) WILD-TYPE 
                           138                            278 
  AMP PEAK 18(12Q14.1) MUTATED AMP PEAK 18(12Q14.1) WILD-TYPE 
                            28                             59 
$`AMP PEAK 18(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-55-8208 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 
         100           47          674           23           29            8 
TCGA-55-8508 TCGA-55-8615 TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
          15           15           48           28            5           47 
TCGA-62-8398 TCGA-62-8402 TCGA-62-A46V TCGA-62-A471 TCGA-64-1678 TCGA-64-1681 
        1970         1445         2199         1246         1189         1968 
TCGA-64-5775 TCGA-64-5779 TCGA-67-3774 TCGA-69-7760 TCGA-69-7973 TCGA-69-7980 
          62          864          385          202          230          382 
TCGA-69-8255 TCGA-69-A59K TCGA-73-4666 TCGA-73-4670 TCGA-73-4675 TCGA-73-A9RS 
         129          214          800          131           40          305 
TCGA-75-7027 TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 TCGA-78-7161 TCGA-78-7167 
        1956         1973         1988         1944          215         1937 
TCGA-78-7220 TCGA-78-7536 TCGA-78-8655 TCGA-86-7701 TCGA-86-7713 TCGA-86-7953 
        1965         1949         1981           11          422          591 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8278 TCGA-86-8279 TCGA-86-8358 TCGA-86-8359 
        1963          508          476          482           19           26 
TCGA-86-8585 TCGA-86-8669 TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6836 TCGA-91-6840 
          35           34           30          323          417          372 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-93-8067 TCGA-95-7567 TCGA-95-7944 
         224           35          492          186          568          377 
TCGA-95-8494 TCGA-95-A4VP TCGA-97-8177 TCGA-97-8552 TCGA-97-A4M7 TCGA-99-8032 
          84          605          147          115          271           44 
TCGA-99-8033 TCGA-L9-A443 TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
         170          116          102          827         1175           84 
TCGA-MP-A4SV TCGA-MP-A4T7 TCGA-MP-A4TE TCGA-MP-A4TI TCGA-MP-A4TK TCGA-S2-AA1A 
        1946         1954         1970         1955         1971          121 

$`AMP PEAK 18(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-49-AARQ TCGA-50-5049 TCGA-50-5066 TCGA-50-5068 
         890          354         6443         2146          944         1499 
TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 
         282         1091         2370          653          567          883 
TCGA-50-7109 TCGA-50-8460 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-5899 
         255          105         1971          280          701           87 
TCGA-55-6543 TCGA-55-6969 TCGA-55-6972 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 
           2         1239         1475         1826         1233         2151 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
          18           35            6            4           95           40 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7727 TCGA-55-7903 TCGA-55-7911 TCGA-55-7914 
         705           39           34           19           21            3 
TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
          31           33          462            6          600           26 
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-55-8506 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
          44           11          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-A4DG 
          33           42           29         1952            1          162 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 TCGA-62-A46U TCGA-62-A472 TCGA-64-1676 
        1216         1289         2696         2067          910         1728 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1680 TCGA-64-5774 TCGA-64-5778 TCGA-64-5781 
         628         1686         1126         1959         1305         1559 
TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
         866           31          610          573          427          174 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
         141          422          186          690          414          165 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-71-6725 
         184           70           89          100           77           61 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4668 TCGA-73-4676 TCGA-73-4677 
        1600          711          912          467          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-78-7154 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-78-7535 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
        1934         1972         1944          327          881         1952 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 
         994         1949         1971         1954         1964         1965 
TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 TCGA-86-7711 TCGA-86-7714 TCGA-86-8054 
        1972          824         1959          630         1968          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-86-8280 TCGA-86-8281 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
          16         1955           45           18           15          455 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 
         405           10           14           39         1940           60 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6847 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
         310           79          842          505          174           36 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-95-7039 TCGA-95-7043 
          44          218          297          127           34            2 
TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-A4VK TCGA-95-A4VN 
        1973          477          476          830          121          553 
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-97-7941 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-A4M2 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-J2-8192 
         148          197          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-A444 TCGA-L9-A50W TCGA-L9-A743 TCGA-L9-A7SV TCGA-MP-A4SW TCGA-MP-A4T2 
           6          266          312          111         1967         1951 
TCGA-MP-A4T4 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-A5C7 
         142         1490 

  AMP PEAK 18(12Q14.1) MUTATED AMP PEAK 18(12Q14.1) WILD-TYPE 
                             5                              1 
  AMP PEAK 18(12Q14.1) MUTATED AMP PEAK 18(12Q14.1) WILD-TYPE 
                          2199                           6443 
  AMP PEAK 18(12Q14.1) MUTATED AMP PEAK 18(12Q14.1) WILD-TYPE 
                           450                            512 
[1] "5.0 - 2199.0 (450.0)" "1.0 - 6443.0 (512.0)"
[1] "hr=" "1.1"
D18V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 18(12Q14.1) MUTATED         2       33       41        18        25
  AMP PEAK 18(12Q14.1) WILD-TYPE       3       83       91        31        45
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 18(12Q14.1) MUTATED           26          3       11
  AMP PEAK 18(12Q14.1) WILD-TYPE         42          8       13
D18V3, multiclass
            clus
vv           AMP PEAK 18(12Q14.1) MUTATED AMP PEAK 18(12Q14.1) WILD-TYPE
  STAGE I                               2                              3
  STAGE IA                             33                             83
  STAGE IB                             41                             91
  STAGE IIA                            18                             31
  STAGE IIB                            25                             45
  STAGE IIIA                           26                             42
  STAGE IIIB                            3                              8
  STAGE IV                             11                             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(12Q14.1) MUTATED    40  96  16   6
  AMP PEAK 18(12Q14.1) WILD-TYPE 107 171  26  12
D18V4, multiclass
    clus
vv   AMP PEAK 18(12Q14.1) MUTATED AMP PEAK 18(12Q14.1) WILD-TYPE
  T1                           40                            107
  T2                           96                            171
  T3                           16                             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 18(12Q14.1) MUTATED    98  32    26
  AMP PEAK 18(12Q14.1) WILD-TYPE 203  59    48
D18V5, multiclass
       clus
vv      AMP PEAK 18(12Q14.1) MUTATED AMP PEAK 18(12Q14.1) WILD-TYPE
  N0                              98                            203
  N1                              32                             59
  N2+N3                           26                             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 18(12Q14.1) MUTATED   109  10   0   1  38
  AMP PEAK 18(12Q14.1) WILD-TYPE 217   8   1   3  85
D18V6, multiclass
     clus
vv    AMP PEAK 18(12Q14.1) MUTATED AMP PEAK 18(12Q14.1) WILD-TYPE
  M0                           109                            217
  M1                            10                              8
  M1A                            0                              1
  M1B                            1                              3
  MX                            38                             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"
D18V7, binary
                                cls
clus                               0   1
  AMP PEAK 18(12Q14.1) MUTATED    78  81
  AMP PEAK 18(12Q14.1) WILD-TYPE 177 140
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(12Q14.1) MUTATED     78   81
  AMP PEAK 18(12Q14.1) WILD-TYPE  177  140
        clus
vv       AMP PEAK 18(12Q14.1) MUTATED AMP PEAK 18(12Q14.1) WILD-TYPE
  FEMALE                           78                            177
  MALE                             81                            140
[1] 2 2
[1] FALSE
D18V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 18(12Q14.1) MUTATED                            5
  AMP PEAK 18(12Q14.1) WILD-TYPE                         10
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 18(12Q14.1) MUTATED                                  28
  AMP PEAK 18(12Q14.1) WILD-TYPE                                66
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 18(12Q14.1) MUTATED                                                  111
  AMP PEAK 18(12Q14.1) WILD-TYPE                                                192
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 18(12Q14.1) MUTATED                                            1
  AMP PEAK 18(12Q14.1) WILD-TYPE                                          4
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 18(12Q14.1) MUTATED                                               5
  AMP PEAK 18(12Q14.1) WILD-TYPE                                            14
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 18(12Q14.1) MUTATED                                1
  AMP PEAK 18(12Q14.1) WILD-TYPE                              1
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 18(12Q14.1) MUTATED                                    0
  AMP PEAK 18(12Q14.1) WILD-TYPE                                  4
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 18(12Q14.1) MUTATED                              0
  AMP PEAK 18(12Q14.1) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 18(12Q14.1) MUTATED                               3
  AMP PEAK 18(12Q14.1) WILD-TYPE                            16
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 18(12Q14.1) MUTATED                                 0
  AMP PEAK 18(12Q14.1) WILD-TYPE                               1
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 18(12Q14.1) MUTATED                                               2
  AMP PEAK 18(12Q14.1) WILD-TYPE                                             3
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 18(12Q14.1) MUTATED                              3
  AMP PEAK 18(12Q14.1) WILD-TYPE                            4
D18V9, multiclass
                                                    clus
vv                                                   AMP PEAK 18(12Q14.1) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            28
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          111
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 5
  LUNG CLEAR CELL ADENOCARCINOMA                                                1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            0
  LUNG MUCINOUS ADENOCARCINOMA                                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                                 3
  LUNG SIGNET RING ADENOCARCINOMA                                               0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 2
  MUCINOUS (COLLOID) CARCINOMA                                                  3
                                                    clus
vv                                                   AMP PEAK 18(12Q14.1) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              66
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            192
  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                                   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"
D18V10, binary
                                cls
clus                               0   1
  AMP PEAK 18(12Q14.1) MUTATED     7 152
  AMP PEAK 18(12Q14.1) WILD-TYPE  14 303
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(12Q14.1) MUTATED      7  152
  AMP PEAK 18(12Q14.1) WILD-TYPE   14  303
     clus
vv    AMP PEAK 18(12Q14.1) MUTATED AMP PEAK 18(12Q14.1) WILD-TYPE
  NO                             7                             14
  YES                          152                            303
[1] 2 2
[1] FALSE
D18V11, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 18(12Q14.1) MUTATED   110   3   3   7
  AMP PEAK 18(12Q14.1) WILD-TYPE 217   9   1  14
D18V12, multiclass
    clus
vv   AMP PEAK 18(12Q14.1) MUTATED AMP PEAK 18(12Q14.1) WILD-TYPE
  R0                          110                            217
  R1                            3                              9
  R2                            3                              1
  RX                            7                             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 18(12Q14.1) MUTATED                                  0     3
  AMP PEAK 18(12Q14.1) WILD-TYPE                                1     3
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 18(12Q14.1) MUTATED                          14   116
  AMP PEAK 18(12Q14.1) WILD-TYPE                        21   251
D18V13, multiclass
                                  clus
vv                                 AMP PEAK 18(12Q14.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  14
  WHITE                                                     116
                                  clus
vv                                 AMP PEAK 18(12Q14.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         3
  BLACK OR AFRICAN AMERICAN                                    21
  WHITE                                                       251
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V14, binary
                                cls
clus                               0   1
  AMP PEAK 18(12Q14.1) MUTATED     3 107
  AMP PEAK 18(12Q14.1) WILD-TYPE   4 238
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(12Q14.1) MUTATED      3  107
  AMP PEAK 18(12Q14.1) WILD-TYPE    4  238
                        clus
vv                       AMP PEAK 18(12Q14.1) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          107
                        clus
vv                       AMP PEAK 18(12Q14.1) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            238
[1] 2 2
[1] FALSE

Clustering(19) Variable = AMP PEAK 19(12Q15) MUTATION ANALYSIS
D19V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 19(12Q15) MUTATED   110  28
  AMP PEAK 19(12Q15) WILD-TYPE 219  59
  AMP PEAK 19(12Q15) MUTATED AMP PEAK 19(12Q15) WILD-TYPE 
                         138                          278 
  AMP PEAK 19(12Q15) MUTATED AMP PEAK 19(12Q15) WILD-TYPE 
                          28                           59 
$`AMP PEAK 19(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-55-8208 TCGA-55-8302 TCGA-55-8505 
          33          100            6          674           23           29 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8615 TCGA-55-A48Y TCGA-55-A490 TCGA-55-A491 
           8           15           15           42           48         1952 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-62-8398 TCGA-62-8402 TCGA-62-A46V 
          28            5           47         1970         1445         2199 
TCGA-62-A471 TCGA-64-1678 TCGA-64-1681 TCGA-64-5779 TCGA-67-3774 TCGA-69-7760 
        1246         1189         1968          864          385          202 
TCGA-69-7973 TCGA-69-7980 TCGA-69-8255 TCGA-69-A59K TCGA-73-4666 TCGA-73-4675 
         230          382          129          214          800           40 
TCGA-73-A9RS TCGA-75-7027 TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 TCGA-78-7161 
         305         1956         1973         1988         1944          215 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 TCGA-78-8655 TCGA-86-6851 TCGA-86-7701 
        1937         1965         1949         1981         1959           11 
TCGA-86-7713 TCGA-86-7953 TCGA-86-8074 TCGA-86-8278 TCGA-86-8279 TCGA-86-8358 
         422          591           24          476          482           19 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8669 TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6831 
          26           35           34           30          323          310 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6848 TCGA-91-7771 TCGA-91-8499 TCGA-93-8067 
         417          372          224          492           36          186 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-8494 TCGA-95-A4VP TCGA-97-8177 
         568          377          477           84          605          147 
TCGA-97-8552 TCGA-97-A4M7 TCGA-99-8032 TCGA-99-8033 TCGA-L9-A443 TCGA-L9-A8F4 
         115          271           44          170          116          102 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T7 TCGA-MP-A4TE TCGA-MP-A4TI TCGA-S2-AA1A 
        1946         1967         1954         1970         1955          121 

$`AMP PEAK 19(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-49-AARQ TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 TCGA-50-5932 
         354         6443          944         1499          282         1091 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 TCGA-50-7109 TCGA-50-8460 
        2370          653          567          883          255          105 
TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-5899 TCGA-55-6543 TCGA-55-6969 
        1971          280          701           87            2         1239 
TCGA-55-6972 TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 TCGA-55-7281 
        1475           67         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          705 
TCGA-55-7725 TCGA-55-7727 TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 TCGA-55-7914 
          39           34           19           16           21            3 
TCGA-55-7994 TCGA-55-8087 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
          31          462          600           26            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-55-8506 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-A48Z TCGA-55-A492 TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 
          29            1          162         1216         1289         2696 
TCGA-62-A46U TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1680 
        2067          910         1728          628         1686         1126 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 
        1959           62         1305         1559          866           31 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
         610          573          427          174          141          422 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 
         186          690          414          165          184           70 
TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 
          89          100           77           61         1600          711 
TCGA-73-4662 TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
         912          467          131          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-86-7711 TCGA-86-7714 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
         824          630         1968         1963          508          745 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 TCGA-86-8076 TCGA-86-8280 
          10         1963           13          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-91-6835 
          10           14           39         1940           60           79 
TCGA-91-6847 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD 
         842           35          505          174           44          218 
TCGA-93-7347 TCGA-93-7348 TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7948 
         297          127           34            2         1973          476 
TCGA-95-8039 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
         830          121          553          964         1965         1932 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
        1332          775          181           22          107          182 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8179 TCGA-97-8547 TCGA-97-A4M2 TCGA-99-7458 
        1965           87           15          148          197          392 
TCGA-99-8025 TCGA-99-8028 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
         427          459          154          114          287          282 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A743 
         238          578          435            6          266          312 
TCGA-L9-A7SV TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4T2 TCGA-MP-A4T4 
         111          827         1175           84         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-A4TK TCGA-MP-A5C7 
        1971         1490 

  AMP PEAK 19(12Q15) MUTATED AMP PEAK 19(12Q15) WILD-TYPE 
                           5                            1 
  AMP PEAK 19(12Q15) MUTATED AMP PEAK 19(12Q15) WILD-TYPE 
                        2199                         6443 
  AMP PEAK 19(12Q15) MUTATED AMP PEAK 19(12Q15) WILD-TYPE 
                       461.5                        484.0 
[1] "5.0 - 2199.0 (461.5)" "1.0 - 6443.0 (484.0)"
[1] "hr=" "1.2"
D19V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 19(12Q15) MUTATED         2       36       41        20        24
  AMP PEAK 19(12Q15) WILD-TYPE       3       80       91        29        46
                              vv
clus                           STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 19(12Q15) MUTATED           26          3       10
  AMP PEAK 19(12Q15) WILD-TYPE         42          8       14
D19V3, multiclass
            clus
vv           AMP PEAK 19(12Q15) MUTATED AMP PEAK 19(12Q15) WILD-TYPE
  STAGE I                             2                            3
  STAGE IA                           36                           80
  STAGE IB                           41                           91
  STAGE IIA                          20                           29
  STAGE IIB                          24                           46
  STAGE IIIA                         26                           42
  STAGE IIIB                          3                            8
  STAGE IV                           10                           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 19(12Q15) MUTATED    44  97  15   5
  AMP PEAK 19(12Q15) WILD-TYPE 103 170  27  13
D19V4, multiclass
    clus
vv   AMP PEAK 19(12Q15) MUTATED AMP PEAK 19(12Q15) WILD-TYPE
  T1                         44                          103
  T2                         97                          170
  T3                         15                           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 19(12Q15) MUTATED   100  33    27
  AMP PEAK 19(12Q15) WILD-TYPE 201  58    47
D19V5, multiclass
       clus
vv      AMP PEAK 19(12Q15) MUTATED AMP PEAK 19(12Q15) WILD-TYPE
  N0                           100                          201
  N1                            33                           58
  N2+N3                         27                           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 19(12Q15) MUTATED   112   9   0   1  39
  AMP PEAK 19(12Q15) WILD-TYPE 214   9   1   3  84
D19V6, multiclass
     clus
vv    AMP PEAK 19(12Q15) MUTATED AMP PEAK 19(12Q15) WILD-TYPE
  M0                         112                          214
  M1                           9                            9
  M1A                          0                            1
  M1B                          1                            3
  MX                          39                           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"
D19V7, binary
                              cls
clus                             0   1
  AMP PEAK 19(12Q15) MUTATED    80  82
  AMP PEAK 19(12Q15) WILD-TYPE 175 139
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(12Q15) MUTATED     80   82
  AMP PEAK 19(12Q15) WILD-TYPE  175  139
        clus
vv       AMP PEAK 19(12Q15) MUTATED AMP PEAK 19(12Q15) WILD-TYPE
  FEMALE                         80                          175
  MALE                           82                          139
[1] 2 2
[1] FALSE
D19V8, continuous
                              vv
clus                           LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 19(12Q15) MUTATED                            5
  AMP PEAK 19(12Q15) WILD-TYPE                         10
                              vv
clus                           LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 19(12Q15) MUTATED                                  32
  AMP PEAK 19(12Q15) WILD-TYPE                                62
                              vv
clus                           LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 19(12Q15) MUTATED                                                  110
  AMP PEAK 19(12Q15) WILD-TYPE                                                193
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 19(12Q15) MUTATED                                            1
  AMP PEAK 19(12Q15) WILD-TYPE                                          4
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 19(12Q15) MUTATED                                               4
  AMP PEAK 19(12Q15) WILD-TYPE                                            15
                              vv
clus                           LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 19(12Q15) MUTATED                                1
  AMP PEAK 19(12Q15) WILD-TYPE                              1
                              vv
clus                           LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 19(12Q15) MUTATED                                    0
  AMP PEAK 19(12Q15) WILD-TYPE                                  4
                              vv
clus                           LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 19(12Q15) MUTATED                              0
  AMP PEAK 19(12Q15) WILD-TYPE                            2
                              vv
clus                           LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 19(12Q15) MUTATED                               4
  AMP PEAK 19(12Q15) WILD-TYPE                            15
                              vv
clus                           LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 19(12Q15) MUTATED                                 0
  AMP PEAK 19(12Q15) WILD-TYPE                               1
                              vv
clus                           LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 19(12Q15) MUTATED                                               2
  AMP PEAK 19(12Q15) WILD-TYPE                                             3
                              vv
clus                           MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 19(12Q15) MUTATED                              3
  AMP PEAK 19(12Q15) WILD-TYPE                            4
D19V9, multiclass
                                                    clus
vv                                                   AMP PEAK 19(12Q15) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                  5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                          32
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                        110
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                  1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                               4
  LUNG CLEAR CELL ADENOCARCINOMA                                              1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                          0
  LUNG MUCINOUS ADENOCARCINOMA                                                0
  LUNG PAPILLARY ADENOCARCINOMA                                               4
  LUNG SIGNET RING ADENOCARCINOMA                                             0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                               2
  MUCINOUS (COLLOID) CARCINOMA                                                3
                                                    clus
vv                                                   AMP PEAK 19(12Q15) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                   10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            62
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          193
  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                                 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(12Q15) MUTATED     8 154
  AMP PEAK 19(12Q15) WILD-TYPE  13 301
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(12Q15) MUTATED      8  154
  AMP PEAK 19(12Q15) WILD-TYPE   13  301
     clus
vv    AMP PEAK 19(12Q15) MUTATED AMP PEAK 19(12Q15) WILD-TYPE
  NO                           8                           13
  YES                        154                          301
[1] 2 2
[1] FALSE
D19V11, continuous
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 19(12Q15) MUTATED   111   4   3   6
  AMP PEAK 19(12Q15) WILD-TYPE 216   8   1  15
D19V12, multiclass
    clus
vv   AMP PEAK 19(12Q15) MUTATED AMP PEAK 19(12Q15) WILD-TYPE
  R0                        111                          216
  R1                          4                            8
  R2                          3                            1
  RX                          6                           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 19(12Q15) MUTATED                                  0     3
  AMP PEAK 19(12Q15) WILD-TYPE                                1     3
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 19(12Q15) MUTATED                          12   120
  AMP PEAK 19(12Q15) WILD-TYPE                        23   247
D19V13, multiclass
                                  clus
vv                                 AMP PEAK 19(12Q15) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     3
  BLACK OR AFRICAN AMERICAN                                12
  WHITE                                                   120
                                  clus
vv                                 AMP PEAK 19(12Q15) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  23
  WHITE                                                     247
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V14, binary
                              cls
clus                             0   1
  AMP PEAK 19(12Q15) MUTATED     3 108
  AMP PEAK 19(12Q15) WILD-TYPE   4 237
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(12Q15) MUTATED      3  108
  AMP PEAK 19(12Q15) WILD-TYPE    4  237
                        clus
vv                       AMP PEAK 19(12Q15) MUTATED
  HISPANIC OR LATINO                              3
  NOT HISPANIC OR LATINO                        108
                        clus
vv                       AMP PEAK 19(12Q15) WILD-TYPE
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          237
[1] 2 2
[1] FALSE

Clustering(20) Variable = AMP PEAK 20(13Q33.3) MUTATION ANALYSIS
D20V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 20(13Q33.3) MUTATED    51  15
  AMP PEAK 20(13Q33.3) WILD-TYPE 278  72
  AMP PEAK 20(13Q33.3) MUTATED AMP PEAK 20(13Q33.3) WILD-TYPE 
                            66                            350 
  AMP PEAK 20(13Q33.3) MUTATED AMP PEAK 20(13Q33.3) WILD-TYPE 
                            15                             72 
$`AMP PEAK 20(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         1175         1967         1954 

$`AMP PEAK 20(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-49-AARQ 
         157         1700          890          522          354         6443 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
        2146          455          785          944         1499          246 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5942 TCGA-50-5944 
         267         1091         2370          653          883          764 
TCGA-50-5946 TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 TCGA-53-7813 TCGA-53-A4EZ 
         686         1015          255          105          424          280 
TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-6543 TCGA-55-6642 
         701         1178         1479         1375            2          993 
TCGA-55-6712 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 TCGA-55-6983 
          24         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-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7727 
           4           95           40          705           39           34 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
          24           54           19           21            3           31 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
           5           33          462            6          600           26 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
          47           15           46           66          674          216 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8510 TCGA-55-8512 
          44           23           29           11          228            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-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A491 TCGA-55-A493 TCGA-55-A494 
         106           33           42         1952           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-A46V TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 
        2199         1246          910         1728          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-67-3773 TCGA-67-3774 TCGA-67-6216 
        1559          866           31          427          385          141 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
         422          202          186          690          414          165 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
         230          184           70           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-73-4675 TCGA-73-4676 TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS 
         131           40          164          621          519          305 
TCGA-75-7025 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7150 
        1967         1973         1988         1950         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-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7535 
         678          215         1940         1950         1934         1972 
TCGA-78-7536 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
        1949          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-83-5908 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
         824           11          630          422         1968          591 
TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8076 
        1963          745           10         1963           13          489 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8281 TCGA-86-8358 TCGA-86-8359 
         476          482           16         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-91-6828 
         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-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
         224           35          492          505          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-95-7562 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
           2         1973          377          477          476          830 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7552 TCGA-97-7553 
          84          121          553          605         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-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 
          87           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-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
         114          287          238          578          435          116 
TCGA-L9-A50W TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N5 
         266          312          111          102          827           84 
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 TCGA-S2-AA1A 
        1490          121 

  AMP PEAK 20(13Q33.3) MUTATED AMP PEAK 20(13Q33.3) WILD-TYPE 
                             1                              2 
  AMP PEAK 20(13Q33.3) MUTATED AMP PEAK 20(13Q33.3) WILD-TYPE 
                          2174                           6443 
  AMP PEAK 20(13Q33.3) MUTATED AMP PEAK 20(13Q33.3) WILD-TYPE 
                         570.5                          458.0 
[1] "1.0 - 2174.0 (570.5)" "2.0 - 6443.0 (458.0)"
[1] "hr=" "1.1"
D20V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 20(13Q33.3) MUTATED         1       16       22        10         9
  AMP PEAK 20(13Q33.3) WILD-TYPE       4      100      110        39        61
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 20(13Q33.3) MUTATED            7          3        8
  AMP PEAK 20(13Q33.3) WILD-TYPE         61          8       16
D20V3, multiclass
            clus
vv           AMP PEAK 20(13Q33.3) MUTATED AMP PEAK 20(13Q33.3) WILD-TYPE
  STAGE I                               1                              4
  STAGE IA                             16                            100
  STAGE IB                             22                            110
  STAGE IIA                            10                             39
  STAGE IIB                             9                             61
  STAGE IIIA                            7                             61
  STAGE IIIB                            3                              8
  STAGE IV                              8                             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 20(13Q33.3) MUTATED    26  46   2   2
  AMP PEAK 20(13Q33.3) WILD-TYPE 121 221  40  16
D20V4, multiclass
    clus
vv   AMP PEAK 20(13Q33.3) MUTATED AMP PEAK 20(13Q33.3) WILD-TYPE
  T1                           26                            121
  T2                           46                            221
  T3                            2                             40
  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 20(13Q33.3) MUTATED    48  18    10
  AMP PEAK 20(13Q33.3) WILD-TYPE 253  73    64
D20V5, multiclass
       clus
vv      AMP PEAK 20(13Q33.3) MUTATED AMP PEAK 20(13Q33.3) WILD-TYPE
  N0                              48                            253
  N1                              18                             73
  N2+N3                           10                             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
  AMP PEAK 20(13Q33.3) MUTATED    49   6   0   2  19
  AMP PEAK 20(13Q33.3) WILD-TYPE 277  12   1   2 104
D20V6, multiclass
     clus
vv    AMP PEAK 20(13Q33.3) MUTATED AMP PEAK 20(13Q33.3) WILD-TYPE
  M0                            49                            277
  M1                             6                             12
  M1A                            0                              1
  M1B                            2                              2
  MX                            19                            104
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V7, binary
                                cls
clus                               0   1
  AMP PEAK 20(13Q33.3) MUTATED    46  30
  AMP PEAK 20(13Q33.3) WILD-TYPE 209 191
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(13Q33.3) MUTATED     46   30
  AMP PEAK 20(13Q33.3) WILD-TYPE  209  191
        clus
vv       AMP PEAK 20(13Q33.3) MUTATED AMP PEAK 20(13Q33.3) WILD-TYPE
  FEMALE                           46                            209
  MALE                             30                            191
[1] 2 2
[1] FALSE
D20V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 20(13Q33.3) MUTATED                            3
  AMP PEAK 20(13Q33.3) WILD-TYPE                         12
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 20(13Q33.3) MUTATED                                  17
  AMP PEAK 20(13Q33.3) WILD-TYPE                                77
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 20(13Q33.3) MUTATED                                                   48
  AMP PEAK 20(13Q33.3) WILD-TYPE                                                255
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 20(13Q33.3) MUTATED                                            0
  AMP PEAK 20(13Q33.3) WILD-TYPE                                          5
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 20(13Q33.3) MUTATED                                               2
  AMP PEAK 20(13Q33.3) WILD-TYPE                                            17
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 20(13Q33.3) MUTATED                                1
  AMP PEAK 20(13Q33.3) WILD-TYPE                              1
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 20(13Q33.3) MUTATED                                    0
  AMP PEAK 20(13Q33.3) WILD-TYPE                                  4
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 20(13Q33.3) MUTATED                              0
  AMP PEAK 20(13Q33.3) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 20(13Q33.3) MUTATED                               3
  AMP PEAK 20(13Q33.3) WILD-TYPE                            16
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 20(13Q33.3) MUTATED                                 0
  AMP PEAK 20(13Q33.3) WILD-TYPE                               1
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 20(13Q33.3) MUTATED                                               0
  AMP PEAK 20(13Q33.3) WILD-TYPE                                             5
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 20(13Q33.3) MUTATED                              2
  AMP PEAK 20(13Q33.3) WILD-TYPE                            5
D20V9, multiclass
                                                    clus
vv                                                   AMP PEAK 20(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 20(13Q33.3) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              77
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            255
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      5
  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                                   5
  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"
D20V10, binary
                                cls
clus                               0   1
  AMP PEAK 20(13Q33.3) MUTATED     4  72
  AMP PEAK 20(13Q33.3) WILD-TYPE  17 383
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(13Q33.3) MUTATED      4   72
  AMP PEAK 20(13Q33.3) WILD-TYPE   17  383
     clus
vv    AMP PEAK 20(13Q33.3) MUTATED AMP PEAK 20(13Q33.3) WILD-TYPE
  NO                             4                             17
  YES                           72                            383
[1] 2 2
[1] FALSE
D20V11, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 20(13Q33.3) MUTATED    55   0   1   2
  AMP PEAK 20(13Q33.3) WILD-TYPE 272  12   3  19
D20V12, multiclass
    clus
vv   AMP PEAK 20(13Q33.3) MUTATED AMP PEAK 20(13Q33.3) WILD-TYPE
  R0                           55                            272
  R1                            0                             12
  R2                            1                              3
  RX                            2                             19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 20(13Q33.3) MUTATED                                  0     0
  AMP PEAK 20(13Q33.3) WILD-TYPE                                1     6
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 20(13Q33.3) MUTATED                           6    60
  AMP PEAK 20(13Q33.3) WILD-TYPE                        29   307
D20V13, multiclass
                                  clus
vv                                 AMP PEAK 20(13Q33.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   6
  WHITE                                                      60
                                  clus
vv                                 AMP PEAK 20(13Q33.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         6
  BLACK OR AFRICAN AMERICAN                                    29
  WHITE                                                       307
[1] 4 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(13Q33.3) MUTATED     3  53
  AMP PEAK 20(13Q33.3) WILD-TYPE   4 292
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(13Q33.3) MUTATED      3   53
  AMP PEAK 20(13Q33.3) WILD-TYPE    4  292
                        clus
vv                       AMP PEAK 20(13Q33.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           53
                        clus
vv                       AMP PEAK 20(13Q33.3) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            292
[1] 2 2
[1] FALSE

Clustering(21) Variable = AMP PEAK 21(14Q13.3) MUTATION ANALYSIS
D21V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 21(14Q13.3) MUTATED   146  42
  AMP PEAK 21(14Q13.3) WILD-TYPE 183  45
  AMP PEAK 21(14Q13.3) MUTATED AMP PEAK 21(14Q13.3) WILD-TYPE 
                           188                            228 
  AMP PEAK 21(14Q13.3) MUTATED AMP PEAK 21(14Q13.3) WILD-TYPE 
                            42                             45 
$`AMP PEAK 21(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-49-AARQ TCGA-50-5045 TCGA-50-5935 TCGA-50-5941 
         157          354         6443         2174          653          567 
TCGA-50-5946 TCGA-50-7109 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1595 
         686          255          424          280         1178         1479 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6971 TCGA-55-6983 
          87            2          993           24           25         1826 
TCGA-55-7281 TCGA-55-7724 TCGA-55-7727 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 
          18          705           34           54           19           16 
TCGA-55-7910 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 TCGA-55-8091 TCGA-55-8096 
         197            3            5           33          600           47 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8507 
          46           66           44           23           11            8 
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-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A4DF TCGA-55-A4DG 
          42           29           48           28           47          162 
TCGA-62-8402 TCGA-62-A46U TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-5774 
        1445         2067         1728          628         1189         1959 
TCGA-64-5775 TCGA-64-5779 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 
          62          864          866           31          610          573 
TCGA-67-3773 TCGA-67-6217 TCGA-69-7760 TCGA-69-7763 TCGA-69-7973 TCGA-69-7974 
         427          422          202          690          230          184 
TCGA-69-7979 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
          89          214           61         1600          711          912 
TCGA-73-4666 TCGA-73-4677 TCGA-73-7499 TCGA-73-A9RS TCGA-75-7025 TCGA-75-7031 
         800           38          519          305         1967         1965 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 TCGA-78-7155 TCGA-78-7159 
        1973         1988         1944         1093         1957         1221 
TCGA-78-7161 TCGA-78-7167 TCGA-78-7536 TCGA-78-7539 TCGA-78-8640 TCGA-78-8660 
         215         1937         1949          327         1949         1954 
TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-7701 TCGA-86-7713 TCGA-86-7953 
        1964         1972          824           11          422          591 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8074 TCGA-86-8278 TCGA-86-8279 
         508          745           10           24          476          482 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8585 TCGA-86-8669 TCGA-86-8673 TCGA-86-A4D0 
          16           19           35           34          455           30 
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-91-6848 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
         842          224          492          505          174           36 
TCGA-91-A4BC TCGA-93-8067 TCGA-95-7562 TCGA-95-7567 TCGA-95-8494 TCGA-95-A4VP 
          44          186         1973          568           84          605 
TCGA-97-7546 TCGA-97-7554 TCGA-97-7937 TCGA-97-8171 TCGA-97-8179 TCGA-99-7458 
         964          775          181          107           15          392 
TCGA-99-8032 TCGA-J2-8192 TCGA-J2-A4AG TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
          44          154          238          116            6          827 
TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TE 
        1175         1946         1954         1957         1980         1970 
TCGA-MP-A4TF TCGA-MP-A4TK 
        1970         1971 

$`AMP PEAK 21(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          462          100 
TCGA-55-8090 TCGA-55-8092 TCGA-55-8094 TCGA-55-8097 TCGA-55-8205 TCGA-55-8208 
           6           26            4           15           33          674 
TCGA-55-8299 TCGA-55-8505 TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 TCGA-55-8619 
         216           29           15            3          146           49 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A494 
          66          106           33         1952            1            5 
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-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5778 TCGA-64-5781 
         910         1686         1126         1968         1305         1559 
TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 
         385          174          141          186          414          165 
TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-73-4668 
          70          382          100           77          129          467 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-7498 TCGA-75-6214 TCGA-75-7027 
         131           40          164          621         1970         1956 
TCGA-78-7147 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 
        1950         1963         1202          760         1948         1961 
TCGA-78-7158 TCGA-78-7160 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7220 
        1963          678         1940         1950         1934         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-80-5607 TCGA-86-6851 TCGA-86-7711 TCGA-86-7714 TCGA-86-7954 
        1981         1965         1959          630         1968         1963 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 TCGA-86-8076 TCGA-86-8281 TCGA-86-8359 
        1963           13          479          489         1955           26 
TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 
          45           18           15          405           10           14 
TCGA-86-A4P8 TCGA-91-6830 TCGA-91-6849 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
          39           60           35          218          297          127 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
          34            2          377          477          476          830 
TCGA-95-A4VK TCGA-95-A4VN TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7941 
         121          553         1965         1932         1332           22 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 TCGA-97-8547 TCGA-97-8552 
         182         1965           87          147          148          115 
TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-8025 TCGA-99-8028 TCGA-99-8033 TCGA-J2-8194 
         197          271          427          459          170          114 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A743 
         287          282          578          435          266          312 
TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T7 
         111          102           84         1967         1951         1954 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A5C7 TCGA-S2-AA1A 
        1951         1944          142         1955         1490          121 

  AMP PEAK 21(14Q13.3) MUTATED AMP PEAK 21(14Q13.3) WILD-TYPE 
                             2                              1 
  AMP PEAK 21(14Q13.3) MUTATED AMP PEAK 21(14Q13.3) WILD-TYPE 
                          6443                           2696 
  AMP PEAK 21(14Q13.3) MUTATED AMP PEAK 21(14Q13.3) WILD-TYPE 
                         484.0                          464.5 
[1] "2.0 - 6443.0 (484.0)" "1.0 - 2696.0 (464.5)"
[1] "hr=" "1.2"
D21V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 21(14Q13.3) MUTATED         2       50       56        29        29
  AMP PEAK 21(14Q13.3) WILD-TYPE       3       66       76        20        41
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 21(14Q13.3) MUTATED           30          6        9
  AMP PEAK 21(14Q13.3) WILD-TYPE         38          5       15
D21V3, multiclass
            clus
vv           AMP PEAK 21(14Q13.3) MUTATED AMP PEAK 21(14Q13.3) WILD-TYPE
  STAGE I                               2                              3
  STAGE IA                             50                             66
  STAGE IB                             56                             76
  STAGE IIA                            29                             20
  STAGE IIB                            29                             41
  STAGE IIIA                           30                             38
  STAGE IIIB                            6                              5
  STAGE IV                              9                             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 21(14Q13.3) MUTATED    63 125  15   8
  AMP PEAK 21(14Q13.3) WILD-TYPE  84 142  27  10
D21V4, multiclass
    clus
vv   AMP PEAK 21(14Q13.3) MUTATED AMP PEAK 21(14Q13.3) WILD-TYPE
  T1                           63                             84
  T2                          125                            142
  T3                           15                             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
  AMP PEAK 21(14Q13.3) MUTATED   133  40    34
  AMP PEAK 21(14Q13.3) WILD-TYPE 168  51    40
D21V5, multiclass
       clus
vv      AMP PEAK 21(14Q13.3) MUTATED AMP PEAK 21(14Q13.3) WILD-TYPE
  N0                             133                            168
  N1                              40                             51
  N2+N3                           34                             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
  AMP PEAK 21(14Q13.3) MUTATED   133   8   1   0  69
  AMP PEAK 21(14Q13.3) WILD-TYPE 193  10   0   4  54
D21V6, multiclass
     clus
vv    AMP PEAK 21(14Q13.3) MUTATED AMP PEAK 21(14Q13.3) WILD-TYPE
  M0                           133                            193
  M1                             8                             10
  M1A                            1                              0
  M1B                            0                              4
  MX                            69                             54
[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(14Q13.3) MUTATED   114  97
  AMP PEAK 21(14Q13.3) WILD-TYPE 141 124
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(14Q13.3) MUTATED    114   97
  AMP PEAK 21(14Q13.3) WILD-TYPE  141  124
        clus
vv       AMP PEAK 21(14Q13.3) MUTATED AMP PEAK 21(14Q13.3) WILD-TYPE
  FEMALE                          114                            141
  MALE                             97                            124
[1] 2 2
[1] FALSE
D21V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 21(14Q13.3) MUTATED                            9
  AMP PEAK 21(14Q13.3) WILD-TYPE                          6
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 21(14Q13.3) MUTATED                                  31
  AMP PEAK 21(14Q13.3) WILD-TYPE                                63
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 21(14Q13.3) MUTATED                                                  151
  AMP PEAK 21(14Q13.3) WILD-TYPE                                                152
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 21(14Q13.3) MUTATED                                            1
  AMP PEAK 21(14Q13.3) WILD-TYPE                                          4
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 21(14Q13.3) MUTATED                                               6
  AMP PEAK 21(14Q13.3) WILD-TYPE                                            13
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 21(14Q13.3) MUTATED                                1
  AMP PEAK 21(14Q13.3) WILD-TYPE                              1
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 21(14Q13.3) MUTATED                                    2
  AMP PEAK 21(14Q13.3) WILD-TYPE                                  2
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 21(14Q13.3) MUTATED                              0
  AMP PEAK 21(14Q13.3) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 21(14Q13.3) MUTATED                               7
  AMP PEAK 21(14Q13.3) WILD-TYPE                            12
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 21(14Q13.3) MUTATED                                 0
  AMP PEAK 21(14Q13.3) WILD-TYPE                               1
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 21(14Q13.3) MUTATED                                               2
  AMP PEAK 21(14Q13.3) WILD-TYPE                                             3
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 21(14Q13.3) MUTATED                              1
  AMP PEAK 21(14Q13.3) WILD-TYPE                            6
D21V9, multiclass
                                                    clus
vv                                                   AMP PEAK 21(14Q13.3) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            31
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          151
  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 21(14Q13.3) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              63
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            152
  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                                                 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"
D21V10, binary
                                cls
clus                               0   1
  AMP PEAK 21(14Q13.3) MUTATED     7 204
  AMP PEAK 21(14Q13.3) WILD-TYPE  14 251
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(14Q13.3) MUTATED      7  204
  AMP PEAK 21(14Q13.3) WILD-TYPE   14  251
     clus
vv    AMP PEAK 21(14Q13.3) MUTATED AMP PEAK 21(14Q13.3) WILD-TYPE
  NO                             7                             14
  YES                          204                            251
[1] 2 2
[1] FALSE
D21V11, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 21(14Q13.3) MUTATED   144   6   1   9
  AMP PEAK 21(14Q13.3) WILD-TYPE 183   6   3  12
D21V12, multiclass
    clus
vv   AMP PEAK 21(14Q13.3) MUTATED AMP PEAK 21(14Q13.3) WILD-TYPE
  R0                          144                            183
  R1                            6                              6
  R2                            1                              3
  RX                            9                             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 21(14Q13.3) MUTATED                                  0     4
  AMP PEAK 21(14Q13.3) WILD-TYPE                                1     2
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 21(14Q13.3) MUTATED                          14   166
  AMP PEAK 21(14Q13.3) WILD-TYPE                        21   201
D21V13, multiclass
                                  clus
vv                                 AMP PEAK 21(14Q13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  14
  WHITE                                                     166
                                  clus
vv                                 AMP PEAK 21(14Q13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         2
  BLACK OR AFRICAN AMERICAN                                    21
  WHITE                                                       201
[1] 4 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(14Q13.3) MUTATED     2 157
  AMP PEAK 21(14Q13.3) WILD-TYPE   5 188
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(14Q13.3) MUTATED      2  157
  AMP PEAK 21(14Q13.3) WILD-TYPE    5  188
                        clus
vv                       AMP PEAK 21(14Q13.3) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          157
                        clus
vv                       AMP PEAK 21(14Q13.3) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            188
[1] 2 2
[1] FALSE

Clustering(22) Variable = AMP PEAK 22(16P11.2) MUTATION ANALYSIS
D22V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 22(16P11.2) MUTATED   110  28
  AMP PEAK 22(16P11.2) WILD-TYPE 219  59
  AMP PEAK 22(16P11.2) MUTATED AMP PEAK 22(16P11.2) WILD-TYPE 
                           138                            278 
  AMP PEAK 22(16P11.2) MUTATED AMP PEAK 22(16P11.2) WILD-TYPE 
                            28                             59 
$`AMP PEAK 22(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          600           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-73-A9RS 
         214           61         1600          467           40          305 
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-78-7154 TCGA-78-7156 TCGA-78-7159 TCGA-78-7161 TCGA-78-7163 
        1202         1948         1961         1221          215         1950 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7542 TCGA-78-8640 TCGA-86-7701 TCGA-86-7713 
        1972         1949         1952         1949           11          422 
TCGA-86-7953 TCGA-86-7955 TCGA-86-8055 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
         591          508           10          476          482           16 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8673 TCGA-86-A456 
          26           35           45           34          455           10 
TCGA-86-A4D0 TCGA-91-6840 TCGA-91-8499 TCGA-93-7348 TCGA-95-7562 TCGA-95-7947 
          30          372           36          127         1973          477 
TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 TCGA-97-7937 TCGA-97-7941 TCGA-97-8177 
         121          964         1965          181           22          147 
TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M7 TCGA-99-8025 TCGA-99-8033 TCGA-J2-A4AD 
          15          115          271          427          170          287 
TCGA-J2-A4AG TCGA-L9-A443 TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4SW TCGA-S2-AA1A 
         238          116          102         1175         1967          121 

$`AMP PEAK 22(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-49-AARQ TCGA-50-5045 TCGA-50-5049 
         369          522          354         6443         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-50-5931 TCGA-50-5932 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-7109 
         267         1091          883          764          686          255 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1595 TCGA-55-1596 
        1986         1971          424          280         1479         1375 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 
          87            2          993         1239           25         1475 
TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7283 TCGA-55-7570 
        1826         1233         2151         1170           35            6 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7727 TCGA-55-7728 
          95           40          705           39           34           24 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-8085 
          54           19           21            3           31           33 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8094 TCGA-55-8205 TCGA-55-8207 
         462          100            6            4           33           66 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 
         674          216           44           23           29            8 
TCGA-55-8508 TCGA-55-8511 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
          15            9          146          202          536           15 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A491 
          48           49          106           33           42         1952 
TCGA-55-A492 TCGA-55-A494 TCGA-55-A4DF TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 
           1            5           47         1216         1289         2696 
TCGA-62-8402 TCGA-62-A46U TCGA-62-A471 TCGA-62-A472 TCGA-64-1677 TCGA-64-1678 
        1445         2067         1246          910          628         1189 
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-67-3773 TCGA-67-3774 TCGA-67-6216 TCGA-69-7761 TCGA-69-7763 
         610          427          385          141          186          690 
TCGA-69-7765 TCGA-69-7974 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
         165          184           89          100           77          129 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 
         711          912          800          131          164           38 
TCGA-73-7498 TCGA-73-7499 TCGA-75-7027 TCGA-75-7031 TCGA-78-7147 TCGA-78-7148 
         621          519         1956         1965         1950         1944 
TCGA-78-7153 TCGA-78-7155 TCGA-78-7158 TCGA-78-7160 TCGA-78-7162 TCGA-78-7166 
         760         1957         1963          678         1940         1934 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7633 
        1937         1965         1944          327          881          994 
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-86-6851 TCGA-86-7711 TCGA-86-7714 TCGA-86-7954 TCGA-86-8054 
         824         1959          630         1968         1963          745 
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-86-8358 TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 TCGA-86-A4P7 TCGA-86-A4P8 
          19           18           15          405           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-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
         842          224           35          492          505          174 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 
          44          218          297          186           34            2 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VN 
         568          377          476          830           84          553 
TCGA-95-A4VP TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-8171 TCGA-97-8172 
         605         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-L9-A50W TCGA-L9-A743 TCGA-L9-A7SV TCGA-MN-A4N1 TCGA-MN-A4N5 
           6          266          312          111          827           84 
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 22(16P11.2) MUTATED AMP PEAK 22(16P11.2) WILD-TYPE 
                             3                              1 
  AMP PEAK 22(16P11.2) MUTATED AMP PEAK 22(16P11.2) WILD-TYPE 
                          2370                           6443 
  AMP PEAK 22(16P11.2) MUTATED AMP PEAK 22(16P11.2) WILD-TYPE 
                         398.5                          544.5 
[1] "3.0 - 2370.0 (398.5)" "1.0 - 6443.0 (544.5)"
[1] "hr=" "1"  
D22V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 22(16P11.2) MUTATED         2       42       39        15        20
  AMP PEAK 22(16P11.2) WILD-TYPE       3       74       93        34        50
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 22(16P11.2) MUTATED           22          4        9
  AMP PEAK 22(16P11.2) WILD-TYPE         46          7       15
D22V3, multiclass
            clus
vv           AMP PEAK 22(16P11.2) MUTATED AMP PEAK 22(16P11.2) WILD-TYPE
  STAGE I                               2                              3
  STAGE IA                             42                             74
  STAGE IB                             39                             93
  STAGE IIA                            15                             34
  STAGE IIB                            20                             50
  STAGE IIIA                           22                             46
  STAGE IIIB                            4                              7
  STAGE IV                              9                             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(16P11.2) MUTATED    53  78  16   5
  AMP PEAK 22(16P11.2) WILD-TYPE  94 189  26  13
D22V4, multiclass
    clus
vv   AMP PEAK 22(16P11.2) MUTATED AMP PEAK 22(16P11.2) WILD-TYPE
  T1                           53                             94
  T2                           78                            189
  T3                           16                             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 22(16P11.2) MUTATED    94  28    26
  AMP PEAK 22(16P11.2) WILD-TYPE 207  63    48
D22V5, multiclass
       clus
vv      AMP PEAK 22(16P11.2) MUTATED AMP PEAK 22(16P11.2) WILD-TYPE
  N0                              94                            207
  N1                              28                             63
  N2+N3                           26                             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 22(16P11.2) MUTATED   104   6   0   3  37
  AMP PEAK 22(16P11.2) WILD-TYPE 222  12   1   1  86
D22V6, multiclass
     clus
vv    AMP PEAK 22(16P11.2) MUTATED AMP PEAK 22(16P11.2) WILD-TYPE
  M0                           104                            222
  M1                             6                             12
  M1A                            0                              1
  M1B                            3                              1
  MX                            37                             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"
D22V7, binary
                                cls
clus                               0   1
  AMP PEAK 22(16P11.2) MUTATED    86  67
  AMP PEAK 22(16P11.2) WILD-TYPE 169 154
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(16P11.2) MUTATED     86   67
  AMP PEAK 22(16P11.2) WILD-TYPE  169  154
        clus
vv       AMP PEAK 22(16P11.2) MUTATED AMP PEAK 22(16P11.2) WILD-TYPE
  FEMALE                           86                            169
  MALE                             67                            154
[1] 2 2
[1] FALSE
D22V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 22(16P11.2) MUTATED                            4
  AMP PEAK 22(16P11.2) WILD-TYPE                         11
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 22(16P11.2) MUTATED                                  24
  AMP PEAK 22(16P11.2) WILD-TYPE                                70
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 22(16P11.2) MUTATED                                                  108
  AMP PEAK 22(16P11.2) WILD-TYPE                                                195
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 22(16P11.2) MUTATED                                            2
  AMP PEAK 22(16P11.2) WILD-TYPE                                          3
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 22(16P11.2) MUTATED                                               6
  AMP PEAK 22(16P11.2) WILD-TYPE                                            13
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 22(16P11.2) MUTATED                                0
  AMP PEAK 22(16P11.2) WILD-TYPE                              2
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 22(16P11.2) MUTATED                                    2
  AMP PEAK 22(16P11.2) WILD-TYPE                                  2
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 22(16P11.2) MUTATED                              0
  AMP PEAK 22(16P11.2) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 22(16P11.2) MUTATED                               6
  AMP PEAK 22(16P11.2) WILD-TYPE                            13
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 22(16P11.2) MUTATED                                 0
  AMP PEAK 22(16P11.2) WILD-TYPE                               1
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 22(16P11.2) MUTATED                                               1
  AMP PEAK 22(16P11.2) WILD-TYPE                                             4
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 22(16P11.2) MUTATED                              0
  AMP PEAK 22(16P11.2) WILD-TYPE                            7
D22V9, multiclass
                                                    clus
vv                                                   AMP PEAK 22(16P11.2) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            24
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          108
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 6
  LUNG CLEAR CELL ADENOCARCINOMA                                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            2
  LUNG MUCINOUS ADENOCARCINOMA                                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                                 6
  LUNG SIGNET RING ADENOCARCINOMA                                               0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 1
  MUCINOUS (COLLOID) CARCINOMA                                                  0
                                                    clus
vv                                                   AMP PEAK 22(16P11.2) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              70
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            195
  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                                   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"
D22V10, binary
                                cls
clus                               0   1
  AMP PEAK 22(16P11.2) MUTATED     6 147
  AMP PEAK 22(16P11.2) WILD-TYPE  15 308
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(16P11.2) MUTATED      6  147
  AMP PEAK 22(16P11.2) WILD-TYPE   15  308
     clus
vv    AMP PEAK 22(16P11.2) MUTATED AMP PEAK 22(16P11.2) WILD-TYPE
  NO                             6                             15
  YES                          147                            308
[1] 2 2
[1] FALSE
D22V11, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 22(16P11.2) MUTATED   110   5   1   9
  AMP PEAK 22(16P11.2) WILD-TYPE 217   7   3  12
D22V12, multiclass
    clus
vv   AMP PEAK 22(16P11.2) MUTATED AMP PEAK 22(16P11.2) WILD-TYPE
  R0                          110                            217
  R1                            5                              7
  R2                            1                              3
  RX                            9                             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 22(16P11.2) MUTATED                                  1     2
  AMP PEAK 22(16P11.2) WILD-TYPE                                0     4
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 22(16P11.2) MUTATED                          10   125
  AMP PEAK 22(16P11.2) WILD-TYPE                        25   242
D22V13, multiclass
                                  clus
vv                                 AMP PEAK 22(16P11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  10
  WHITE                                                     125
                                  clus
vv                                 AMP PEAK 22(16P11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    25
  WHITE                                                       242
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V14, binary
                                cls
clus                               0   1
  AMP PEAK 22(16P11.2) MUTATED     2 113
  AMP PEAK 22(16P11.2) WILD-TYPE   5 232
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(16P11.2) MUTATED      2  113
  AMP PEAK 22(16P11.2) WILD-TYPE    5  232
                        clus
vv                       AMP PEAK 22(16P11.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          113
                        clus
vv                       AMP PEAK 22(16P11.2) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            232
[1] 2 2
[1] FALSE

Clustering(23) Variable = AMP PEAK 23(17Q12) MUTATION ANALYSIS
D23V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 23(17Q12) MUTATED   151  38
  AMP PEAK 23(17Q12) WILD-TYPE 178  49
  AMP PEAK 23(17Q12) MUTATED AMP PEAK 23(17Q12) WILD-TYPE 
                         189                          227 
  AMP PEAK 23(17Q12) MUTATED AMP PEAK 23(17Q12) WILD-TYPE 
                          38                           49 
$`AMP PEAK 23(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-49-AARQ TCGA-50-5049 TCGA-50-5930 TCGA-50-5931 
         890          522         6443         2146          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-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-55-7281 TCGA-55-7576 TCGA-55-7727 TCGA-55-7815 
         993           24           18           40           34           54 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
          19           16           21           31            5           33 
TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8205 TCGA-55-8207 TCGA-55-8208 
         100           26            4           33           66          674 
TCGA-55-8302 TCGA-55-8507 TCGA-55-8510 TCGA-55-8511 TCGA-55-8514 TCGA-55-8616 
          23            8          228            9          202           48 
TCGA-55-8620 TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A494 TCGA-55-A4DG 
          66           29           48         1952            5          162 
TCGA-62-8398 TCGA-62-8402 TCGA-62-A471 TCGA-64-1676 TCGA-64-1677 TCGA-64-1680 
        1970         1445         1246         1728          628         1126 
TCGA-64-5774 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-6215 TCGA-69-7760 
        1959           31          610          573          174          202 
TCGA-69-7761 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-A59K 
         186          230          184           70          382          214 
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-75-7031 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
         164          519         1965         1973         1988         1950 
TCGA-78-7149 TCGA-78-7154 TCGA-78-7156 TCGA-78-7159 TCGA-78-7161 TCGA-78-7167 
        1093         1948         1961         1221          215         1937 
TCGA-78-7220 TCGA-78-7536 TCGA-78-7539 TCGA-78-7633 TCGA-78-8640 TCGA-78-8660 
        1965         1949          327          994         1949         1954 
TCGA-78-8662 TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 
        1964         1959          630          422          591         1963 
TCGA-86-7955 TCGA-86-8055 TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 TCGA-86-8358 
         508           10           24          479          482           19 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-91-6828 
          35           45           34           30           14          323 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-93-7348 
          79          417          372          842          224          127 
TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
         186           34            2          568          377          477 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VN TCGA-97-7553 TCGA-97-7554 TCGA-97-8175 
         830           84          553         1332          775           87 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-99-8025 TCGA-99-8032 
         147           15          148          115          427           44 
TCGA-J2-A4AD TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 
         287          116            6          312          111          102 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4T4 TCGA-MP-A4T8 
         827         1175           84         1946         1954         1957 
TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TK 
        1980         1970         1971 

$`AMP PEAK 23(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          705           39           39           24 
TCGA-55-7910 TCGA-55-7914 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8096 
         197            3          462            6          600           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-73-A9RS 
         129          711          131           38          621          305 
TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7148 TCGA-78-7150 TCGA-78-7152 
        1970         1967         1956         1944         1963         1202 
TCGA-78-7153 TCGA-78-7155 TCGA-78-7158 TCGA-78-7160 TCGA-78-7162 TCGA-78-7163 
         760         1957         1963          678         1940         1950 
TCGA-78-7166 TCGA-78-7535 TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-8648 
        1934         1972         1944          881         1952         1971 
TCGA-78-8655 TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 TCGA-86-7701 TCGA-86-7714 
        1981         1965         1972          824           11         1968 
TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 
         745         1963           13          489          476           16 
TCGA-86-8281 TCGA-86-8359 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
        1955           26           18           15          455          405 
TCGA-86-A456 TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6849 
          10           39         1940           60          310           35 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
         492          505          174           36           44          218 
TCGA-93-7347 TCGA-95-7562 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VP TCGA-97-7546 
         297         1973          476          121          605          964 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
        1965         1932          181           22          107          182 
TCGA-97-8174 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8028 TCGA-99-8033 
        1965          197          271          392          459          170 
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-L9-A50W TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T7 TCGA-MP-A4TA TCGA-MP-A4TC 
         266         1967         1951         1954         1951         1944 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A5C7 TCGA-S2-AA1A 
        1970          142         1955         1490          121 

  AMP PEAK 23(17Q12) MUTATED AMP PEAK 23(17Q12) WILD-TYPE 
                           2                            1 
  AMP PEAK 23(17Q12) MUTATED AMP PEAK 23(17Q12) WILD-TYPE 
                        6443                         2696 
  AMP PEAK 23(17Q12) MUTATED AMP PEAK 23(17Q12) WILD-TYPE 
                         455                          486 
[1] "2.0 - 6443.0 (455.0)" "1.0 - 2696.0 (486.0)"
[1] "hr=" "1.1"
D23V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 23(17Q12) MUTATED         3       49       60        23        29
  AMP PEAK 23(17Q12) WILD-TYPE       2       67       72        26        41
                              vv
clus                           STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 23(17Q12) MUTATED           33          8       12
  AMP PEAK 23(17Q12) WILD-TYPE         35          3       12
D23V3, multiclass
            clus
vv           AMP PEAK 23(17Q12) MUTATED AMP PEAK 23(17Q12) WILD-TYPE
  STAGE I                             3                            2
  STAGE IA                           49                           67
  STAGE IB                           60                           72
  STAGE IIA                          23                           26
  STAGE IIB                          29                           41
  STAGE IIIA                         33                           35
  STAGE IIIB                          8                            3
  STAGE IV                           12                           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 23(17Q12) MUTATED    59 130  18   9
  AMP PEAK 23(17Q12) WILD-TYPE  88 137  24   9
D23V4, multiclass
    clus
vv   AMP PEAK 23(17Q12) MUTATED AMP PEAK 23(17Q12) WILD-TYPE
  T1                         59                           88
  T2                        130                          137
  T3                         18                           24
  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 23(17Q12) MUTATED   133  43    38
  AMP PEAK 23(17Q12) WILD-TYPE 168  48    36
D23V5, multiclass
       clus
vv      AMP PEAK 23(17Q12) MUTATED AMP PEAK 23(17Q12) WILD-TYPE
  N0                           133                          168
  N1                            43                           48
  N2+N3                         38                           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 23(17Q12) MUTATED   152  10   0   2  53
  AMP PEAK 23(17Q12) WILD-TYPE 174   8   1   2  70
D23V6, multiclass
     clus
vv    AMP PEAK 23(17Q12) MUTATED AMP PEAK 23(17Q12) WILD-TYPE
  M0                         152                          174
  M1                          10                            8
  M1A                          0                            1
  M1B                          2                            2
  MX                          53                           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"
D23V7, binary
                              cls
clus                             0   1
  AMP PEAK 23(17Q12) MUTATED   111 106
  AMP PEAK 23(17Q12) WILD-TYPE 144 115
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 23(17Q12) MUTATED    111  106
  AMP PEAK 23(17Q12) WILD-TYPE  144  115
        clus
vv       AMP PEAK 23(17Q12) MUTATED AMP PEAK 23(17Q12) WILD-TYPE
  FEMALE                        111                          144
  MALE                          106                          115
[1] 2 2
[1] FALSE
D23V8, continuous
                              vv
clus                           LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 23(17Q12) MUTATED                            7
  AMP PEAK 23(17Q12) WILD-TYPE                          8
                              vv
clus                           LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 23(17Q12) MUTATED                                  45
  AMP PEAK 23(17Q12) WILD-TYPE                                49
                              vv
clus                           LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 23(17Q12) MUTATED                                                  143
  AMP PEAK 23(17Q12) WILD-TYPE                                                160
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 23(17Q12) MUTATED                                            1
  AMP PEAK 23(17Q12) WILD-TYPE                                          4
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 23(17Q12) MUTATED                                               5
  AMP PEAK 23(17Q12) WILD-TYPE                                            14
                              vv
clus                           LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 23(17Q12) MUTATED                                2
  AMP PEAK 23(17Q12) WILD-TYPE                              0
                              vv
clus                           LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 23(17Q12) MUTATED                                    2
  AMP PEAK 23(17Q12) WILD-TYPE                                  2
                              vv
clus                           LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 23(17Q12) MUTATED                              1
  AMP PEAK 23(17Q12) WILD-TYPE                            1
                              vv
clus                           LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 23(17Q12) MUTATED                               6
  AMP PEAK 23(17Q12) WILD-TYPE                            13
                              vv
clus                           LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 23(17Q12) MUTATED                                 0
  AMP PEAK 23(17Q12) WILD-TYPE                               1
                              vv
clus                           LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 23(17Q12) MUTATED                                               4
  AMP PEAK 23(17Q12) WILD-TYPE                                             1
                              vv
clus                           MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 23(17Q12) MUTATED                              1
  AMP PEAK 23(17Q12) WILD-TYPE                            6
D23V9, multiclass
                                                    clus
vv                                                   AMP PEAK 23(17Q12) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                  7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                          45
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                        143
  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                               4
  MUCINOUS (COLLOID) CARCINOMA                                                1
                                                    clus
vv                                                   AMP PEAK 23(17Q12) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                    8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            49
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          160
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                14
  LUNG CLEAR CELL ADENOCARCINOMA                                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            2
  LUNG MUCINOUS ADENOCARCINOMA                                                  1
  LUNG PAPILLARY ADENOCARCINOMA                                                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"
D23V10, binary
                              cls
clus                             0   1
  AMP PEAK 23(17Q12) MUTATED    12 205
  AMP PEAK 23(17Q12) WILD-TYPE   9 250
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 23(17Q12) MUTATED     12  205
  AMP PEAK 23(17Q12) WILD-TYPE    9  250
     clus
vv    AMP PEAK 23(17Q12) MUTATED AMP PEAK 23(17Q12) WILD-TYPE
  NO                          12                            9
  YES                        205                          250
[1] 2 2
[1] FALSE
D23V11, continuous
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 23(17Q12) MUTATED   145   5   2  15
  AMP PEAK 23(17Q12) WILD-TYPE 182   7   2   6
D23V12, multiclass
    clus
vv   AMP PEAK 23(17Q12) MUTATED AMP PEAK 23(17Q12) WILD-TYPE
  R0                        145                          182
  R1                          5                            7
  R2                          2                            2
  RX                         15                            6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 23(17Q12) MUTATED                                  1     4
  AMP PEAK 23(17Q12) WILD-TYPE                                0     2
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 23(17Q12) MUTATED                          14   167
  AMP PEAK 23(17Q12) WILD-TYPE                        21   200
D23V13, multiclass
                                  clus
vv                                 AMP PEAK 23(17Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          1
  ASIAN                                                     4
  BLACK OR AFRICAN AMERICAN                                14
  WHITE                                                   167
                                  clus
vv                                 AMP PEAK 23(17Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  21
  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"
D23V14, binary
                              cls
clus                             0   1
  AMP PEAK 23(17Q12) MUTATED     3 153
  AMP PEAK 23(17Q12) WILD-TYPE   4 192
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 23(17Q12) MUTATED      3  153
  AMP PEAK 23(17Q12) WILD-TYPE    4  192
                        clus
vv                       AMP PEAK 23(17Q12) MUTATED
  HISPANIC OR LATINO                              3
  NOT HISPANIC OR LATINO                        153
                        clus
vv                       AMP PEAK 23(17Q12) WILD-TYPE
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          192
[1] 2 2
[1] FALSE

Clustering(24) Variable = AMP PEAK 24(17Q23.1) MUTATION ANALYSIS
D24V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 24(17Q23.1) MUTATED   164  39
  AMP PEAK 24(17Q23.1) WILD-TYPE 165  48
  AMP PEAK 24(17Q23.1) MUTATED AMP PEAK 24(17Q23.1) WILD-TYPE 
                           203                            213 
  AMP PEAK 24(17Q23.1) MUTATED AMP PEAK 24(17Q23.1) WILD-TYPE 
                            39                             48 
$`AMP PEAK 24(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-55-8208 TCGA-55-8302 TCGA-55-8506 
           4           33           66          674           23           11 
TCGA-55-8507 TCGA-55-8510 TCGA-55-8514 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Z 
           8          228          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-A46U TCGA-62-A471 TCGA-64-1676 TCGA-64-1677 TCGA-64-1680 TCGA-64-5774 
        2067         1246         1728          628         1126         1959 
TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-6215 TCGA-67-6217 
         866           31          610          573          174          422 
TCGA-69-7760 TCGA-69-7764 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 
         202          414          230          184           70          382 
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-73-4675 TCGA-73-4676 TCGA-73-7499 TCGA-75-6214 TCGA-75-7031 TCGA-78-7145 
          40          164          519         1970         1965         1973 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 TCGA-78-7154 TCGA-78-7159 TCGA-78-7161 
        1988         1950         1093         1948         1221          215 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7539 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
        1937         1965          327         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-86-7955 TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 TCGA-86-8075 
         591          508           10         1963           24          479 
TCGA-86-8279 TCGA-86-8358 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8672 
         482           19           35           45           34           15 
TCGA-86-8673 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-91-6828 TCGA-91-6835 
         455           10           30           14          323           79 
TCGA-91-6836 TCGA-91-6847 TCGA-91-6848 TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 
         417          842          224          127          186           34 
TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
           2          568          377          830           84          121 
TCGA-95-A4VN TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-8175 TCGA-97-8177 
         553         1332          775          181           87          147 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
          15          148          115          427          459           44 
TCGA-99-8033 TCGA-J2-A4AD TCGA-L4-A4E5 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 
         170          287          578          116            6          312 
TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
         111          102          827         1175           84         1946 
TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TK 
        1954         1957         1980         1970         1971 

$`AMP PEAK 24(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-49-AARQ TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
        6443         2174         2146          455          785          944 
TCGA-50-5072 TCGA-50-5932 TCGA-50-5942 TCGA-50-7109 TCGA-50-8460 TCGA-53-7626 
         246         1091          883          255          105         1971 
TCGA-53-A4EZ TCGA-55-1596 TCGA-55-6543 TCGA-55-6969 TCGA-55-6972 TCGA-55-6980 
         280         1375            2         1239         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-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 
           4           95          705           39           39           24 
TCGA-55-7910 TCGA-55-7914 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 
         197            3           33          462            6          600 
TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8299 TCGA-55-8301 
          26           47           15           46          216           44 
TCGA-55-8505 TCGA-55-8508 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 
          29           15            9            3          146          536 
TCGA-55-8615 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A492 
          15           49          106           33           42            1 
TCGA-55-A493 TCGA-55-A4DF TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 TCGA-62-A46V 
          28           47         1216         1289         2696         2199 
TCGA-62-A472 TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 TCGA-64-5775 TCGA-64-5778 
         910         1189         1686         1968           62         1305 
TCGA-64-5779 TCGA-64-5781 TCGA-67-3773 TCGA-67-3774 TCGA-67-6216 TCGA-69-7761 
         864         1559          427          385          141          186 
TCGA-69-7763 TCGA-69-7765 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-69-A59K 
         690          165           89          100           77          214 
TCGA-73-4659 TCGA-73-4670 TCGA-73-4677 TCGA-73-7498 TCGA-73-A9RS TCGA-75-7025 
         711          131           38          621          305         1967 
TCGA-75-7027 TCGA-78-7148 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7155 
        1956         1944         1963         1202          760         1957 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
        1961         1963          678         1940         1950         1934 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 TCGA-78-8648 TCGA-80-5607 
        1972         1949         1944          881         1971         1965 
TCGA-80-5608 TCGA-83-5908 TCGA-86-7701 TCGA-86-7714 TCGA-86-7954 TCGA-86-8054 
        1972          824           11         1968         1963          745 
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-86-8671 TCGA-86-8674 TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
          18          405           39         1940           60          310 
TCGA-91-6840 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
         372           35          492          505          174           36 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 
          44          218          297         1973          477          476 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7941 TCGA-97-8171 
         605          964         1965         1932           22          107 
TCGA-97-8172 TCGA-97-8174 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 TCGA-J2-8192 
         182         1965          197          271          392          154 
TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A50W TCGA-MP-A4SW 
         114          282          238          435          266         1967 
TCGA-MP-A4T2 TCGA-MP-A4T7 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TF TCGA-MP-A4TH 
        1951         1954         1951         1944         1970          142 
TCGA-MP-A4TI TCGA-MP-A5C7 TCGA-S2-AA1A 
        1955         1490          121 

  AMP PEAK 24(17Q23.1) MUTATED AMP PEAK 24(17Q23.1) WILD-TYPE 
                             2                              1 
  AMP PEAK 24(17Q23.1) MUTATED AMP PEAK 24(17Q23.1) WILD-TYPE 
                          2370                           6443 
  AMP PEAK 24(17Q23.1) MUTATED AMP PEAK 24(17Q23.1) WILD-TYPE 
                           455                            492 
[1] "2.0 - 2370.0 (455.0)" "1.0 - 6443.0 (492.0)"
[1] "hr=" "1"  
D24V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 24(17Q23.1) MUTATED         3       49       67        24        33
  AMP PEAK 24(17Q23.1) WILD-TYPE       2       67       65        25        37
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 24(17Q23.1) MUTATED           37          8       13
  AMP PEAK 24(17Q23.1) WILD-TYPE         31          3       11
D24V3, multiclass
            clus
vv           AMP PEAK 24(17Q23.1) MUTATED AMP PEAK 24(17Q23.1) WILD-TYPE
  STAGE I                               3                              2
  STAGE IA                             49                             67
  STAGE IB                             67                             65
  STAGE IIA                            24                             25
  STAGE IIB                            33                             37
  STAGE IIIA                           37                             31
  STAGE IIIB                            8                              3
  STAGE IV                             13                             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 24(17Q23.1) MUTATED    62 142  19   9
  AMP PEAK 24(17Q23.1) WILD-TYPE  85 125  23   9
D24V4, multiclass
    clus
vv   AMP PEAK 24(17Q23.1) MUTATED AMP PEAK 24(17Q23.1) WILD-TYPE
  T1                           62                             85
  T2                          142                            125
  T3                           19                             23
  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 24(17Q23.1) MUTATED   141  47    41
  AMP PEAK 24(17Q23.1) WILD-TYPE 160  44    33
D24V5, multiclass
       clus
vv      AMP PEAK 24(17Q23.1) MUTATED AMP PEAK 24(17Q23.1) WILD-TYPE
  N0                             141                            160
  N1                              47                             44
  N2+N3                           41                             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
  AMP PEAK 24(17Q23.1) MUTATED   164  11   0   2  57
  AMP PEAK 24(17Q23.1) WILD-TYPE 162   7   1   2  66
D24V6, multiclass
     clus
vv    AMP PEAK 24(17Q23.1) MUTATED AMP PEAK 24(17Q23.1) WILD-TYPE
  M0                           164                            162
  M1                            11                              7
  M1A                            0                              1
  M1B                            2                              2
  MX                            57                             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"
D24V7, binary
                                cls
clus                               0   1
  AMP PEAK 24(17Q23.1) MUTATED   127 107
  AMP PEAK 24(17Q23.1) WILD-TYPE 128 114
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(17Q23.1) MUTATED    127  107
  AMP PEAK 24(17Q23.1) WILD-TYPE  128  114
        clus
vv       AMP PEAK 24(17Q23.1) MUTATED AMP PEAK 24(17Q23.1) WILD-TYPE
  FEMALE                          127                            128
  MALE                            107                            114
[1] 2 2
[1] FALSE
D24V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 24(17Q23.1) MUTATED                            6
  AMP PEAK 24(17Q23.1) WILD-TYPE                          9
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 24(17Q23.1) MUTATED                                  49
  AMP PEAK 24(17Q23.1) WILD-TYPE                                45
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 24(17Q23.1) MUTATED                                                  155
  AMP PEAK 24(17Q23.1) WILD-TYPE                                                148
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 24(17Q23.1) MUTATED                                            1
  AMP PEAK 24(17Q23.1) WILD-TYPE                                          4
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 24(17Q23.1) MUTATED                                               6
  AMP PEAK 24(17Q23.1) WILD-TYPE                                            13
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 24(17Q23.1) MUTATED                                2
  AMP PEAK 24(17Q23.1) WILD-TYPE                              0
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 24(17Q23.1) MUTATED                                    3
  AMP PEAK 24(17Q23.1) WILD-TYPE                                  1
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 24(17Q23.1) MUTATED                              1
  AMP PEAK 24(17Q23.1) WILD-TYPE                            1
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 24(17Q23.1) MUTATED                               5
  AMP PEAK 24(17Q23.1) WILD-TYPE                            14
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 24(17Q23.1) MUTATED                                 0
  AMP PEAK 24(17Q23.1) WILD-TYPE                               1
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 24(17Q23.1) MUTATED                                               5
  AMP PEAK 24(17Q23.1) WILD-TYPE                                             0
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 24(17Q23.1) MUTATED                              1
  AMP PEAK 24(17Q23.1) WILD-TYPE                            6
D24V9, multiclass
                                                    clus
vv                                                   AMP PEAK 24(17Q23.1) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            49
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          155
  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                                 5
  MUCINOUS (COLLOID) CARCINOMA                                                  1
                                                    clus
vv                                                   AMP PEAK 24(17Q23.1) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              45
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            148
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  13
  LUNG CLEAR CELL ADENOCARCINOMA                                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              1
  LUNG MUCINOUS ADENOCARCINOMA                                                    1
  LUNG PAPILLARY ADENOCARCINOMA                                                  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"
D24V10, binary
                                cls
clus                               0   1
  AMP PEAK 24(17Q23.1) MUTATED    10 224
  AMP PEAK 24(17Q23.1) WILD-TYPE  11 231
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(17Q23.1) MUTATED     10  224
  AMP PEAK 24(17Q23.1) WILD-TYPE   11  231
     clus
vv    AMP PEAK 24(17Q23.1) MUTATED AMP PEAK 24(17Q23.1) WILD-TYPE
  NO                            10                             11
  YES                          224                            231
[1] 2 2
[1] FALSE
D24V11, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 24(17Q23.1) MUTATED   159   4   2  16
  AMP PEAK 24(17Q23.1) WILD-TYPE 168   8   2   5
D24V12, multiclass
    clus
vv   AMP PEAK 24(17Q23.1) MUTATED AMP PEAK 24(17Q23.1) WILD-TYPE
  R0                          159                            168
  R1                            4                              8
  R2                            2                              2
  RX                           16                              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 24(17Q23.1) MUTATED                                  1     4
  AMP PEAK 24(17Q23.1) WILD-TYPE                                0     2
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 24(17Q23.1) MUTATED                          13   181
  AMP PEAK 24(17Q23.1) WILD-TYPE                        22   186
D24V13, multiclass
                                  clus
vv                                 AMP PEAK 24(17Q23.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  13
  WHITE                                                     181
                                  clus
vv                                 AMP PEAK 24(17Q23.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         2
  BLACK OR AFRICAN AMERICAN                                    22
  WHITE                                                       186
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V14, binary
                                cls
clus                               0   1
  AMP PEAK 24(17Q23.1) MUTATED     5 164
  AMP PEAK 24(17Q23.1) WILD-TYPE   2 181
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(17Q23.1) MUTATED      5  164
  AMP PEAK 24(17Q23.1) WILD-TYPE    2  181
                        clus
vv                       AMP PEAK 24(17Q23.1) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          164
                        clus
vv                       AMP PEAK 24(17Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            181
[1] 2 2
[1] FALSE

Clustering(25) Variable = AMP PEAK 25(18Q11.2) MUTATION ANALYSIS
D25V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 25(18Q11.2) MUTATED    73  20
  AMP PEAK 25(18Q11.2) WILD-TYPE 256  67
  AMP PEAK 25(18Q11.2) MUTATED AMP PEAK 25(18Q11.2) WILD-TYPE 
                            93                            323 
  AMP PEAK 25(18Q11.2) MUTATED AMP PEAK 25(18Q11.2) WILD-TYPE 
                            20                             67 
$`AMP PEAK 25(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-95-7562 TCGA-97-7546 TCGA-97-7547 TCGA-97-7554 TCGA-97-8175 TCGA-97-8179 
        1973          964         1965          775           87           15 
TCGA-97-8552 TCGA-L9-A7SV TCGA-S2-AA1A 
         115          111          121 

$`AMP PEAK 25(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-49-AARQ TCGA-50-5045 TCGA-50-5049 
         157          445          890         6443         2174         2146 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 TCGA-50-5932 
         455          785          944          246          282         1091 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        2370          653          567          883          764          686 
TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ 
        1015          255          105         1986         1971          280 
TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6712 TCGA-55-6969 
        1178         1375           87            2           24         1239 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
          25         1475         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-55-7815 
          40          705           39           39           34           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-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
          33          462            6          600           26            4 
TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
          15           33           46           66          674          216 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 
          44           23           29           11            8          228 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 
           3          146          202          536           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-62-8395 TCGA-62-8397 TCGA-62-A46U 
        1952            1           28         1216         1289         2067 
TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 
        2199         1246          910         1686         1126         1968 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 
        1959           62         1305         1559          866           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-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7765 TCGA-69-7974 
         422          202          186          690          165          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-73-4666 TCGA-73-4670 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
         711          800          131           38          621          519 
TCGA-73-A9RS TCGA-75-7025 TCGA-75-7027 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
         305         1967         1956         1973         1988         1950 
TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 
        1093         1202          760         1948         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-78-7220 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-78-8660 TCGA-80-5607 TCGA-80-5608 
         994         1949         1971         1954         1965         1972 
TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 TCGA-86-7953 
         824         1959           11          630         1968          591 
TCGA-86-7954 TCGA-86-8054 TCGA-86-8056 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
        1963          745         1963          489          476          482 
TCGA-86-8280 TCGA-86-8281 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
          16         1955           45           34           18           15 
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-91-6830 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          505          174           44          218          297 
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-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
         477          476          830           84          121          553 
TCGA-95-A4VP TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 
         605         1932         1332          181           22          107 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8177 TCGA-97-8547 TCGA-97-A4M2 TCGA-97-A4M7 
         182         1965          147          148          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-L9-A50W TCGA-L9-A743 TCGA-L9-A8F4 TCGA-MN-A4N1 
         116            6          266          312          102          827 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 
        1175           84         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 

  AMP PEAK 25(18Q11.2) MUTATED AMP PEAK 25(18Q11.2) WILD-TYPE 
                             5                              1 
  AMP PEAK 25(18Q11.2) MUTATED AMP PEAK 25(18Q11.2) WILD-TYPE 
                          2696                           6443 
  AMP PEAK 25(18Q11.2) MUTATED AMP PEAK 25(18Q11.2) WILD-TYPE 
                           522                            459 
[1] "5.0 - 2696.0 (522.0)" "1.0 - 6443.0 (459.0)"
[1] "hr=" "1"  
D25V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 25(18Q11.2) MUTATED         2       20       32        13        11
  AMP PEAK 25(18Q11.2) WILD-TYPE       3       96      100        36        59
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 25(18Q11.2) MUTATED           15          3        2
  AMP PEAK 25(18Q11.2) WILD-TYPE         53          8       22
D25V3, multiclass
            clus
vv           AMP PEAK 25(18Q11.2) MUTATED AMP PEAK 25(18Q11.2) WILD-TYPE
  STAGE I                               2                              3
  STAGE IA                             20                             96
  STAGE IB                             32                            100
  STAGE IIA                            13                             36
  STAGE IIB                            11                             59
  STAGE IIIA                           15                             53
  STAGE IIIB                            3                              8
  STAGE IV                              2                             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 25(18Q11.2) MUTATED    29  59   7   3
  AMP PEAK 25(18Q11.2) WILD-TYPE 118 208  35  15
D25V4, multiclass
    clus
vv   AMP PEAK 25(18Q11.2) MUTATED AMP PEAK 25(18Q11.2) WILD-TYPE
  T1                           29                            118
  T2                           59                            208
  T3                            7                             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 25(18Q11.2) MUTATED    63  20    15
  AMP PEAK 25(18Q11.2) WILD-TYPE 238  71    59
D25V5, multiclass
       clus
vv      AMP PEAK 25(18Q11.2) MUTATED AMP PEAK 25(18Q11.2) WILD-TYPE
  N0                              63                            238
  N1                              20                             71
  N2+N3                           15                             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 25(18Q11.2) MUTATED    67   2   0   0  28
  AMP PEAK 25(18Q11.2) WILD-TYPE 259  16   1   4  95
D25V6, multiclass
     clus
vv    AMP PEAK 25(18Q11.2) MUTATED AMP PEAK 25(18Q11.2) WILD-TYPE
  M0                            67                            259
  M1                             2                             16
  M1A                            0                              1
  M1B                            0                              4
  MX                            28                             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"
D25V7, binary
                                cls
clus                               0   1
  AMP PEAK 25(18Q11.2) MUTATED    47  51
  AMP PEAK 25(18Q11.2) WILD-TYPE 208 170
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 25(18Q11.2) MUTATED     47   51
  AMP PEAK 25(18Q11.2) WILD-TYPE  208  170
        clus
vv       AMP PEAK 25(18Q11.2) MUTATED AMP PEAK 25(18Q11.2) WILD-TYPE
  FEMALE                           47                            208
  MALE                             51                            170
[1] 2 2
[1] FALSE
D25V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 25(18Q11.2) MUTATED                            4
  AMP PEAK 25(18Q11.2) WILD-TYPE                         11
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 25(18Q11.2) MUTATED                                  16
  AMP PEAK 25(18Q11.2) WILD-TYPE                                78
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 25(18Q11.2) MUTATED                                                   58
  AMP PEAK 25(18Q11.2) WILD-TYPE                                                245
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 25(18Q11.2) MUTATED                                            1
  AMP PEAK 25(18Q11.2) WILD-TYPE                                          4
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 25(18Q11.2) MUTATED                                               5
  AMP PEAK 25(18Q11.2) WILD-TYPE                                            14
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 25(18Q11.2) MUTATED                                2
  AMP PEAK 25(18Q11.2) WILD-TYPE                              0
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 25(18Q11.2) MUTATED                                    1
  AMP PEAK 25(18Q11.2) WILD-TYPE                                  3
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 25(18Q11.2) MUTATED                              1
  AMP PEAK 25(18Q11.2) WILD-TYPE                            1
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 25(18Q11.2) MUTATED                               6
  AMP PEAK 25(18Q11.2) WILD-TYPE                            13
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 25(18Q11.2) MUTATED                                 0
  AMP PEAK 25(18Q11.2) WILD-TYPE                               1
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 25(18Q11.2) MUTATED                                               2
  AMP PEAK 25(18Q11.2) WILD-TYPE                                             3
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 25(18Q11.2) MUTATED                              2
  AMP PEAK 25(18Q11.2) WILD-TYPE                            5
D25V9, multiclass
                                                    clus
vv                                                   AMP PEAK 25(18Q11.2) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            16
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           58
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 5
  LUNG CLEAR CELL ADENOCARCINOMA                                                2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            1
  LUNG MUCINOUS ADENOCARCINOMA                                                  1
  LUNG PAPILLARY ADENOCARCINOMA                                                 6
  LUNG SIGNET RING ADENOCARCINOMA                                               0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 2
  MUCINOUS (COLLOID) CARCINOMA                                                  2
                                                    clus
vv                                                   AMP PEAK 25(18Q11.2) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              78
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            245
  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                                   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"
D25V10, binary
                                cls
clus                               0   1
  AMP PEAK 25(18Q11.2) MUTATED     2  96
  AMP PEAK 25(18Q11.2) WILD-TYPE  19 359
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 25(18Q11.2) MUTATED      2   96
  AMP PEAK 25(18Q11.2) WILD-TYPE   19  359
     clus
vv    AMP PEAK 25(18Q11.2) MUTATED AMP PEAK 25(18Q11.2) WILD-TYPE
  NO                             2                             19
  YES                           96                            359
[1] 2 2
[1] FALSE
D25V11, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 25(18Q11.2) MUTATED    63   2   0   6
  AMP PEAK 25(18Q11.2) WILD-TYPE 264  10   4  15
D25V12, multiclass
    clus
vv   AMP PEAK 25(18Q11.2) MUTATED AMP PEAK 25(18Q11.2) WILD-TYPE
  R0                           63                            264
  R1                            2                             10
  R2                            0                              4
  RX                            6                             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 25(18Q11.2) MUTATED                                  1     1
  AMP PEAK 25(18Q11.2) WILD-TYPE                                0     5
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 25(18Q11.2) MUTATED                           8    72
  AMP PEAK 25(18Q11.2) WILD-TYPE                        27   295
D25V13, multiclass
                                  clus
vv                                 AMP PEAK 25(18Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   8
  WHITE                                                      72
                                  clus
vv                                 AMP PEAK 25(18Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         5
  BLACK OR AFRICAN AMERICAN                                    27
  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"
D25V14, binary
                                cls
clus                               0   1
  AMP PEAK 25(18Q11.2) MUTATED     1  67
  AMP PEAK 25(18Q11.2) WILD-TYPE   6 278
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 25(18Q11.2) MUTATED      1   67
  AMP PEAK 25(18Q11.2) WILD-TYPE    6  278
                        clus
vv                       AMP PEAK 25(18Q11.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           67
                        clus
vv                       AMP PEAK 25(18Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            278
[1] 2 2
[1] FALSE

Clustering(26) Variable = AMP PEAK 26(19Q12) MUTATION ANALYSIS
D26V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 26(19Q12) MUTATED    96  17
  AMP PEAK 26(19Q12) WILD-TYPE 233  70
  AMP PEAK 26(19Q12) MUTATED AMP PEAK 26(19Q12) WILD-TYPE 
                         113                          303 
  AMP PEAK 26(19Q12) MUTATED AMP PEAK 26(19Q12) WILD-TYPE 
                          17                           70 
$`AMP PEAK 26(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-L9-A8F4 
          87           15          427          170          116          102 
TCGA-MN-A4N4 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4TH TCGA-S2-AA1A 
        1175         1954         1954          142          121 

$`AMP PEAK 26(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-49-AARQ TCGA-50-5045 TCGA-50-5051 
        1700          522          354         6443         2174          455 
TCGA-50-5055 TCGA-50-5068 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
         785         1499          267         1091         2370          653 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-7109 TCGA-50-8460 TCGA-53-7626 
         567          883          764          255          105         1971 
TCGA-55-1592 TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
         701         1479         1375           87            2          993 
TCGA-55-6712 TCGA-55-6969 TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 
          24         1239           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-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
          95           40          705           39           39           34 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
          24           54           19          197           21            3 
TCGA-55-7994 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8094 
          31          462          100            6          600            4 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
          47           15           33           46           66          674 
TCGA-55-8299 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
         216           29           11           15          228            9 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8616 TCGA-55-8619 TCGA-55-8621 
           3          146          202           48           49          106 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A490 TCGA-55-A492 TCGA-55-A494 TCGA-55-A4DG 
          33           42           48            1            5          162 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8402 TCGA-62-A46U TCGA-62-A46V 
        1216         1289         1970         1445         2067         2199 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1680 TCGA-64-1681 
        1246          910         1728          628         1126         1968 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 
        1959           62          866           31          610          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-69-7974 TCGA-69-8254 TCGA-69-8255 TCGA-71-6725 TCGA-73-4658 
         165          184           77          129           61         1600 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 
         711          912          800          467          131          164 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS TCGA-75-6214 TCGA-75-7025 
          38          621          519          305         1970         1967 
TCGA-75-7027 TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 
        1956         1965         1973         1988         1950         1093 
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-78-7160 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-78-7542 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-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
        1964         1965          824         1959           11          630 
TCGA-86-7714 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8056 TCGA-86-8076 
        1968         1963          508          745         1963          489 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8281 TCGA-86-8668 TCGA-86-8669 
         476          482           16         1955           45           34 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 
          18           15          405           30           14           39 
TCGA-91-6828 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6847 TCGA-91-6848 
         323          310           79          417          842          224 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
          35          492          505          174           36           44 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7562 
         218          297          127          186           34         1973 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VN TCGA-95-A4VP 
         477          476          830           84          553          605 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7941 TCGA-97-8171 
         964         1965         1932         1332           22          107 
TCGA-97-8177 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 
         147          148          115          197          271          392 
TCGA-99-8028 TCGA-99-8032 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
         459           44          154          114          287          282 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A743 
         238          578          435            6          266          312 
TCGA-L9-A7SV TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 
         111          827           84         1946         1967         1951 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TF 
        1957         1980         1951         1944         1970         1970 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
        1955         1971         1490 

  AMP PEAK 26(19Q12) MUTATED AMP PEAK 26(19Q12) WILD-TYPE 
                           2                            1 
  AMP PEAK 26(19Q12) MUTATED AMP PEAK 26(19Q12) WILD-TYPE 
                        2696                         6443 
  AMP PEAK 26(19Q12) MUTATED AMP PEAK 26(19Q12) WILD-TYPE 
                         424                          489 
[1] "2.0 - 2696.0 (424.0)" "1.0 - 6443.0 (489.0)"
[1] "hr=" "1.3"
D26V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 26(19Q12) MUTATED         1       30       37        12        18
  AMP PEAK 26(19Q12) WILD-TYPE       4       86       95        37        52
                              vv
clus                           STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 26(19Q12) MUTATED           21          5        7
  AMP PEAK 26(19Q12) WILD-TYPE         47          6       17
D26V3, multiclass
            clus
vv           AMP PEAK 26(19Q12) MUTATED AMP PEAK 26(19Q12) WILD-TYPE
  STAGE I                             1                            4
  STAGE IA                           30                           86
  STAGE IB                           37                           95
  STAGE IIA                          12                           37
  STAGE IIB                          18                           52
  STAGE IIIA                         21                           47
  STAGE IIIB                          5                            6
  STAGE IV                            7                           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 26(19Q12) MUTATED    38  72  15   4
  AMP PEAK 26(19Q12) WILD-TYPE 109 195  27  14
D26V4, multiclass
    clus
vv   AMP PEAK 26(19Q12) MUTATED AMP PEAK 26(19Q12) WILD-TYPE
  T1                         38                          109
  T2                         72                          195
  T3                         15                           27
  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 26(19Q12) MUTATED    81  24    24
  AMP PEAK 26(19Q12) WILD-TYPE 220  67    50
D26V5, multiclass
       clus
vv      AMP PEAK 26(19Q12) MUTATED AMP PEAK 26(19Q12) WILD-TYPE
  N0                            81                          220
  N1                            24                           67
  N2+N3                         24                           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 26(19Q12) MUTATED    92   5   0   2  31
  AMP PEAK 26(19Q12) WILD-TYPE 234  13   1   2  92
D26V6, multiclass
     clus
vv    AMP PEAK 26(19Q12) MUTATED AMP PEAK 26(19Q12) WILD-TYPE
  M0                          92                          234
  M1                           5                           13
  M1A                          0                            1
  M1B                          2                            2
  MX                          31                           92
[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(19Q12) MUTATED    61  70
  AMP PEAK 26(19Q12) WILD-TYPE 194 151
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 26(19Q12) MUTATED     61   70
  AMP PEAK 26(19Q12) WILD-TYPE  194  151
        clus
vv       AMP PEAK 26(19Q12) MUTATED AMP PEAK 26(19Q12) WILD-TYPE
  FEMALE                         61                          194
  MALE                           70                          151
[1] 2 2
[1] FALSE
D26V8, continuous
                              vv
clus                           LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 26(19Q12) MUTATED                            6
  AMP PEAK 26(19Q12) WILD-TYPE                          9
                              vv
clus                           LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 26(19Q12) MUTATED                                  28
  AMP PEAK 26(19Q12) WILD-TYPE                                66
                              vv
clus                           LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 26(19Q12) MUTATED                                                   75
  AMP PEAK 26(19Q12) WILD-TYPE                                                228
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 26(19Q12) MUTATED                                            1
  AMP PEAK 26(19Q12) WILD-TYPE                                          4
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 26(19Q12) MUTATED                                               5
  AMP PEAK 26(19Q12) WILD-TYPE                                            14
                              vv
clus                           LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 26(19Q12) MUTATED                                1
  AMP PEAK 26(19Q12) WILD-TYPE                              1
                              vv
clus                           LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 26(19Q12) MUTATED                                    1
  AMP PEAK 26(19Q12) WILD-TYPE                                  3
                              vv
clus                           LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 26(19Q12) MUTATED                              0
  AMP PEAK 26(19Q12) WILD-TYPE                            2
                              vv
clus                           LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 26(19Q12) MUTATED                               9
  AMP PEAK 26(19Q12) WILD-TYPE                            10
                              vv
clus                           LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 26(19Q12) MUTATED                                 1
  AMP PEAK 26(19Q12) WILD-TYPE                               0
                              vv
clus                           LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 26(19Q12) MUTATED                                               2
  AMP PEAK 26(19Q12) WILD-TYPE                                             3
                              vv
clus                           MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 26(19Q12) MUTATED                              2
  AMP PEAK 26(19Q12) WILD-TYPE                            5
D26V9, multiclass
                                                    clus
vv                                                   AMP PEAK 26(19Q12) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                  6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                          28
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         75
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                  1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                               5
  LUNG CLEAR CELL ADENOCARCINOMA                                              1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                          1
  LUNG MUCINOUS ADENOCARCINOMA                                                0
  LUNG PAPILLARY ADENOCARCINOMA                                               9
  LUNG SIGNET RING ADENOCARCINOMA                                             1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                               2
  MUCINOUS (COLLOID) CARCINOMA                                                2
                                                    clus
vv                                                   AMP PEAK 26(19Q12) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                    9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            66
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          228
  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                                 3
  MUCINOUS (COLLOID) CARCINOMA                                                  5
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V10, binary
                              cls
clus                             0   1
  AMP PEAK 26(19Q12) MUTATED     4 127
  AMP PEAK 26(19Q12) WILD-TYPE  17 328
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 26(19Q12) MUTATED      4  127
  AMP PEAK 26(19Q12) WILD-TYPE   17  328
     clus
vv    AMP PEAK 26(19Q12) MUTATED AMP PEAK 26(19Q12) WILD-TYPE
  NO                           4                           17
  YES                        127                          328
[1] 2 2
[1] FALSE
D26V11, continuous
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 26(19Q12) MUTATED    82   4   1   6
  AMP PEAK 26(19Q12) WILD-TYPE 245   8   3  15
D26V12, multiclass
    clus
vv   AMP PEAK 26(19Q12) MUTATED AMP PEAK 26(19Q12) WILD-TYPE
  R0                         82                          245
  R1                          4                            8
  R2                          1                            3
  RX                          6                           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 26(19Q12) MUTATED                                  0     1
  AMP PEAK 26(19Q12) WILD-TYPE                                1     5
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 26(19Q12) MUTATED                          11   101
  AMP PEAK 26(19Q12) WILD-TYPE                        24   266
D26V13, multiclass
                                  clus
vv                                 AMP PEAK 26(19Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     1
  BLACK OR AFRICAN AMERICAN                                11
  WHITE                                                   101
                                  clus
vv                                 AMP PEAK 26(19Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  24
  WHITE                                                     266
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V14, binary
                              cls
clus                             0   1
  AMP PEAK 26(19Q12) MUTATED     2  99
  AMP PEAK 26(19Q12) WILD-TYPE   5 246
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 26(19Q12) MUTATED      2   99
  AMP PEAK 26(19Q12) WILD-TYPE    5  246
                        clus
vv                       AMP PEAK 26(19Q12) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                         99
                        clus
vv                       AMP PEAK 26(19Q12) WILD-TYPE
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          246
[1] 2 2
[1] FALSE

Clustering(27) Variable = AMP PEAK 27(20Q13.33) MUTATION ANALYSIS
D27V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 27(20Q13.33) MUTATED   164  39
  AMP PEAK 27(20Q13.33) WILD-TYPE 165  48
  AMP PEAK 27(20Q13.33) MUTATED AMP PEAK 27(20Q13.33) WILD-TYPE 
                            203                             213 
  AMP PEAK 27(20Q13.33) MUTATED AMP PEAK 27(20Q13.33) WILD-TYPE 
                             39                              48 
$`AMP PEAK 27(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-49-AARQ TCGA-50-5045 TCGA-50-5049 TCGA-50-5066 TCGA-50-5068 
        1700         6443         2174         2146          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-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 
        1015          424          280          701         1178         1375 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6972 
          87            2          993           24         1239         1475 
TCGA-55-7284 TCGA-55-7724 TCGA-55-7726 TCGA-55-7907 TCGA-55-7910 TCGA-55-7995 
         121          705           39           16          197            5 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 
          33          462           26           47           15           33 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8302 TCGA-55-8507 TCGA-55-8508 
          46           66          674           23            8           15 
TCGA-55-8512 TCGA-55-8514 TCGA-55-8615 TCGA-55-8620 TCGA-55-A48Z TCGA-55-A491 
           3          202           15           66           29         1952 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8397 TCGA-62-8399 
          28            5           47          162         1289         2696 
TCGA-62-8402 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-1681 TCGA-64-5774 
        1445         1728          628         1189         1968         1959 
TCGA-64-5779 TCGA-64-5781 TCGA-67-3771 TCGA-67-3772 TCGA-67-6215 TCGA-67-6216 
         864         1559          610          573          174          141 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 
         186          690          414          230           70           89 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8255 TCGA-71-6725 TCGA-73-4658 TCGA-73-4662 
         382          100          129           61         1600          912 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4677 TCGA-73-7499 
         800          467          131           40           38          519 
TCGA-73-A9RS TCGA-75-6214 TCGA-75-7031 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
         305         1970         1965         1202          760         1948 
TCGA-78-7155 TCGA-78-7159 TCGA-78-7161 TCGA-78-7163 TCGA-78-7220 TCGA-78-7535 
        1957         1221          215         1950         1965         1972 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7542 TCGA-78-8640 TCGA-78-8660 TCGA-80-5608 
        1949         1944         1952         1949         1954         1972 
TCGA-83-5908 TCGA-86-6851 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
         824         1959         1963          508          745           10 
TCGA-86-8073 TCGA-86-8075 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 
          13          479          476          482           16           26 
TCGA-86-8585 TCGA-86-8669 TCGA-91-6828 TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 
          35           34          323         1940          310           79 
TCGA-91-6836 TCGA-91-6847 TCGA-91-7771 TCGA-91-8499 TCGA-91-A4BC TCGA-93-8067 
         417          842          492           36           44          186 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7947 TCGA-95-8494 
          34            2         1973          568          477           84 
TCGA-97-7546 TCGA-97-7553 TCGA-97-7937 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 
         964         1332          181           87          147           15 
TCGA-97-8552 TCGA-99-8025 TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L9-A444 TCGA-L9-A7SV 
         115          427          282          578            6          111 
TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4T2 
         102          827         1175           84         1946         1951 
TCGA-MP-A4T7 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-S2-AA1A 
        1954         1970         1970          142          121 

$`AMP PEAK 27(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          600            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          505          174          218 
TCGA-93-7347 TCGA-93-7348 TCGA-95-7944 TCGA-95-7948 TCGA-95-8039 TCGA-95-A4VK 
         297          127          377          476          830          121 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7547 TCGA-97-7552 TCGA-97-7554 TCGA-97-7941 
         553          605         1965         1932          775           22 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8547 TCGA-97-A4M2 TCGA-97-A4M7 
         107          182         1965          148          197          271 
TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
         392          459           44          170          154          114 
TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A50W TCGA-L9-A743 
         287          238          435          116          266          312 
TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
        1967         1954         1957         1980         1951         1944 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
        1955         1971         1490 

  AMP PEAK 27(20Q13.33) MUTATED AMP PEAK 27(20Q13.33) WILD-TYPE 
                              2                               1 
  AMP PEAK 27(20Q13.33) MUTATED AMP PEAK 27(20Q13.33) WILD-TYPE 
                           6443                            2199 
  AMP PEAK 27(20Q13.33) MUTATED AMP PEAK 27(20Q13.33) WILD-TYPE 
                            535                             435 
[1] "2.0 - 6443.0 (535.0)" "1.0 - 2199.0 (435.0)"
[1] "hr=" "1.1"
D27V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 27(20Q13.33) MUTATED         4       59       75        24        32
  AMP PEAK 27(20Q13.33) WILD-TYPE       1       57       57        25        38
                                 vv
clus                              STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 27(20Q13.33) MUTATED           25          5        8
  AMP PEAK 27(20Q13.33) WILD-TYPE         43          6       16
D27V3, multiclass
            clus
vv           AMP PEAK 27(20Q13.33) MUTATED AMP PEAK 27(20Q13.33) WILD-TYPE
  STAGE I                                4                               1
  STAGE IA                              59                              57
  STAGE IB                              75                              57
  STAGE IIA                             24                              25
  STAGE IIB                             32                              38
  STAGE IIIA                            25                              43
  STAGE IIIB                             5                               6
  STAGE IV                               8                              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 27(20Q13.33) MUTATED    70 136  21   4
  AMP PEAK 27(20Q13.33) WILD-TYPE  77 131  21  14
D27V4, multiclass
    clus
vv   AMP PEAK 27(20Q13.33) MUTATED AMP PEAK 27(20Q13.33) WILD-TYPE
  T1                            70                              77
  T2                           136                             131
  T3                            21                              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 27(20Q13.33) MUTATED   157  42    29
  AMP PEAK 27(20Q13.33) WILD-TYPE 144  49    45
D27V5, multiclass
       clus
vv      AMP PEAK 27(20Q13.33) MUTATED AMP PEAK 27(20Q13.33) WILD-TYPE
  N0                              157                             144
  N1                               42                              49
  N2+N3                            29                              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 27(20Q13.33) MUTATED   159   5   0   3  62
  AMP PEAK 27(20Q13.33) WILD-TYPE 167  13   1   1  61
D27V6, multiclass
     clus
vv    AMP PEAK 27(20Q13.33) MUTATED AMP PEAK 27(20Q13.33) WILD-TYPE
  M0                            159                             167
  M1                              5                              13
  M1A                             0                               1
  M1B                             3                               1
  MX                             62                              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"
D27V7, binary
                                 cls
clus                                0   1
  AMP PEAK 27(20Q13.33) MUTATED   124 108
  AMP PEAK 27(20Q13.33) WILD-TYPE 131 113
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(20Q13.33) MUTATED    124  108
  AMP PEAK 27(20Q13.33) WILD-TYPE  131  113
        clus
vv       AMP PEAK 27(20Q13.33) MUTATED AMP PEAK 27(20Q13.33) WILD-TYPE
  FEMALE                           124                             131
  MALE                             108                             113
[1] 2 2
[1] FALSE
D27V8, continuous
                                 vv
clus                              LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 27(20Q13.33) MUTATED                            9
  AMP PEAK 27(20Q13.33) WILD-TYPE                          6
                                 vv
clus                              LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 27(20Q13.33) MUTATED                                  38
  AMP PEAK 27(20Q13.33) WILD-TYPE                                56
                                 vv
clus                              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 27(20Q13.33) MUTATED                                                  157
  AMP PEAK 27(20Q13.33) WILD-TYPE                                                146
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 27(20Q13.33) MUTATED                                            2
  AMP PEAK 27(20Q13.33) WILD-TYPE                                          3
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 27(20Q13.33) MUTATED                                              10
  AMP PEAK 27(20Q13.33) WILD-TYPE                                             9
                                 vv
clus                              LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 27(20Q13.33) MUTATED                                0
  AMP PEAK 27(20Q13.33) WILD-TYPE                              2
                                 vv
clus                              LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 27(20Q13.33) MUTATED                                    2
  AMP PEAK 27(20Q13.33) WILD-TYPE                                  2
                                 vv
clus                              LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 27(20Q13.33) MUTATED                              0
  AMP PEAK 27(20Q13.33) WILD-TYPE                            2
                                 vv
clus                              LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 27(20Q13.33) MUTATED                               8
  AMP PEAK 27(20Q13.33) WILD-TYPE                            11
                                 vv
clus                              LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 27(20Q13.33) MUTATED                                 1
  AMP PEAK 27(20Q13.33) WILD-TYPE                               0
                                 vv
clus                              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 27(20Q13.33) MUTATED                                               4
  AMP PEAK 27(20Q13.33) WILD-TYPE                                             1
                                 vv
clus                              MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 27(20Q13.33) MUTATED                              1
  AMP PEAK 27(20Q13.33) WILD-TYPE                            6
D27V9, multiclass
                                                    clus
vv                                                   AMP PEAK 27(20Q13.33) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                     9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             38
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           157
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 10
  LUNG CLEAR CELL ADENOCARCINOMA                                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             2
  LUNG MUCINOUS ADENOCARCINOMA                                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                                  8
  LUNG SIGNET RING ADENOCARCINOMA                                                1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                  4
  MUCINOUS (COLLOID) CARCINOMA                                                   1
                                                    clus
vv                                                   AMP PEAK 27(20Q13.33) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                       6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                               56
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             146
  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                                                     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"
D27V10, binary
                                 cls
clus                                0   1
  AMP PEAK 27(20Q13.33) MUTATED     9 223
  AMP PEAK 27(20Q13.33) WILD-TYPE  12 232
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(20Q13.33) MUTATED      9  223
  AMP PEAK 27(20Q13.33) WILD-TYPE   12  232
     clus
vv    AMP PEAK 27(20Q13.33) MUTATED AMP PEAK 27(20Q13.33) WILD-TYPE
  NO                              9                              12
  YES                           223                             232
[1] 2 2
[1] FALSE
D27V11, continuous
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 27(20Q13.33) MUTATED   152   7   2  10
  AMP PEAK 27(20Q13.33) WILD-TYPE 175   5   2  11
D27V12, multiclass
    clus
vv   AMP PEAK 27(20Q13.33) MUTATED AMP PEAK 27(20Q13.33) WILD-TYPE
  R0                           152                             175
  R1                             7                               5
  R2                             2                               2
  RX                            10                              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 27(20Q13.33) MUTATED                                  1     3
  AMP PEAK 27(20Q13.33) WILD-TYPE                                0     3
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 27(20Q13.33) MUTATED                          22   177
  AMP PEAK 27(20Q13.33) WILD-TYPE                        13   190
D27V13, multiclass
                                  clus
vv                                 AMP PEAK 27(20Q13.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        3
  BLACK OR AFRICAN AMERICAN                                   22
  WHITE                                                      177
                                  clus
vv                                 AMP PEAK 27(20Q13.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          3
  BLACK OR AFRICAN AMERICAN                                     13
  WHITE                                                        190
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V14, binary
                                 cls
clus                                0   1
  AMP PEAK 27(20Q13.33) MUTATED     4 173
  AMP PEAK 27(20Q13.33) WILD-TYPE   3 172
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(20Q13.33) MUTATED      4  173
  AMP PEAK 27(20Q13.33) WILD-TYPE    3  172
                        clus
vv                       AMP PEAK 27(20Q13.33) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           173
                        clus
vv                       AMP PEAK 27(20Q13.33) WILD-TYPE
  HISPANIC OR LATINO                                   3
  NOT HISPANIC OR LATINO                             172
[1] 2 2
[1] FALSE

Clustering(28) Variable = AMP PEAK 28(22Q11.22) MUTATION ANALYSIS
D28V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 28(22Q11.22) MUTATED    57  17
  AMP PEAK 28(22Q11.22) WILD-TYPE 272  70
  AMP PEAK 28(22Q11.22) MUTATED AMP PEAK 28(22Q11.22) WILD-TYPE 
                             74                             342 
  AMP PEAK 28(22Q11.22) MUTATED AMP PEAK 28(22Q11.22) WILD-TYPE 
                             17                              70 
$`AMP PEAK 28(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          705           39 
TCGA-55-7907 TCGA-55-8091 TCGA-55-8096 TCGA-55-8208 TCGA-55-8506 TCGA-55-8511 
          16          600           47          674           11            9 
TCGA-55-8514 TCGA-55-8614 TCGA-55-A490 TCGA-55-A491 TCGA-62-8397 TCGA-62-8398 
         202          536           48         1952         1289         1970 
TCGA-62-8402 TCGA-64-1679 TCGA-67-3770 TCGA-67-3771 TCGA-69-7979 TCGA-69-8253 
        1445         1686           31          610           89          100 
TCGA-73-4675 TCGA-75-7031 TCGA-78-7150 TCGA-78-7154 TCGA-78-7155 TCGA-78-7536 
          40         1965         1963         1948         1957         1949 
TCGA-78-8662 TCGA-86-7713 TCGA-86-7955 TCGA-86-8055 TCGA-86-8280 TCGA-86-8358 
        1964          422          508           10           16           19 
TCGA-86-A4D0 TCGA-91-6847 TCGA-95-7567 TCGA-95-7944 TCGA-95-8494 TCGA-97-7553 
          30          842          568          377           84         1332 
TCGA-97-8174 TCGA-97-8552 TCGA-J2-A4AE TCGA-L9-A8F4 TCGA-MP-A4SW TCGA-MP-A4T7 
        1965          115          282          102         1967         1954 
TCGA-MP-A4TC TCGA-MP-A5C7 
        1944         1490 

$`AMP PEAK 28(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-49-AARQ TCGA-50-5045 
        1700          890          522          354         6443         2174 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
        2146          455          785          944         1499          246 
TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 
         282         1091         2370          653          567          883 
TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
        1015          255          105         1986         1971          424 
TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
         280         1178         1479           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-55-7283 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-55-7815 
           4           40           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-55-8089 TCGA-55-8090 TCGA-55-8092 TCGA-55-8094 
          33          462          100            6           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-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 
          23           29            8           15          228            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-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
          33           42           29            1           28            5 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 TCGA-62-8399 TCGA-62-A46U TCGA-62-A46V 
          47          162         1216         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-64-1681 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-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 
         866          573          427          385          174          141 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
         422          202          186          690          414          165 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8254 TCGA-69-8255 
         230          184           70          382           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-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
         467          131          164           38          621          519 
TCGA-73-A9RS TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7145 TCGA-78-7146 
         305         1970         1967         1956         1973         1988 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7156 
        1950         1944         1093         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-78-7220 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-78-8655 
         881         1952          994         1949         1971         1981 
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-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
          13           24          479          489          476          482 
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-A4P7 TCGA-86-A4P8 
          15          455          405           10           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-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
         372          224           35          492          505          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-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
          34            2         1973          477          476          830 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
         121          553          605          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-L9-A50W TCGA-L9-A743 TCGA-L9-A7SV TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
         266          312          111          827         1175           84 
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-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-S2-AA1A 
        1970         1970          142         1955         1971          121 

  AMP PEAK 28(22Q11.22) MUTATED AMP PEAK 28(22Q11.22) WILD-TYPE 
                              9                               1 
  AMP PEAK 28(22Q11.22) MUTATED AMP PEAK 28(22Q11.22) WILD-TYPE 
                           1978                            6443 
  AMP PEAK 28(22Q11.22) MUTATED AMP PEAK 28(22Q11.22) WILD-TYPE 
                            640                             456 
[1] "9.0 - 1978.0 (640.0)" "1.0 - 6443.0 (456.0)"
[1] "hr=" "1.2"
D28V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 28(22Q11.22) MUTATED         1       17       29        14        12
  AMP PEAK 28(22Q11.22) WILD-TYPE       4       99      103        35        58
                                 vv
clus                              STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 28(22Q11.22) MUTATED           12          1        1
  AMP PEAK 28(22Q11.22) WILD-TYPE         56         10       23
D28V3, multiclass
            clus
vv           AMP PEAK 28(22Q11.22) MUTATED AMP PEAK 28(22Q11.22) WILD-TYPE
  STAGE I                                1                               4
  STAGE IA                              17                              99
  STAGE IB                              29                             103
  STAGE IIA                             14                              35
  STAGE IIB                             12                              58
  STAGE IIIA                            12                              56
  STAGE IIIB                             1                              10
  STAGE IV                               1                              23
[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(22Q11.22) MUTATED    25  55   6   1
  AMP PEAK 28(22Q11.22) WILD-TYPE 122 212  36  17
D28V4, multiclass
    clus
vv   AMP PEAK 28(22Q11.22) MUTATED AMP PEAK 28(22Q11.22) WILD-TYPE
  T1                            25                             122
  T2                            55                             212
  T3                             6                              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
  AMP PEAK 28(22Q11.22) MUTATED    54  19    12
  AMP PEAK 28(22Q11.22) WILD-TYPE 247  72    62
D28V5, multiclass
       clus
vv      AMP PEAK 28(22Q11.22) MUTATED AMP PEAK 28(22Q11.22) WILD-TYPE
  N0                               54                             247
  N1                               19                              72
  N2+N3                            12                              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 28(22Q11.22) MUTATED    56   1   0   0  29
  AMP PEAK 28(22Q11.22) WILD-TYPE 270  17   1   4  94
D28V6, multiclass
     clus
vv    AMP PEAK 28(22Q11.22) MUTATED AMP PEAK 28(22Q11.22) WILD-TYPE
  M0                             56                             270
  M1                              1                              17
  M1A                             0                               1
  M1B                             0                               4
  MX                             29                              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"
D28V7, binary
                                 cls
clus                                0   1
  AMP PEAK 28(22Q11.22) MUTATED    52  35
  AMP PEAK 28(22Q11.22) WILD-TYPE 203 186
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 28(22Q11.22) MUTATED     52   35
  AMP PEAK 28(22Q11.22) WILD-TYPE  203  186
        clus
vv       AMP PEAK 28(22Q11.22) MUTATED AMP PEAK 28(22Q11.22) WILD-TYPE
  FEMALE                            52                             203
  MALE                              35                             186
[1] 2 2
[1] FALSE
D28V8, continuous
                                 vv
clus                              LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 28(22Q11.22) MUTATED                            2
  AMP PEAK 28(22Q11.22) WILD-TYPE                         13
                                 vv
clus                              LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 28(22Q11.22) MUTATED                                  11
  AMP PEAK 28(22Q11.22) WILD-TYPE                                83
                                 vv
clus                              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 28(22Q11.22) MUTATED                                                   67
  AMP PEAK 28(22Q11.22) WILD-TYPE                                                236
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 28(22Q11.22) MUTATED                                            0
  AMP PEAK 28(22Q11.22) WILD-TYPE                                          5
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 28(22Q11.22) MUTATED                                               3
  AMP PEAK 28(22Q11.22) WILD-TYPE                                            16
                                 vv
clus                              LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 28(22Q11.22) MUTATED                                1
  AMP PEAK 28(22Q11.22) WILD-TYPE                              1
                                 vv
clus                              LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 28(22Q11.22) MUTATED                                    1
  AMP PEAK 28(22Q11.22) WILD-TYPE                                  3
                                 vv
clus                              LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 28(22Q11.22) MUTATED                              0
  AMP PEAK 28(22Q11.22) WILD-TYPE                            2
                                 vv
clus                              LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 28(22Q11.22) MUTATED                               1
  AMP PEAK 28(22Q11.22) WILD-TYPE                            18
                                 vv
clus                              LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 28(22Q11.22) MUTATED                                 0
  AMP PEAK 28(22Q11.22) WILD-TYPE                               1
                                 vv
clus                              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 28(22Q11.22) MUTATED                                               0
  AMP PEAK 28(22Q11.22) WILD-TYPE                                             5
                                 vv
clus                              MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 28(22Q11.22) MUTATED                              1
  AMP PEAK 28(22Q11.22) WILD-TYPE                            6
D28V9, multiclass
                                                    clus
vv                                                   AMP PEAK 28(22Q11.22) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                     2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             11
  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                                             1
  LUNG MUCINOUS ADENOCARCINOMA                                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                                  1
  LUNG SIGNET RING ADENOCARCINOMA                                                0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                  0
  MUCINOUS (COLLOID) CARCINOMA                                                   1
                                                    clus
vv                                                   AMP PEAK 28(22Q11.22) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                               83
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             236
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                       5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                   16
  LUNG CLEAR CELL ADENOCARCINOMA                                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                               3
  LUNG MUCINOUS ADENOCARCINOMA                                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                                   18
  LUNG SIGNET RING ADENOCARCINOMA                                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                    5
  MUCINOUS (COLLOID) CARCINOMA                                                     6
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V10, binary
                                 cls
clus                                0   1
  AMP PEAK 28(22Q11.22) MUTATED     3  84
  AMP PEAK 28(22Q11.22) WILD-TYPE  18 371
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 28(22Q11.22) MUTATED      3   84
  AMP PEAK 28(22Q11.22) WILD-TYPE   18  371
     clus
vv    AMP PEAK 28(22Q11.22) MUTATED AMP PEAK 28(22Q11.22) WILD-TYPE
  NO                              3                              18
  YES                            84                             371
[1] 2 2
[1] FALSE
D28V11, continuous
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 28(22Q11.22) MUTATED    60   1   0   3
  AMP PEAK 28(22Q11.22) WILD-TYPE 267  11   4  18
D28V12, multiclass
    clus
vv   AMP PEAK 28(22Q11.22) MUTATED AMP PEAK 28(22Q11.22) WILD-TYPE
  R0                            60                             267
  R1                             1                              11
  R2                             0                               4
  RX                             3                              18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 28(22Q11.22) MUTATED                                  0     1
  AMP PEAK 28(22Q11.22) WILD-TYPE                                1     5
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 28(22Q11.22) MUTATED                           6    69
  AMP PEAK 28(22Q11.22) WILD-TYPE                        29   298
D28V13, multiclass
                                  clus
vv                                 AMP PEAK 28(22Q11.22) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                    6
  WHITE                                                       69
                                  clus
vv                                 AMP PEAK 28(22Q11.22) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          5
  BLACK OR AFRICAN AMERICAN                                     29
  WHITE                                                        298
[1] 4 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(22Q11.22) MUTATED     1  61
  AMP PEAK 28(22Q11.22) WILD-TYPE   6 284
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 28(22Q11.22) MUTATED      1   61
  AMP PEAK 28(22Q11.22) WILD-TYPE    6  284
                        clus
vv                       AMP PEAK 28(22Q11.22) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            61
                        clus
vv                       AMP PEAK 28(22Q11.22) WILD-TYPE
  HISPANIC OR LATINO                                   6
  NOT HISPANIC OR LATINO                             284
[1] 2 2
[1] FALSE

Clustering(29) Variable = AMP PEAK 29(XQ28) MUTATION ANALYSIS
D29V1, survival
                             sevent
clus2                           0   1
  AMP PEAK 29(XQ28) MUTATED    99  30
  AMP PEAK 29(XQ28) WILD-TYPE 230  57
  AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE 
                        129                         287 
  AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE 
                         30                          57 
$`AMP PEAK 29(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-49-AARQ TCGA-50-5045 TCGA-50-5933 TCGA-50-5941 
         890          354         6443         2174         2370          567 
TCGA-50-5946 TCGA-50-7109 TCGA-53-7624 TCGA-55-1592 TCGA-55-1595 TCGA-55-1596 
         686          255         1986          701         1479         1375 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6985 TCGA-55-6987 
          87            2          993           24         1233         1170 
TCGA-55-7281 TCGA-55-7576 TCGA-55-7726 TCGA-55-7907 TCGA-55-7994 TCGA-55-8090 
          18           40           39           16           31            6 
TCGA-55-8092 TCGA-55-8096 TCGA-55-A48Z TCGA-55-A491 TCGA-55-A494 TCGA-55-A4DF 
          26           47           29         1952            5           47 
TCGA-55-A4DG TCGA-62-8399 TCGA-62-A46U TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 
         162         2696         2067         1728          628         1189 
TCGA-64-1680 TCGA-64-5815 TCGA-67-3772 TCGA-67-6215 TCGA-69-7764 TCGA-69-7979 
        1126          866          573          174          414           89 
TCGA-71-6725 TCGA-73-4666 TCGA-73-4670 TCGA-73-4676 TCGA-73-7499 TCGA-75-6214 
          61          800          131          164          519         1970 
TCGA-75-7025 TCGA-75-7031 TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 TCGA-78-7154 
        1967         1965         1988         1950         1093         1948 
TCGA-78-7155 TCGA-78-7161 TCGA-78-7163 TCGA-78-7166 TCGA-78-7220 TCGA-78-7535 
        1957          215         1950         1934         1965         1972 
TCGA-78-7542 TCGA-78-8640 TCGA-78-8655 TCGA-83-5908 TCGA-86-7955 TCGA-86-8054 
        1952         1949         1981          824          508          745 
TCGA-86-8055 TCGA-86-8075 TCGA-86-8280 TCGA-86-8281 TCGA-86-8358 TCGA-86-8359 
          10          479           16         1955           19           26 
TCGA-86-8673 TCGA-86-A4P7 TCGA-91-6829 TCGA-91-7771 TCGA-91-8496 TCGA-91-8499 
         455           14         1940          492          505           36 
TCGA-95-7043 TCGA-95-7567 TCGA-95-8039 TCGA-95-8494 TCGA-97-7554 TCGA-97-7937 
           2          568          830           84          775          181 
TCGA-97-8172 TCGA-97-8179 TCGA-97-8547 TCGA-97-A4M7 TCGA-L9-A444 TCGA-L9-A7SV 
         182           15          148          271            6          111 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4TF 
         827         1175           84         1967         1954         1970 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-S2-AA1A 
        1955         1971          121 

$`AMP PEAK 29(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          705           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          462          100          600 
TCGA-55-8094 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
           4           15           33           46           66          674 
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-A490 TCGA-55-A492 TCGA-55-A493 TCGA-62-8395 
          33           42           48            1           28         1216 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8402 TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 
        1289         1970         1445         2199         1246          910 
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-67-3770 TCGA-67-3771 TCGA-67-3773 TCGA-67-3774 TCGA-67-6216 
        1559           31          610          427          385          141 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7765 TCGA-69-7973 
         422          202          186          690          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-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4668 TCGA-73-4675 
         214         1600          711          912          467           40 
TCGA-73-4677 TCGA-73-7498 TCGA-73-A9RS TCGA-75-7027 TCGA-78-7145 TCGA-78-7148 
          38          621          305         1956         1973         1944 
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-78-7160 TCGA-78-7162 TCGA-78-7167 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
         678         1940         1937         1949         1944          327 
TCGA-78-7540 TCGA-78-7633 TCGA-78-8648 TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 
         881          994         1971         1954         1964         1965 
TCGA-80-5608 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
        1972         1959           11          630          422         1968 
TCGA-86-7953 TCGA-86-7954 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8076 
         591         1963         1963           13           24          489 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
         476          482           35           45           34           18 
TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P8 TCGA-91-6828 
          15          405           10           30           39          323 
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-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
         224           35          174           44          218          297 
TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7562 TCGA-95-7944 TCGA-95-7947 
         127          186           34         1973          377          477 
TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
         476          121          553          605          964         1965 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 
        1932         1332           22          107         1965           87 
TCGA-97-8177 TCGA-97-8552 TCGA-97-A4M2 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
         147          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-L4-A4E6 TCGA-L9-A443 TCGA-L9-A50W TCGA-L9-A743 
         238          578          435          116          266          312 
TCGA-L9-A8F4 TCGA-MP-A4SV TCGA-MP-A4T2 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
         102         1946         1951         1954         1957         1980 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A5C7 
        1951         1944         1970          142         1490 

  AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE 
                          2                           1 
  AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE 
                       6443                        2199 
  AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE 
                        607                         445 
[1] "2.0 - 6443.0 (607.0)" "1.0 - 2199.0 (445.0)"
[1] "hr=" "1.5"
D29V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 29(XQ28) MUTATED         2       35       40        16        23
  AMP PEAK 29(XQ28) WILD-TYPE       3       81       92        33        47
                             vv
clus                          STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 29(XQ28) MUTATED           19          3        9
  AMP PEAK 29(XQ28) WILD-TYPE         49          8       15
D29V3, multiclass
            clus
vv           AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE
  STAGE I                            2                           3
  STAGE IA                          35                          81
  STAGE IB                          40                          92
  STAGE IIA                         16                          33
  STAGE IIB                         23                          47
  STAGE IIIA                        19                          49
  STAGE IIIB                         3                           8
  STAGE IV                           9                          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 29(XQ28) MUTATED    41  89  13   3
  AMP PEAK 29(XQ28) WILD-TYPE 106 178  29  15
D29V4, multiclass
    clus
vv   AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE
  T1                        41                         106
  T2                        89                         178
  T3                        13                          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
  AMP PEAK 29(XQ28) MUTATED    87  34    23
  AMP PEAK 29(XQ28) WILD-TYPE 214  57    51
D29V5, multiclass
       clus
vv      AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE
  N0                           87                         214
  N1                           34                          57
  N2+N3                        23                          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
  AMP PEAK 29(XQ28) MUTATED    96   8   0   1  40
  AMP PEAK 29(XQ28) WILD-TYPE 230  10   1   3  83
D29V6, multiclass
     clus
vv    AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE
  M0                         96                         230
  M1                          8                          10
  M1A                         0                           1
  M1B                         1                           3
  MX                         40                          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"
D29V7, binary
                             cls
clus                            0   1
  AMP PEAK 29(XQ28) MUTATED    74  73
  AMP PEAK 29(XQ28) WILD-TYPE 181 148
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 29(XQ28) MUTATED     74   73
  AMP PEAK 29(XQ28) WILD-TYPE  181  148
        clus
vv       AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE
  FEMALE                        74                         181
  MALE                          73                         148
[1] 2 2
[1] FALSE
D29V8, continuous
                             vv
clus                          LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 29(XQ28) MUTATED                            5
  AMP PEAK 29(XQ28) WILD-TYPE                         10
                             vv
clus                          LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 29(XQ28) MUTATED                                  27
  AMP PEAK 29(XQ28) WILD-TYPE                                67
                             vv
clus                          LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 29(XQ28) MUTATED                                                  102
  AMP PEAK 29(XQ28) WILD-TYPE                                                201
                             vv
clus                          LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 29(XQ28) MUTATED                                            2
  AMP PEAK 29(XQ28) WILD-TYPE                                          3
                             vv
clus                          LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 29(XQ28) MUTATED                                               4
  AMP PEAK 29(XQ28) WILD-TYPE                                            15
                             vv
clus                          LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 29(XQ28) MUTATED                                1
  AMP PEAK 29(XQ28) WILD-TYPE                              1
                             vv
clus                          LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 29(XQ28) MUTATED                                    2
  AMP PEAK 29(XQ28) WILD-TYPE                                  2
                             vv
clus                          LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 29(XQ28) MUTATED                              0
  AMP PEAK 29(XQ28) WILD-TYPE                            2
                             vv
clus                          LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 29(XQ28) MUTATED                               4
  AMP PEAK 29(XQ28) WILD-TYPE                            15
                             vv
clus                          LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 29(XQ28) MUTATED                                 0
  AMP PEAK 29(XQ28) WILD-TYPE                               1
                             vv
clus                          LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 29(XQ28) MUTATED                                               0
  AMP PEAK 29(XQ28) WILD-TYPE                                             5
                             vv
clus                          MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 29(XQ28) MUTATED                              0
  AMP PEAK 29(XQ28) WILD-TYPE                            7
D29V9, multiclass
                                                    clus
vv                                                   AMP PEAK 29(XQ28) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                 5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                         27
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                       102
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                 2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                              4
  LUNG CLEAR CELL ADENOCARCINOMA                                             1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                         2
  LUNG MUCINOUS ADENOCARCINOMA                                               0
  LUNG PAPILLARY ADENOCARCINOMA                                              4
  LUNG SIGNET RING ADENOCARCINOMA                                            0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                              0
  MUCINOUS (COLLOID) CARCINOMA                                               0
                                                    clus
vv                                                   AMP PEAK 29(XQ28) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                  10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           67
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         201
  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                                5
  MUCINOUS (COLLOID) CARCINOMA                                                 7
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V10, binary
                             cls
clus                            0   1
  AMP PEAK 29(XQ28) MUTATED     9 138
  AMP PEAK 29(XQ28) WILD-TYPE  12 317
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 29(XQ28) MUTATED      9  138
  AMP PEAK 29(XQ28) WILD-TYPE   12  317
     clus
vv    AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE
  NO                          9                          12
  YES                       138                         317
[1] 2 2
[1] FALSE
D29V11, continuous
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK 29(XQ28) MUTATED   102   5   1   4
  AMP PEAK 29(XQ28) WILD-TYPE 225   7   3  17
D29V12, multiclass
    clus
vv   AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE
  R0                       102                         225
  R1                         5                           7
  R2                         1                           3
  RX                         4                          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 29(XQ28) MUTATED                                  0     3
  AMP PEAK 29(XQ28) WILD-TYPE                                1     3
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 29(XQ28) MUTATED                          11   110
  AMP PEAK 29(XQ28) WILD-TYPE                        24   257
D29V13, multiclass
                                  clus
vv                                 AMP PEAK 29(XQ28) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    3
  BLACK OR AFRICAN AMERICAN                               11
  WHITE                                                  110
                                  clus
vv                                 AMP PEAK 29(XQ28) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 24
  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"
D29V14, binary
                             cls
clus                            0   1
  AMP PEAK 29(XQ28) MUTATED     1  98
  AMP PEAK 29(XQ28) WILD-TYPE   6 247
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 29(XQ28) MUTATED      1   98
  AMP PEAK 29(XQ28) WILD-TYPE    6  247
                        clus
vv                       AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE
  HISPANIC OR LATINO                             1                           6
  NOT HISPANIC OR LATINO                        98                         247
[1] 2 2
[1] FALSE

Clustering(30) Variable = DEL PEAK  1(1P36.13) MUTATION ANALYSIS
D30V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  1(1P36.13) MUTATED    75  22
  DEL PEAK  1(1P36.13) WILD-TYPE 254  65
  DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE 
                            97                            319 
  DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE 
                            22                             65 
$`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-73-A9RS TCGA-75-7027 TCGA-75-7031 TCGA-78-7146 TCGA-78-7148 TCGA-78-7153 
         305         1956         1965         1988         1944          760 
TCGA-78-7154 TCGA-78-7159 TCGA-78-7160 TCGA-78-7536 TCGA-78-8655 TCGA-80-5608 
        1948         1221          678         1949         1981         1972 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7713 TCGA-86-8054 TCGA-86-8358 TCGA-86-8669 
        1959           11          422          745           19           34 
TCGA-91-6828 TCGA-91-6830 TCGA-91-7771 TCGA-91-8499 TCGA-95-7043 TCGA-95-7944 
         323           60          492           36            2          377 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-8172 TCGA-L9-A743 TCGA-MP-A4T7 TCGA-MP-A4TC 
         553          605          182          312         1954         1944 
TCGA-MP-A4TE 
        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-49-AARQ TCGA-50-5045 
        1700          445          369          890         6443         2174 
TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
        2146          785          944         1499          246          282 
TCGA-50-5931 TCGA-50-5933 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
         267         2370          567          883          764          686 
TCGA-50-6597 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        1015          105         1986         1971          424          280 
TCGA-55-1592 TCGA-55-1594 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 
         701         1178            2          993           24         1239 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 TCGA-55-6987 
          25         1475           67         1826         1233         1170 
TCGA-55-7281 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
          18          121            6            4           95           40 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
         705           39           39           34           24           54 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
          19           16          197           31            5           33 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
         462          100          600           26            4           47 
TCGA-55-8097 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
          15           46           66          674          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-55-8514 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-A490 TCGA-55-A493 TCGA-55-A4DF TCGA-55-A4DG 
         106           33           48           28           47          162 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 TCGA-62-8402 TCGA-62-A471 TCGA-64-1676 
        1216         1289         2696         1445         1246         1728 
TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5775 TCGA-64-5779 
        1189         1686         1126         1968           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-69-7764 TCGA-69-7765 TCGA-69-7974 
         174          141          422          414          165          184 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
          89          382          100           77          129          214 
TCGA-71-6725 TCGA-73-4658 TCGA-73-4662 TCGA-73-4668 TCGA-73-4676 TCGA-73-7498 
          61         1600          912          467          164          621 
TCGA-73-7499 TCGA-75-6214 TCGA-75-7025 TCGA-78-7145 TCGA-78-7147 TCGA-78-7149 
         519         1970         1967         1973         1950         1093 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7161 
        1963         1202         1957         1961         1963          215 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
        1940         1950         1934         1937         1965         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-83-5908 TCGA-86-7711 
        1971         1954         1964         1965          824          630 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 
        1968          591         1963          508           10         1963 
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-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 
          16         1955           26           35           45           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-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
          39         1940          310           79          417          372 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC 
         842          224           35          505          174           44 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7562 
         218          297          127          186           34         1973 
TCGA-95-7567 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
         568          477          476          830           84          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-97-7941 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-L9-A444 
         282          238          578          435          116            6 
TCGA-L9-A50W TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
         266          111          102          827         1175           84 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4T9 
        1946         1967         1951         1954         1957         1980 
TCGA-MP-A4TA TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
        1951         1970          142         1955         1971         1490 
TCGA-S2-AA1A 
         121 

  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                           6443 
  DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE 
                           628                            448 
[1] "1.0 - 2199.0 (628.0)" "2.0 - 6443.0 (448.0)"
[1] "hr=" "1.3"
D30V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK  1(1P36.13) MUTATED         1       23       22        10        19
  DEL PEAK  1(1P36.13) WILD-TYPE       4       93      110        39        51
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK  1(1P36.13) MUTATED           25          4        7
  DEL PEAK  1(1P36.13) WILD-TYPE         43          7       17
D30V3, multiclass
            clus
vv           DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE
  STAGE I                               1                              4
  STAGE IA                             23                             93
  STAGE IB                             22                            110
  STAGE IIA                            10                             39
  STAGE IIB                            19                             51
  STAGE IIIA                           25                             43
  STAGE IIIB                            4                              7
  STAGE IV                              7                             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  1(1P36.13) MUTATED    29  60  16   5
  DEL PEAK  1(1P36.13) WILD-TYPE 118 207  26  13
D30V4, multiclass
    clus
vv   DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE
  T1                           29                            118
  T2                           60                            207
  T3                           16                             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
  DEL PEAK  1(1P36.13) MUTATED    60  24    26
  DEL PEAK  1(1P36.13) WILD-TYPE 241  67    48
D30V5, multiclass
       clus
vv      DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE
  N0                              60                            241
  N1                              24                             67
  N2+N3                           26                             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
  DEL PEAK  1(1P36.13) MUTATED    80   7   0   0  24
  DEL PEAK  1(1P36.13) WILD-TYPE 246  11   1   4  99
D30V6, multiclass
     clus
vv    DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE
  M0                            80                            246
  M1                             7                             11
  M1A                            0                              1
  M1B                            0                              4
  MX                            24                             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"
D30V7, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.13) MUTATED    51  60
  DEL PEAK  1(1P36.13) WILD-TYPE 204 161
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.13) MUTATED     51   60
  DEL PEAK  1(1P36.13) WILD-TYPE  204  161
        clus
vv       DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE
  FEMALE                           51                            204
  MALE                             60                            161
[1] 2 2
[1] FALSE
D30V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK  1(1P36.13) MUTATED                            5
  DEL PEAK  1(1P36.13) WILD-TYPE                         10
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK  1(1P36.13) MUTATED                                  26
  DEL PEAK  1(1P36.13) WILD-TYPE                                68
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  1(1P36.13) MUTATED                                                   70
  DEL PEAK  1(1P36.13) WILD-TYPE                                                233
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK  1(1P36.13) MUTATED                                            0
  DEL PEAK  1(1P36.13) WILD-TYPE                                          5
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK  1(1P36.13) MUTATED                                               3
  DEL PEAK  1(1P36.13) WILD-TYPE                                            16
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK  1(1P36.13) MUTATED                                1
  DEL PEAK  1(1P36.13) WILD-TYPE                              1
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK  1(1P36.13) MUTATED                                    0
  DEL PEAK  1(1P36.13) WILD-TYPE                                  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                                               2
  DEL PEAK  1(1P36.13) WILD-TYPE                                             3
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK  1(1P36.13) MUTATED                              2
  DEL PEAK  1(1P36.13) WILD-TYPE                            5
D30V9, multiclass
                                                    clus
vv                                                   DEL PEAK  1(1P36.13) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            26
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           70
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 3
  LUNG CLEAR CELL ADENOCARCINOMA                                                1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            0
  LUNG MUCINOUS ADENOCARCINOMA                                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                                 1
  LUNG SIGNET RING ADENOCARCINOMA                                               1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 2
  MUCINOUS (COLLOID) CARCINOMA                                                  2
                                                    clus
vv                                                   DEL PEAK  1(1P36.13) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              68
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            233
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      5
  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"
D30V10, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.13) MUTATED     5 106
  DEL PEAK  1(1P36.13) WILD-TYPE  16 349
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.13) MUTATED      5  106
  DEL PEAK  1(1P36.13) WILD-TYPE   16  349
     clus
vv    DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE
  NO                             5                             16
  YES                          106                            349
[1] 2 2
[1] FALSE
D30V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK  1(1P36.13) MUTATED    76   3   2   4
  DEL PEAK  1(1P36.13) WILD-TYPE 251   9   2  17
D30V12, multiclass
    clus
vv   DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE
  R0                           76                            251
  R1                            3                              9
  R2                            2                              2
  RX                            4                             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  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                           6    81
  DEL PEAK  1(1P36.13) WILD-TYPE                        29   286
D30V13, multiclass
                                  clus
vv                                 DEL PEAK  1(1P36.13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   6
  WHITE                                                      81
                                  clus
vv                                 DEL PEAK  1(1P36.13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    29
  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"
D30V14, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.13) MUTATED     1  75
  DEL PEAK  1(1P36.13) WILD-TYPE   6 270
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.13) MUTATED      1   75
  DEL PEAK  1(1P36.13) WILD-TYPE    6  270
                        clus
vv                       DEL PEAK  1(1P36.13) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           75
                        clus
vv                       DEL PEAK  1(1P36.13) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            270
[1] 2 2
[1] FALSE

Clustering(31) Variable = DEL PEAK  2(1P13.1) MUTATION ANALYSIS
D31V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  2(1P13.1) MUTATED   102  26
  DEL PEAK  2(1P13.1) WILD-TYPE 227  61
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                          128                           288 
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                           26                            61 
$`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-49-AARQ TCGA-50-5051 
        1700          369          522          354         6443          455 
TCGA-50-5932 TCGA-50-5935 TCGA-50-5946 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1596 
        1091          653          686          424          280         1375 
TCGA-55-5899 TCGA-55-6971 TCGA-55-6972 TCGA-55-6986 TCGA-55-7283 TCGA-55-7907 
          87           25         1475         2151           35           16 
TCGA-55-7911 TCGA-55-7994 TCGA-55-7995 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
          21           31            5            6          600           26 
TCGA-55-8094 TCGA-55-8205 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8512 
           4           33           29            8           15            3 
TCGA-55-8615 TCGA-55-A48Y TCGA-55-A492 TCGA-55-A4DF TCGA-62-8402 TCGA-62-A46U 
          15           42            1           47         1445         2067 
TCGA-62-A46V TCGA-64-1678 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
        2199         1189         1959           62         1305          864 
TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3774 TCGA-69-7761 TCGA-69-7763 
          31          610          573          385          186          690 
TCGA-69-7973 TCGA-71-6725 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4670 
         230           61          711          912          800          131 
TCGA-73-4675 TCGA-73-4677 TCGA-73-7498 TCGA-73-A9RS TCGA-75-7027 TCGA-75-7031 
          40           38          621          305         1956         1965 
TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 TCGA-78-7153 TCGA-78-7154 TCGA-78-7160 
        1988         1944         1093          760         1948          678 
TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7539 TCGA-80-5608 TCGA-86-6851 
        1950         1937         1965          327         1972         1959 
TCGA-86-7701 TCGA-86-8054 TCGA-86-8278 TCGA-86-8668 TCGA-86-8669 TCGA-86-A4D0 
          11          745          476           45           34           30 
TCGA-91-6828 TCGA-91-6836 TCGA-91-6848 TCGA-91-7771 TCGA-91-8497 TCGA-93-7348 
         323          417          224          492          174          127 
TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-95-7947 TCGA-95-8039 
         186           34            2          568          477          830 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7554 TCGA-97-8172 TCGA-97-8547 TCGA-97-8552 
         553          605          775          182          148          115 
TCGA-J2-8192 TCGA-L9-A444 TCGA-L9-A50W TCGA-MP-A4SW TCGA-MP-A4T7 TCGA-MP-A4TH 
         154            6          266         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          705           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          462 
TCGA-55-8089 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
         100           47           15           46           66          674 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8510 TCGA-55-8511 
         216           44           23           11          228            9 
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-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A493 
         106           33           29           48         1952           28 
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-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-64-5781 TCGA-64-5815 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
        1968         1559          866          427          174          141 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 
         422          202          414          165          184           70 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
          89          382          100           77          129          214 
TCGA-73-4658 TCGA-73-4668 TCGA-73-4676 TCGA-73-7499 TCGA-75-6214 TCGA-75-7025 
        1600          467          164          519         1970         1967 
TCGA-78-7145 TCGA-78-7147 TCGA-78-7150 TCGA-78-7152 TCGA-78-7155 TCGA-78-7156 
        1973         1950         1963         1202         1957         1961 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7161 TCGA-78-7162 TCGA-78-7166 TCGA-78-7535 
        1963         1221          215         1940         1934         1972 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
        1949         1944          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-86-7711 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-86-8074 TCGA-86-8075 TCGA-86-8076 
          10         1963           13           24          479          489 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8281 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
         482           16         1955           19           26           35 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 
          18           15          455          405           10           14 
TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 
          39         1940           60          310           79          372 
TCGA-91-6847 TCGA-91-6849 TCGA-91-8496 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
         842           35          505           36           44          218 
TCGA-93-7347 TCGA-95-7562 TCGA-95-7944 TCGA-95-7948 TCGA-95-8494 TCGA-95-A4VK 
         297         1973          377          476           84          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-97-8174 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-A4M2 
         107         1965           87          147           15          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-J2-8194 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-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 
         116          312          111          102          827         1175 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4T9 
          84         1946         1951         1954         1957         1980 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TI TCGA-S2-AA1A 
        1951         1944         1970         1970         1955          121 

  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 
                         6443                          2696 
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                          507                           464 
[1] "1.0 - 6443.0 (507.0)" "2.0 - 2696.0 (464.0)"
[1] "hr=" "1.1"
D31V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK  2(1P13.1) MUTATED         2       31       34        11        22
  DEL PEAK  2(1P13.1) WILD-TYPE       3       85       98        38        48
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK  2(1P13.1) MUTATED           29          5       10
  DEL PEAK  2(1P13.1) WILD-TYPE         39          6       14
D31V3, multiclass
            clus
vv           DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  STAGE I                              2                             3
  STAGE IA                            31                            85
  STAGE IB                            34                            98
  STAGE IIA                           11                            38
  STAGE IIB                           22                            48
  STAGE IIIA                          29                            39
  STAGE IIIB                           5                             6
  STAGE IV                            10                            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  2(1P13.1) MUTATED    38  83  14   8
  DEL PEAK  2(1P13.1) WILD-TYPE 109 184  28  10
D31V4, multiclass
    clus
vv   DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  T1                          38                           109
  T2                          83                           184
  T3                          14                            28
  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    87  29    28
  DEL PEAK  2(1P13.1) WILD-TYPE 214  62    46
D31V5, multiclass
       clus
vv      DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  N0                             87                           214
  N1                             29                            62
  N2+N3                          28                            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  2(1P13.1) MUTATED    97   8   0   2  36
  DEL PEAK  2(1P13.1) WILD-TYPE 229  10   1   2  87
D31V6, multiclass
     clus
vv    DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  M0                           97                           229
  M1                            8                            10
  M1A                           0                             1
  M1B                           2                             2
  MX                           36                            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"
D31V7, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.1) MUTATED    77  67
  DEL PEAK  2(1P13.1) WILD-TYPE 178 154
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.1) MUTATED     77   67
  DEL PEAK  2(1P13.1) WILD-TYPE  178  154
        clus
vv       DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  FEMALE                          77                           178
  MALE                            67                           154
[1] 2 2
[1] FALSE
D31V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  DEL PEAK  2(1P13.1) MUTATED                            8
  DEL PEAK  2(1P13.1) WILD-TYPE                          7
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK  2(1P13.1) MUTATED                                  29
  DEL PEAK  2(1P13.1) WILD-TYPE                                65
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  2(1P13.1) MUTATED                                                   86
  DEL PEAK  2(1P13.1) WILD-TYPE                                                217
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK  2(1P13.1) MUTATED                                            1
  DEL PEAK  2(1P13.1) WILD-TYPE                                          4
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK  2(1P13.1) MUTATED                                               7
  DEL PEAK  2(1P13.1) WILD-TYPE                                            12
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK  2(1P13.1) MUTATED                                1
  DEL PEAK  2(1P13.1) WILD-TYPE                              1
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK  2(1P13.1) MUTATED                                    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                                               2
  DEL PEAK  2(1P13.1) WILD-TYPE                                             3
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK  2(1P13.1) MUTATED                              2
  DEL PEAK  2(1P13.1) WILD-TYPE                            5
D31V9, multiclass
                                                    clus
vv                                                   DEL PEAK  2(1P13.1) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           29
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          86
  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                                2
  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)                           217
  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                                                 13
  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"
D31V10, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.1) MUTATED     6 138
  DEL PEAK  2(1P13.1) WILD-TYPE  15 317
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.1) MUTATED      6  138
  DEL PEAK  2(1P13.1) WILD-TYPE   15  317
     clus
vv    DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  NO                            6                            15
  YES                         138                           317
[1] 2 2
[1] FALSE
D31V11, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  2(1P13.1) MUTATED    99   2   2   8
  DEL PEAK  2(1P13.1) WILD-TYPE 228  10   2  13
D31V12, multiclass
    clus
vv   DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  R0                          99                           228
  R1                           2                            10
  R2                           2                             2
  RX                           8                            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  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                           8   112
  DEL PEAK  2(1P13.1) WILD-TYPE                        27   255
D31V13, multiclass
                                  clus
vv                                 DEL PEAK  2(1P13.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                  8
  WHITE                                                    112
                                  clus
vv                                 DEL PEAK  2(1P13.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        3
  BLACK OR AFRICAN AMERICAN                                   27
  WHITE                                                      255
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V14, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.1) MUTATED     1 103
  DEL PEAK  2(1P13.1) WILD-TYPE   6 242
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.1) MUTATED      1  103
  DEL PEAK  2(1P13.1) WILD-TYPE    6  242
                        clus
vv                       DEL PEAK  2(1P13.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                         103
                        clus
vv                       DEL PEAK  2(1P13.1) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           242
[1] 2 2
[1] FALSE

Clustering(32) Variable = DEL PEAK  3(2Q22.1) MUTATION ANALYSIS
D32V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  3(2Q22.1) MUTATED    30   8
  DEL PEAK  3(2Q22.1) WILD-TYPE 299  79
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           38                           378 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                            8                            79 
$`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-49-AARQ TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
        6443         2174         2146          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-50-6597 TCGA-50-7109 TCGA-50-8460 
         567          883          764         1015          255          105 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 
        1971          424          280          701         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-55-6980 TCGA-55-6983 TCGA-55-6985 TCGA-55-6987 
          25         1475           67         1826         1233         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          705           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-55-8087 TCGA-55-8089 TCGA-55-8090 
          31            5           33          462          100            6 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8205 TCGA-55-8206 
         600           26            4           47           33           46 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
          66          674          216           44           23           29 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
          11            8          228            9            3          146 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
         202          536           15           48           49           66 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
         106           33           42           29           48         1952 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 
          28            5          162         1216         1970         2696 
TCGA-62-8402 TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 TCGA-64-1677 
        1445         2067         2199         1246          910          628 
TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
        1189         1686         1126         1968         1959           62 
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-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7761 
         427          385          174          141          422          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-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
          89          382          100           77          129          214 
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-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-A9RS TCGA-75-6214 TCGA-75-7025 
         164           38          621          305         1970         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-78-7152 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-78-7535 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-78-8655 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-86-7954 TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
         591         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-86-8669 TCGA-86-8671 TCGA-86-8672 
          26           35           45           34           18           15 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 
         455          405           10           30           14           39 
TCGA-91-6828 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
         323           60          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          505          174           36 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-95-7043 TCGA-95-7562 
          44          218          297          127            2         1973 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
         568          377          477          476          830           84 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
         121          553          605          964         1965         1932 
TCGA-97-7553 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 
        1332          181           22          107         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-99-7458 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-A50W TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 
         116          266          312          111          102          827 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 
        1175           84         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 TCGA-S2-AA1A 
        1970          142         1955         1971         1490          121 

  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                          6443 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                        546.0                         471.5 
[1] "1.0 - 2151.0 (546.0)" "2.0 - 6443.0 (471.5)"
[1] "hr=" "1.5"
D32V2, 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       5      108      119        47        61
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK  3(2Q22.1) MUTATED            7          1        4
  DEL PEAK  3(2Q22.1) WILD-TYPE         61         10       20
D32V3, multiclass
            clus
vv           DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  STAGE I                              0                             5
  STAGE IA                             8                           108
  STAGE IB                            13                           119
  STAGE IIA                            2                            47
  STAGE IIB                            9                            61
  STAGE IIIA                           7                            61
  STAGE IIIB                           1                            10
  STAGE IV                             4                            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  3(2Q22.1) MUTATED    10  28   5   1
  DEL PEAK  3(2Q22.1) WILD-TYPE 137 239  37  17
D32V4, multiclass
    clus
vv   DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  T1                          10                           137
  T2                          28                           239
  T3                           5                            37
  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 272  84    66
D32V5, multiclass
       clus
vv      DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  N0                             29                           272
  N1                              7                            84
  N2+N3                           8                            66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               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 298  14   1   4 111
D32V6, multiclass
     clus
vv    DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  M0                           28                           298
  M1                            4                            14
  M1A                           0                             1
  M1B                           0                             4
  MX                           12                           111
[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
  DEL PEAK  3(2Q22.1) MUTATED    24  20
  DEL PEAK  3(2Q22.1) WILD-TYPE 231 201
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED     24   20
  DEL PEAK  3(2Q22.1) WILD-TYPE  231  201
        clus
vv       DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  FEMALE                          24                           231
  MALE                            20                           201
[1] 2 2
[1] FALSE
D32V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  DEL PEAK  3(2Q22.1) MUTATED                            4
  DEL PEAK  3(2Q22.1) WILD-TYPE                         11
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK  3(2Q22.1) MUTATED                                   8
  DEL PEAK  3(2Q22.1) WILD-TYPE                                86
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  3(2Q22.1) MUTATED                                                   26
  DEL PEAK  3(2Q22.1) WILD-TYPE                                                277
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK  3(2Q22.1) MUTATED                                            0
  DEL PEAK  3(2Q22.1) WILD-TYPE                                          5
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK  3(2Q22.1) MUTATED                                               2
  DEL PEAK  3(2Q22.1) WILD-TYPE                                            17
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK  3(2Q22.1) MUTATED                                0
  DEL PEAK  3(2Q22.1) WILD-TYPE                              2
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK  3(2Q22.1) MUTATED                                    0
  DEL PEAK  3(2Q22.1) WILD-TYPE                                  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                                             5
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK  3(2Q22.1) MUTATED                              2
  DEL PEAK  3(2Q22.1) WILD-TYPE                            5
D32V9, 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                                                    11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             86
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           277
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     5
  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                                  5
  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"
D32V10, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q22.1) MUTATED     2  42
  DEL PEAK  3(2Q22.1) WILD-TYPE  19 413
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED      2   42
  DEL PEAK  3(2Q22.1) WILD-TYPE   19  413
     clus
vv    DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  NO                            2                            19
  YES                          42                           413
[1] 2 2
[1] FALSE
D32V11, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  3(2Q22.1) MUTATED    29   0   0   2
  DEL PEAK  3(2Q22.1) WILD-TYPE 298  12   4  19
D32V12, multiclass
    clus
vv   DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  R0                          29                           298
  R1                           0                            12
  R2                           0                             4
  RX                           2                            19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  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                        33   332
D32V13, 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                                   33
  WHITE                                                      332
[1] 4 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
  DEL PEAK  3(2Q22.1) MUTATED     1  30
  DEL PEAK  3(2Q22.1) WILD-TYPE   6 315
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED      1   30
  DEL PEAK  3(2Q22.1) WILD-TYPE    6  315
                        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                           315
[1] 2 2
[1] FALSE

Clustering(33) Variable = DEL PEAK  4(3P26.2) MUTATION ANALYSIS
D33V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  4(3P26.2) MUTATED   148  36
  DEL PEAK  4(3P26.2) WILD-TYPE 181  51
  DEL PEAK  4(3P26.2) MUTATED DEL PEAK  4(3P26.2) WILD-TYPE 
                          184                           232 
  DEL PEAK  4(3P26.2) MUTATED DEL PEAK  4(3P26.2) WILD-TYPE 
                           36                            51 
$`DEL PEAK  4(3P26.2) 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-50-6597 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-55-6983 TCGA-55-6985 
         424          280         1178         1375         1826         1233 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7576 TCGA-55-7724 TCGA-55-7726 TCGA-55-7727 
           6            4           40          705           39           34 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7914 TCGA-55-7995 TCGA-55-8090 TCGA-55-8092 
          16          197            3            5            6           26 
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-55-8620 TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF 
         536           15           66         1952            1           47 
TCGA-55-A4DG TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-A471 TCGA-64-1676 
         162         1289         1970         2696         1246         1728 
TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 TCGA-64-5774 TCGA-64-5779 TCGA-64-5781 
         628         1189         1686         1959          864         1559 
TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-6217 TCGA-69-7763 TCGA-69-7764 
          31          610          573          422          690          414 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 TCGA-71-6725 
         165          230           70           89          100           61 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-7498 TCGA-73-7499 
         800          467          131           40          621          519 
TCGA-73-A9RS TCGA-75-6214 TCGA-75-7027 TCGA-75-7031 TCGA-78-7146 TCGA-78-7147 
         305         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-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7554 
         830           84          605          964         1965          775 
TCGA-97-7937 TCGA-97-8174 TCGA-97-8177 TCGA-97-A4M7 TCGA-99-8033 TCGA-J2-8192 
         181         1965          147          271          170          154 
TCGA-J2-A4AG TCGA-L9-A50W TCGA-L9-A7SV TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4T4 
         238          266          111          827         1175         1954 
TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-MP-A4TF TCGA-MP-A4TI 
        1957         1944         1970         1955 

$`DEL PEAK  4(3P26.2) 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-49-AARQ TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
         354         6443         2174          455          785          944 
TCGA-50-5930 TCGA-50-5933 TCGA-50-5942 TCGA-50-5946 TCGA-50-8460 TCGA-55-1592 
         282         2370          883          686          105          701 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 
        1479           87            2          993           24         1239 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 
          25         1475           67         2151         1170           18 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7574 TCGA-55-7725 TCGA-55-7728 TCGA-55-7815 
          35          121           95           39           24           54 
TCGA-55-7903 TCGA-55-7911 TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
          19           21           31           33          462          100 
TCGA-55-8091 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8207 TCGA-55-8208 
         600           47           15           33           66          674 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8510 TCGA-55-8511 
         216           44           23           29          228            9 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8616 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
           3          146           48           49          106           33 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-62-8395 
          42           29           48           28            5         1216 
TCGA-62-8402 TCGA-62-A46U TCGA-62-A46V TCGA-62-A472 TCGA-64-1680 TCGA-64-1681 
        1445         2067         2199          910         1126         1968 
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-69-7760 TCGA-69-7761 TCGA-69-7974 TCGA-69-7980 TCGA-69-8254 
         141          202          186          184          382           77 
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-78-7220 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
        1950         1934         1965         1944          327          881 
TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5607 TCGA-86-7714 
         994         1971         1981         1964         1965         1968 
TCGA-86-7955 TCGA-86-8056 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8281 
         508         1963          489          476          482         1955 
TCGA-86-8359 TCGA-86-8668 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
          26           45           18          455          405           10 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6831 TCGA-91-6836 TCGA-91-6848 
          14           39          323          310          417          224 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 
          35          492          505          174          218          297 
TCGA-93-8067 TCGA-95-7562 TCGA-95-7944 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-7552 
         186         1973          377          121          553         1932 
TCGA-97-7553 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 TCGA-97-8179 
        1332           22          107          182           87           15 
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-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 
          44          114          287          282          578          435 
TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 TCGA-L9-A8F4 TCGA-MN-A4N5 TCGA-MP-A4SV 
         116            6          312          102           84         1946 
TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TE 
        1967         1951         1954         1980         1951         1970 
TCGA-MP-A4TH TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-S2-AA1A 
         142         1971         1490          121 

  DEL PEAK  4(3P26.2) MUTATED DEL PEAK  4(3P26.2) WILD-TYPE 
                            1                             2 
  DEL PEAK  4(3P26.2) MUTATED DEL PEAK  4(3P26.2) WILD-TYPE 
                         2696                          6443 
  DEL PEAK  4(3P26.2) MUTATED DEL PEAK  4(3P26.2) WILD-TYPE 
                          582                           427 
[1] "1.0 - 2696.0 (582.0)" "2.0 - 6443.0 (427.0)"
[1] "hr=" "1.1"
D33V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK  4(3P26.2) MUTATED         1       46       53        30        34
  DEL PEAK  4(3P26.2) WILD-TYPE       4       70       79        19        36
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK  4(3P26.2) MUTATED           31          4       15
  DEL PEAK  4(3P26.2) WILD-TYPE         37          7        9
D33V3, multiclass
            clus
vv           DEL PEAK  4(3P26.2) MUTATED DEL PEAK  4(3P26.2) WILD-TYPE
  STAGE I                              1                             4
  STAGE IA                            46                            70
  STAGE IB                            53                            79
  STAGE IIA                           30                            19
  STAGE IIB                           34                            36
  STAGE IIIA                          31                            37
  STAGE IIIB                           4                             7
  STAGE IV                            15                             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  4(3P26.2) MUTATED    65 129  11   7
  DEL PEAK  4(3P26.2) WILD-TYPE  82 138  31  11
D33V4, multiclass
    clus
vv   DEL PEAK  4(3P26.2) MUTATED DEL PEAK  4(3P26.2) WILD-TYPE
  T1                          65                            82
  T2                         129                           138
  T3                          11                            31
  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  4(3P26.2) MUTATED   123  51    35
  DEL PEAK  4(3P26.2) WILD-TYPE 178  40    39
D33V5, multiclass
       clus
vv      DEL PEAK  4(3P26.2) MUTATED DEL PEAK  4(3P26.2) WILD-TYPE
  N0                            123                           178
  N1                             51                            40
  N2+N3                          35                            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  4(3P26.2) MUTATED   148  12   0   2  50
  DEL PEAK  4(3P26.2) WILD-TYPE 178   6   1   2  73
D33V6, multiclass
     clus
vv    DEL PEAK  4(3P26.2) MUTATED DEL PEAK  4(3P26.2) WILD-TYPE
  M0                          148                           178
  M1                           12                             6
  M1A                           0                             1
  M1B                           2                             2
  MX                           50                            73
[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  4(3P26.2) MUTATED   111 103
  DEL PEAK  4(3P26.2) WILD-TYPE 144 118
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(3P26.2) MUTATED    111  103
  DEL PEAK  4(3P26.2) WILD-TYPE  144  118
        clus
vv       DEL PEAK  4(3P26.2) MUTATED DEL PEAK  4(3P26.2) WILD-TYPE
  FEMALE                         111                           144
  MALE                           103                           118
[1] 2 2
[1] FALSE
D33V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  DEL PEAK  4(3P26.2) MUTATED                            9
  DEL PEAK  4(3P26.2) WILD-TYPE                          6
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK  4(3P26.2) MUTATED                                  43
  DEL PEAK  4(3P26.2) WILD-TYPE                                51
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  4(3P26.2) MUTATED                                                  141
  DEL PEAK  4(3P26.2) WILD-TYPE                                                162
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK  4(3P26.2) MUTATED                                            0
  DEL PEAK  4(3P26.2) WILD-TYPE                                          5
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK  4(3P26.2) MUTATED                                               6
  DEL PEAK  4(3P26.2) WILD-TYPE                                            13
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK  4(3P26.2) MUTATED                                1
  DEL PEAK  4(3P26.2) WILD-TYPE                              1
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK  4(3P26.2) MUTATED                                    2
  DEL PEAK  4(3P26.2) WILD-TYPE                                  2
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK  4(3P26.2) MUTATED                              0
  DEL PEAK  4(3P26.2) WILD-TYPE                            2
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK  4(3P26.2) MUTATED                               7
  DEL PEAK  4(3P26.2) WILD-TYPE                            12
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK  4(3P26.2) MUTATED                                 1
  DEL PEAK  4(3P26.2) WILD-TYPE                               0
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK  4(3P26.2) MUTATED                                               1
  DEL PEAK  4(3P26.2) WILD-TYPE                                             4
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK  4(3P26.2) MUTATED                              3
  DEL PEAK  4(3P26.2) WILD-TYPE                            4
D33V9, multiclass
                                                    clus
vv                                                   DEL PEAK  4(3P26.2) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           43
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         141
  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  4(3P26.2) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             51
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           162
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 13
  LUNG CLEAR CELL ADENOCARCINOMA                                                 1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             2
  LUNG MUCINOUS ADENOCARCINOMA                                                   2
  LUNG PAPILLARY ADENOCARCINOMA                                                 12
  LUNG SIGNET RING ADENOCARCINOMA                                                0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                  4
  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"
D33V10, binary
                               cls
clus                              0   1
  DEL PEAK  4(3P26.2) MUTATED     8 206
  DEL PEAK  4(3P26.2) WILD-TYPE  13 249
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(3P26.2) MUTATED      8  206
  DEL PEAK  4(3P26.2) WILD-TYPE   13  249
     clus
vv    DEL PEAK  4(3P26.2) MUTATED DEL PEAK  4(3P26.2) WILD-TYPE
  NO                            8                            13
  YES                         206                           249
[1] 2 2
[1] FALSE
D33V11, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  4(3P26.2) MUTATED   143   2   2   8
  DEL PEAK  4(3P26.2) WILD-TYPE 184  10   2  13
D33V12, multiclass
    clus
vv   DEL PEAK  4(3P26.2) MUTATED DEL PEAK  4(3P26.2) WILD-TYPE
  R0                         143                           184
  R1                           2                            10
  R2                           2                             2
  RX                           8                            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  4(3P26.2) MUTATED                                  1     2
  DEL PEAK  4(3P26.2) WILD-TYPE                                0     4
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(3P26.2) MUTATED                          18   167
  DEL PEAK  4(3P26.2) WILD-TYPE                        17   200
D33V13, multiclass
                                  clus
vv                                 DEL PEAK  4(3P26.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 18
  WHITE                                                    167
                                  clus
vv                                 DEL PEAK  4(3P26.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   17
  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"
D33V14, binary
                               cls
clus                              0   1
  DEL PEAK  4(3P26.2) MUTATED     4 159
  DEL PEAK  4(3P26.2) WILD-TYPE   3 186
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(3P26.2) MUTATED      4  159
  DEL PEAK  4(3P26.2) WILD-TYPE    3  186
                        clus
vv                       DEL PEAK  4(3P26.2) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         159
                        clus
vv                       DEL PEAK  4(3P26.2) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           186
[1] 2 2
[1] FALSE

Clustering(34) Variable = DEL PEAK  5(3P21.31) MUTATION ANALYSIS
D34V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  5(3P21.31) MUTATED   160  39
  DEL PEAK  5(3P21.31) WILD-TYPE 169  48
  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                           199                            217 
  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                            39                             48 
$`DEL PEAK  5(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          705           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-73-A9RS TCGA-75-6214 
         131           40          621          519          305         1970 
TCGA-75-7027 TCGA-75-7031 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7150 
        1956         1965         1988         1950         1944         1963 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
        1221          678         1937         1965         1972         1949 
TCGA-78-7542 TCGA-78-8640 TCGA-78-8660 TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 
        1952         1949         1954         1972          824         1959 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 
          11          630          591         1963          745           10 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8278 TCGA-86-8280 TCGA-86-8358 
          13           24          479          476           16           19 
TCGA-86-8585 TCGA-86-8669 TCGA-86-A4D0 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
          35           34           30         1940           60          310 
TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-8499 TCGA-91-A4BC 
          79          372          842          224           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-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7554 
         830           84          605          964         1965          775 
TCGA-97-7937 TCGA-97-8174 TCGA-97-8177 TCGA-97-A4M7 TCGA-99-8032 TCGA-99-8033 
         181         1965          147          271           44          170 
TCGA-J2-8192 TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L9-A50W TCGA-L9-A7SV TCGA-MN-A4N1 
         154          238          578          266          111          827 
TCGA-MN-A4N4 TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-MP-A4TF 
        1175         1967         1951         1957         1944         1970 
TCGA-MP-A4TI 
        1955 

$`DEL PEAK  5(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-49-AARQ TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
         354         6443         2174          455          785          944 
TCGA-50-5930 TCGA-50-5933 TCGA-50-5942 TCGA-50-5946 TCGA-50-8460 TCGA-55-1592 
         282         2370          883          686          105          701 
TCGA-55-1595 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6971 
        1479            2          993           24         1239           25 
TCGA-55-6972 TCGA-55-6980 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 
        1475           67         2151         1170           18           35 
TCGA-55-7284 TCGA-55-7574 TCGA-55-7725 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 
         121           95           39           24           54           19 
TCGA-55-7911 TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8091 
          21           31           33          462          100          600 
TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8207 TCGA-55-8208 
          26           47           15           33           66          674 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8510 TCGA-55-8511 
         216           44           23           29          228            9 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
           3          146           49          106           33           42 
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-64-1677 TCGA-64-1680 TCGA-64-1681 TCGA-64-5775 TCGA-64-5778 
         910          628         1126         1968           62         1305 
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-69-8255 TCGA-69-A59K TCGA-73-4658 TCGA-73-4659 
         184          382          129          214         1600          711 
TCGA-73-4662 TCGA-73-4676 TCGA-73-4677 TCGA-75-7025 TCGA-78-7145 TCGA-78-7149 
         912          164           38         1967         1973         1093 
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-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7537 TCGA-78-7539 
         215         1940         1950         1934         1944          327 
TCGA-78-7540 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5607 
         881          994         1971         1981         1964         1965 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7955 TCGA-86-8056 TCGA-86-8076 TCGA-86-8279 
         422         1968          508         1963          489          482 
TCGA-86-8281 TCGA-86-8359 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1955           26           45           18           15          455 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6836 
         405           10           14           39          323          417 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 
          35          492          505          174          218          297 
TCGA-93-8067 TCGA-95-7562 TCGA-95-7944 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-7552 
         186         1973          377          121          553         1932 
TCGA-97-7553 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 TCGA-97-8179 
        1332           22          107          182           87           15 
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-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
         114          287          282          435          116            6 
TCGA-L9-A743 TCGA-L9-A8F4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4T4 TCGA-MP-A4T7 
         312          102           84         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 
TCGA-S2-AA1A 
         121 

  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                             1                              2 
  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                          2696                           6443 
  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                           567                            427 
[1] "1.0 - 2696.0 (567.0)" "2.0 - 6443.0 (427.0)"
[1] "hr=" "1.1"
D34V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK  5(3P21.31) MUTATED         2       52       56        30        34
  DEL PEAK  5(3P21.31) WILD-TYPE       3       64       76        19        36
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK  5(3P21.31) MUTATED           35          4       14
  DEL PEAK  5(3P21.31) WILD-TYPE         33          7       10
D34V3, multiclass
            clus
vv           DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE
  STAGE I                               2                              3
  STAGE IA                             52                             64
  STAGE IB                             56                             76
  STAGE IIA                            30                             19
  STAGE IIB                            34                             36
  STAGE IIIA                           35                             33
  STAGE IIIB                            4                              7
  STAGE IV                             14                             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  5(3P21.31) MUTATED    73 137  10   6
  DEL PEAK  5(3P21.31) WILD-TYPE  74 130  32  12
D34V4, multiclass
    clus
vv   DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE
  T1                           73                             74
  T2                          137                            130
  T3                           10                             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
  DEL PEAK  5(3P21.31) MUTATED   130  55    37
  DEL PEAK  5(3P21.31) WILD-TYPE 171  36    37
D34V5, multiclass
       clus
vv      DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE
  N0                             130                            171
  N1                              55                             36
  N2+N3                           37                             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  5(3P21.31) MUTATED   159  11   0   2  53
  DEL PEAK  5(3P21.31) WILD-TYPE 167   7   1   2  70
D34V6, multiclass
     clus
vv    DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE
  M0                           159                            167
  M1                            11                              7
  M1A                            0                              1
  M1B                            2                              2
  MX                            53                             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"
D34V7, binary
                                cls
clus                               0   1
  DEL PEAK  5(3P21.31) MUTATED   116 112
  DEL PEAK  5(3P21.31) WILD-TYPE 139 109
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  5(3P21.31) MUTATED    116  112
  DEL PEAK  5(3P21.31) WILD-TYPE  139  109
        clus
vv       DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE
  FEMALE                          116                            139
  MALE                            112                            109
[1] 2 2
[1] FALSE
D34V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK  5(3P21.31) MUTATED                            9
  DEL PEAK  5(3P21.31) WILD-TYPE                          6
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK  5(3P21.31) MUTATED                                  46
  DEL PEAK  5(3P21.31) WILD-TYPE                                48
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  5(3P21.31) MUTATED                                                  149
  DEL PEAK  5(3P21.31) WILD-TYPE                                                154
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK  5(3P21.31) MUTATED                                            0
  DEL PEAK  5(3P21.31) WILD-TYPE                                          5
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK  5(3P21.31) MUTATED                                               6
  DEL PEAK  5(3P21.31) WILD-TYPE                                            13
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK  5(3P21.31) MUTATED                                1
  DEL PEAK  5(3P21.31) WILD-TYPE                              1
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK  5(3P21.31) MUTATED                                    2
  DEL PEAK  5(3P21.31) WILD-TYPE                                  2
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK  5(3P21.31) MUTATED                              0
  DEL PEAK  5(3P21.31) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK  5(3P21.31) MUTATED                               8
  DEL PEAK  5(3P21.31) WILD-TYPE                            11
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK  5(3P21.31) MUTATED                                 1
  DEL PEAK  5(3P21.31) WILD-TYPE                               0
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK  5(3P21.31) MUTATED                                               2
  DEL PEAK  5(3P21.31) WILD-TYPE                                             3
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK  5(3P21.31) MUTATED                              4
  DEL PEAK  5(3P21.31) WILD-TYPE                            3
D34V9, multiclass
                                                    clus
vv                                                   DEL PEAK  5(3P21.31) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            46
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          149
  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  5(3P21.31) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              48
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            154
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      5
  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                                   3
  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"
D34V10, binary
                                cls
clus                               0   1
  DEL PEAK  5(3P21.31) MUTATED    10 218
  DEL PEAK  5(3P21.31) WILD-TYPE  11 237
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  5(3P21.31) MUTATED     10  218
  DEL PEAK  5(3P21.31) WILD-TYPE   11  237
     clus
vv    DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE
  NO                            10                             11
  YES                          218                            237
[1] 2 2
[1] FALSE
D34V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK  5(3P21.31) MUTATED   154   3   2   7
  DEL PEAK  5(3P21.31) WILD-TYPE 173   9   2  14
D34V12, multiclass
    clus
vv   DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE
  R0                          154                            173
  R1                            3                              9
  R2                            2                              2
  RX                            7                             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  5(3P21.31) MUTATED                                  1     2
  DEL PEAK  5(3P21.31) WILD-TYPE                                0     4
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(3P21.31) MUTATED                          18   181
  DEL PEAK  5(3P21.31) WILD-TYPE                        17   186
D34V13, multiclass
                                  clus
vv                                 DEL PEAK  5(3P21.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  18
  WHITE                                                     181
                                  clus
vv                                 DEL PEAK  5(3P21.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    17
  WHITE                                                       186
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V14, binary
                                cls
clus                               0   1
  DEL PEAK  5(3P21.31) MUTATED     4 172
  DEL PEAK  5(3P21.31) WILD-TYPE   3 173
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  5(3P21.31) MUTATED      4  172
  DEL PEAK  5(3P21.31) WILD-TYPE    3  173
                        clus
vv                       DEL PEAK  5(3P21.31) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          172
                        clus
vv                       DEL PEAK  5(3P21.31) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            173
[1] 2 2
[1] FALSE

Clustering(35) Variable = DEL PEAK  6(3Q11.1) MUTATION ANALYSIS
D35V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  6(3Q11.1) MUTATED    91  24
  DEL PEAK  6(3Q11.1) WILD-TYPE 238  63
  DEL PEAK  6(3Q11.1) MUTATED DEL PEAK  6(3Q11.1) WILD-TYPE 
                          115                           301 
  DEL PEAK  6(3Q11.1) MUTATED DEL PEAK  6(3Q11.1) WILD-TYPE 
                           24                            63 
$`DEL PEAK  6(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-95-8039 TCGA-95-A4VP 
         127           34          568          476          830          605 
TCGA-97-7546 TCGA-97-7554 TCGA-97-7937 TCGA-97-8172 TCGA-97-8174 TCGA-97-8177 
         964          775          181          182         1965          147 
TCGA-99-8032 TCGA-J2-8192 TCGA-J2-A4AG TCGA-MP-A4TC TCGA-MP-A4TF TCGA-MP-A4TI 
          44          154          238         1944         1970         1955 
TCGA-MP-A4TK 
        1971 

$`DEL PEAK  6(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-49-AARQ TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
         522          354         6443         2174         2146          455 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5942 
         785          944          282          267         2370          883 
TCGA-50-5944 TCGA-50-5946 TCGA-50-7109 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 
         764          686          255          105         1971          424 
TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-6543 TCGA-55-6642 
         280         1178         1479         1375            2          993 
TCGA-55-6712 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 TCGA-55-6986 
          24         1239           25         1475           67         2151 
TCGA-55-6987 TCGA-55-7281 TCGA-55-7284 TCGA-55-7570 TCGA-55-7574 TCGA-55-7724 
        1170           18          121            6           95          705 
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-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
          21            3           31            5           33          462 
TCGA-55-8089 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
         100          600           26            4           47           15 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
          66          674          216           44           23           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-55-8513 TCGA-55-8614 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
         146          536           49          106           33           42 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A493 TCGA-55-A494 TCGA-62-8395 TCGA-62-8402 
          48         1952           28            5         1216         1445 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
        2067         2199         1246          910         1728          628 
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-64-5815 TCGA-67-3771 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 
         866          610          427          385          174          141 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8254 
         202          186           70           89          382           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-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-73-A9RS TCGA-75-7025 
         131          164           38          519          305         1967 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
        1988         1950         1093         1963         1202          760 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7162 
        1948         1957         1961         1963         1221         1940 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
        1950         1934         1944          327          881         1952 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5607 
         994         1949         1971         1981         1964         1965 
TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7955 
        1959          630          422         1968          591          508 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
          10         1963           24          489          476          482 
TCGA-86-8281 TCGA-86-8358 TCGA-86-8359 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
        1955           19           26           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-91-6830 TCGA-91-6836 TCGA-91-6840 
          39          323         1940           60          417          372 
TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
         224           35          505           44          218          297 
TCGA-93-8067 TCGA-95-7043 TCGA-95-7562 TCGA-95-7944 TCGA-95-7947 TCGA-95-8494 
         186            2         1973          377          477           84 
TCGA-95-A4VK TCGA-95-A4VN TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7941 
         121          553         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-L9-A50W TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 
         266          312          111          102          827         1175 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 
          84         1946         1967         1951         1954         1954 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A5C7 
        1957         1980         1951         1970          142         1490 
TCGA-S2-AA1A 
         121 

  DEL PEAK  6(3Q11.1) MUTATED DEL PEAK  6(3Q11.1) WILD-TYPE 
                            1                             2 
  DEL PEAK  6(3Q11.1) MUTATED DEL PEAK  6(3Q11.1) WILD-TYPE 
                         2696                          6443 
  DEL PEAK  6(3Q11.1) MUTATED DEL PEAK  6(3Q11.1) WILD-TYPE 
                          535                           459 
[1] "1.0 - 2696.0 (535.0)" "2.0 - 6443.0 (459.0)"
[1] "hr=" "1.2"
D35V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK  6(3Q11.1) MUTATED         0       30       36         9        22
  DEL PEAK  6(3Q11.1) WILD-TYPE       5       86       96        40        48
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK  6(3Q11.1) MUTATED           24          3        8
  DEL PEAK  6(3Q11.1) WILD-TYPE         44          8       16
D35V3, multiclass
            clus
vv           DEL PEAK  6(3Q11.1) MUTATED DEL PEAK  6(3Q11.1) WILD-TYPE
  STAGE I                              0                             5
  STAGE IA                            30                            86
  STAGE IB                            36                            96
  STAGE IIA                            9                            40
  STAGE IIB                           22                            48
  STAGE IIIA                          24                            44
  STAGE IIIB                           3                             8
  STAGE IV                             8                            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  6(3Q11.1) MUTATED    37  81   9   5
  DEL PEAK  6(3Q11.1) WILD-TYPE 110 186  33  13
D35V4, multiclass
    clus
vv   DEL PEAK  6(3Q11.1) MUTATED DEL PEAK  6(3Q11.1) WILD-TYPE
  T1                          37                           110
  T2                          81                           186
  T3                           9                            33
  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  6(3Q11.1) MUTATED    81  24    27
  DEL PEAK  6(3Q11.1) WILD-TYPE 220  67    47
D35V5, multiclass
       clus
vv      DEL PEAK  6(3Q11.1) MUTATED DEL PEAK  6(3Q11.1) WILD-TYPE
  N0                             81                           220
  N1                             24                            67
  N2+N3                          27                            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  6(3Q11.1) MUTATED    93   6   0   1  32
  DEL PEAK  6(3Q11.1) WILD-TYPE 233  12   1   3  91
D35V6, multiclass
     clus
vv    DEL PEAK  6(3Q11.1) MUTATED DEL PEAK  6(3Q11.1) WILD-TYPE
  M0                           93                           233
  M1                            6                            12
  M1A                           0                             1
  M1B                           1                             3
  MX                           32                            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"
D35V7, binary
                               cls
clus                              0   1
  DEL PEAK  6(3Q11.1) MUTATED    73  59
  DEL PEAK  6(3Q11.1) WILD-TYPE 182 162
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3Q11.1) MUTATED     73   59
  DEL PEAK  6(3Q11.1) WILD-TYPE  182  162
        clus
vv       DEL PEAK  6(3Q11.1) MUTATED DEL PEAK  6(3Q11.1) WILD-TYPE
  FEMALE                          73                           182
  MALE                            59                           162
[1] 2 2
[1] FALSE
D35V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  DEL PEAK  6(3Q11.1) MUTATED                            6
  DEL PEAK  6(3Q11.1) WILD-TYPE                          9
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK  6(3Q11.1) MUTATED                                  30
  DEL PEAK  6(3Q11.1) WILD-TYPE                                64
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  6(3Q11.1) MUTATED                                                   80
  DEL PEAK  6(3Q11.1) WILD-TYPE                                                223
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK  6(3Q11.1) MUTATED                                            0
  DEL PEAK  6(3Q11.1) WILD-TYPE                                          5
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK  6(3Q11.1) MUTATED                                               5
  DEL PEAK  6(3Q11.1) WILD-TYPE                                            14
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK  6(3Q11.1) MUTATED                                1
  DEL PEAK  6(3Q11.1) WILD-TYPE                              1
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK  6(3Q11.1) MUTATED                                    1
  DEL PEAK  6(3Q11.1) WILD-TYPE                                  3
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK  6(3Q11.1) MUTATED                              0
  DEL PEAK  6(3Q11.1) WILD-TYPE                            2
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK  6(3Q11.1) MUTATED                               5
  DEL PEAK  6(3Q11.1) WILD-TYPE                            14
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK  6(3Q11.1) MUTATED                                 1
  DEL PEAK  6(3Q11.1) WILD-TYPE                               0
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK  6(3Q11.1) MUTATED                                               1
  DEL PEAK  6(3Q11.1) WILD-TYPE                                             4
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK  6(3Q11.1) MUTATED                              2
  DEL PEAK  6(3Q11.1) WILD-TYPE                            5
D35V9, multiclass
                                                    clus
vv                                                   DEL PEAK  6(3Q11.1) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   6
  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  6(3Q11.1) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             64
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           223
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     5
  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                                  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  6(3Q11.1) MUTATED     6 126
  DEL PEAK  6(3Q11.1) WILD-TYPE  15 329
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3Q11.1) MUTATED      6  126
  DEL PEAK  6(3Q11.1) WILD-TYPE   15  329
     clus
vv    DEL PEAK  6(3Q11.1) MUTATED DEL PEAK  6(3Q11.1) WILD-TYPE
  NO                            6                            15
  YES                         126                           329
[1] 2 2
[1] FALSE
D35V11, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  6(3Q11.1) MUTATED    80   3   0   5
  DEL PEAK  6(3Q11.1) WILD-TYPE 247   9   4  16
D35V12, multiclass
    clus
vv   DEL PEAK  6(3Q11.1) MUTATED DEL PEAK  6(3Q11.1) WILD-TYPE
  R0                          80                           247
  R1                           3                             9
  R2                           0                             4
  RX                           5                            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  6(3Q11.1) MUTATED                                  0     1
  DEL PEAK  6(3Q11.1) WILD-TYPE                                1     5
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(3Q11.1) MUTATED                           8   107
  DEL PEAK  6(3Q11.1) WILD-TYPE                        27   260
D35V13, multiclass
                                  clus
vv                                 DEL PEAK  6(3Q11.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  8
  WHITE                                                    107
                                  clus
vv                                 DEL PEAK  6(3Q11.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                   27
  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"
D35V14, binary
                               cls
clus                              0   1
  DEL PEAK  6(3Q11.1) MUTATED     1  98
  DEL PEAK  6(3Q11.1) WILD-TYPE   6 247
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3Q11.1) MUTATED      1   98
  DEL PEAK  6(3Q11.1) WILD-TYPE    6  247
                        clus
vv                       DEL PEAK  6(3Q11.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          98
                        clus
vv                       DEL PEAK  6(3Q11.1) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           247
[1] 2 2
[1] FALSE

Clustering(36) Variable = DEL PEAK  7(3Q29) MUTATION ANALYSIS
D36V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  7(3Q29) MUTATED    90  25
  DEL PEAK  7(3Q29) WILD-TYPE 239  62
  DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE 
                        115                         301 
  DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE 
                         25                          62 
$`DEL PEAK  7(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-73-A9RS 
         129          711          912           40          621          305 
TCGA-75-7027 TCGA-75-7031 TCGA-78-7147 TCGA-78-7148 TCGA-78-7160 TCGA-78-7161 
        1956         1965         1950         1944          678          215 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7535 TCGA-78-7539 TCGA-78-8660 TCGA-80-5608 
        1934         1937         1972          327         1954         1972 
TCGA-86-7701 TCGA-86-7713 TCGA-86-8054 TCGA-86-8055 TCGA-86-8075 TCGA-86-8280 
          11          422          745           10          479           16 
TCGA-91-6828 TCGA-91-6835 TCGA-91-6836 TCGA-91-6847 TCGA-91-7771 TCGA-91-8497 
         323           79          417          842          492          174 
TCGA-95-7567 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VP TCGA-97-7546 TCGA-97-7554 
         568          476          121          605          964          775 
TCGA-97-7937 TCGA-97-8172 TCGA-97-8174 TCGA-97-8177 TCGA-99-7458 TCGA-99-8032 
         181          182         1965          147          392           44 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AG TCGA-L9-A443 TCGA-MP-A4T8 TCGA-MP-A4TC 
         154          114          238          116         1957         1944 
TCGA-MP-A4TI 
        1955 

$`DEL PEAK  7(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-49-AARQ TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
         354         6443         2174         2146          455          785 
TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5941 
         944          246          282          267         2370          567 
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-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 
         424          280          701         1178         1479         1375 
TCGA-55-6543 TCGA-55-6969 TCGA-55-6971 TCGA-55-6980 TCGA-55-6985 TCGA-55-6986 
           2         1239           25           67         1233         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-55-7726 TCGA-55-7728 TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 
         705           39           24           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          462          100 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8207 
         600           26           47           15           33           66 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
         674          216           44           23           29           11 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-8619 
         228            9            3          146          536           49 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A490 TCGA-55-A491 
          66          106           33           42           48         1952 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 
          28            5           47         2067         2199         1246 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5775 
         910         1728         1686         1126         1968           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-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
         385          174          141          422          202          186 
TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8254 TCGA-69-A59K 
         230           70           89          382           77          214 
TCGA-71-6725 TCGA-73-4658 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 
          61         1600          800          467          131          164 
TCGA-73-4677 TCGA-73-7499 TCGA-75-6214 TCGA-75-7025 TCGA-78-7145 TCGA-78-7146 
          38          519         1970         1967         1973         1988 
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-78-7162 TCGA-78-7163 TCGA-78-7220 
        1961         1963         1221         1940         1950         1965 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
        1949         1944          881         1952          994         1949 
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-86-7711 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8056 
         630         1968          591         1963          508         1963 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8281 
          13           24          489          476          482         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-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6840 TCGA-91-6848 
          39         1940           60          310          372          224 
TCGA-91-6849 TCGA-91-8496 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
          35          505           36           44          218          297 
TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7944 
         127          186           34            2         1973          377 
TCGA-95-7947 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VN TCGA-97-7547 TCGA-97-7552 
         477          830           84          553         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-L9-A50W 
         287          282          578          435            6          266 
TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
         312          111          102          827         1175           84 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T9 
        1946         1967         1951         1954         1954         1980 
TCGA-MP-A4TA TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TK TCGA-MP-A5C7 
        1951         1970         1970          142         1971         1490 
TCGA-S2-AA1A 
         121 

  DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE 
                          1                           2 
  DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE 
                       2696                        6443 
  DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE 
                        476                         476 
[1] "1.0 - 2696.0 (476.0)" "2.0 - 6443.0 (476.0)"
[1] "hr=" "1.2"
D36V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK  7(3Q29) MUTATED         0       28       36        14        23
  DEL PEAK  7(3Q29) WILD-TYPE       5       88       96        35        47
                             vv
clus                          STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK  7(3Q29) MUTATED           20          2        5
  DEL PEAK  7(3Q29) WILD-TYPE         48          9       19
D36V3, multiclass
            clus
vv           DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE
  STAGE I                            0                           5
  STAGE IA                          28                          88
  STAGE IB                          36                          96
  STAGE IIA                         14                          35
  STAGE IIB                         23                          47
  STAGE IIIA                        20                          48
  STAGE IIIB                         2                           9
  STAGE IV                           5                          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  7(3Q29) MUTATED    36  78  10   4
  DEL PEAK  7(3Q29) WILD-TYPE 111 189  32  14
D36V4, multiclass
    clus
vv   DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE
  T1                        36                         111
  T2                        78                         189
  T3                        10                          32
  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  7(3Q29) MUTATED    81  26    21
  DEL PEAK  7(3Q29) WILD-TYPE 220  65    53
D36V5, multiclass
       clus
vv      DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE
  N0                           81                         220
  N1                           26                          65
  N2+N3                        21                          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  7(3Q29) MUTATED    92   3   0   1  31
  DEL PEAK  7(3Q29) WILD-TYPE 234  15   1   3  92
D36V6, multiclass
     clus
vv    DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE
  M0                         92                         234
  M1                          3                          15
  M1A                         0                           1
  M1B                         1                           3
  MX                         31                          92
[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  7(3Q29) MUTATED    66  62
  DEL PEAK  7(3Q29) WILD-TYPE 189 159
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  7(3Q29) MUTATED     66   62
  DEL PEAK  7(3Q29) WILD-TYPE  189  159
        clus
vv       DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE
  FEMALE                        66                         189
  MALE                          62                         159
[1] 2 2
[1] FALSE
D36V8, continuous
                             vv
clus                          LUNG ACINAR ADENOCARCINOMA
  DEL PEAK  7(3Q29) MUTATED                            5
  DEL PEAK  7(3Q29) WILD-TYPE                         10
                             vv
clus                          LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK  7(3Q29) MUTATED                                  30
  DEL PEAK  7(3Q29) WILD-TYPE                                64
                             vv
clus                          LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  7(3Q29) MUTATED                                                   77
  DEL PEAK  7(3Q29) WILD-TYPE                                                226
                             vv
clus                          LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK  7(3Q29) MUTATED                                            0
  DEL PEAK  7(3Q29) WILD-TYPE                                          5
                             vv
clus                          LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK  7(3Q29) MUTATED                                               4
  DEL PEAK  7(3Q29) WILD-TYPE                                            15
                             vv
clus                          LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK  7(3Q29) MUTATED                                0
  DEL PEAK  7(3Q29) WILD-TYPE                              2
                             vv
clus                          LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK  7(3Q29) MUTATED                                    1
  DEL PEAK  7(3Q29) WILD-TYPE                                  3
                             vv
clus                          LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK  7(3Q29) MUTATED                              0
  DEL PEAK  7(3Q29) WILD-TYPE                            2
                             vv
clus                          LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK  7(3Q29) MUTATED                               5
  DEL PEAK  7(3Q29) WILD-TYPE                            14
                             vv
clus                          LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK  7(3Q29) MUTATED                                 1
  DEL PEAK  7(3Q29) WILD-TYPE                               0
                             vv
clus                          LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK  7(3Q29) MUTATED                                               2
  DEL PEAK  7(3Q29) WILD-TYPE                                             3
                             vv
clus                          MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK  7(3Q29) MUTATED                              3
  DEL PEAK  7(3Q29) WILD-TYPE                            4
D36V9, multiclass
                                                    clus
vv                                                   DEL PEAK  7(3Q29) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                 5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                         30
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                        77
  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  7(3Q29) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                  10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           64
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         226
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                   5
  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                                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"
D36V10, binary
                             cls
clus                            0   1
  DEL PEAK  7(3Q29) MUTATED     4 124
  DEL PEAK  7(3Q29) WILD-TYPE  17 331
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  7(3Q29) MUTATED      4  124
  DEL PEAK  7(3Q29) WILD-TYPE   17  331
     clus
vv    DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE
  NO                          4                          17
  YES                       124                         331
[1] 2 2
[1] FALSE
D36V11, continuous
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK  7(3Q29) MUTATED    85   2   0   3
  DEL PEAK  7(3Q29) WILD-TYPE 242  10   4  18
D36V12, multiclass
    clus
vv   DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE
  R0                        85                         242
  R1                         2                          10
  R2                         0                           4
  RX                         3                          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  7(3Q29) MUTATED                                  0     0
  DEL PEAK  7(3Q29) WILD-TYPE                                1     6
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(3Q29) MUTATED                          10   100
  DEL PEAK  7(3Q29) WILD-TYPE                        25   267
D36V13, multiclass
                                  clus
vv                                 DEL PEAK  7(3Q29) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    0
  BLACK OR AFRICAN AMERICAN                               10
  WHITE                                                  100
                                  clus
vv                                 DEL PEAK  7(3Q29) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      6
  BLACK OR AFRICAN AMERICAN                                 25
  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"
D36V14, binary
                             cls
clus                            0   1
  DEL PEAK  7(3Q29) MUTATED     1  95
  DEL PEAK  7(3Q29) WILD-TYPE   6 250
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  7(3Q29) MUTATED      1   95
  DEL PEAK  7(3Q29) WILD-TYPE    6  250
                        clus
vv                       DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE
  HISPANIC OR LATINO                             1                           6
  NOT HISPANIC OR LATINO                        95                         250
[1] 2 2
[1] FALSE

Clustering(37) Variable = DEL PEAK  8(4P16.3) MUTATION ANALYSIS
D37V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  8(4P16.3) MUTATED    89  14
  DEL PEAK  8(4P16.3) WILD-TYPE 240  73
  DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE 
                          103                           313 
  DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE 
                           14                            73 
$`DEL PEAK  8(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          705           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-95-A4VN TCGA-97-8547 
         492            2          568          377          553          148 
TCGA-99-8025 TCGA-99-8033 TCGA-J2-A4AD TCGA-L4-A4E5 TCGA-L9-A7SV TCGA-MN-A4N4 
         427          170          287          578          111         1175 
TCGA-MP-A4T4 
        1954 

$`DEL PEAK  8(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-49-AARQ TCGA-50-5045 
        1700          890          522          354         6443         2174 
TCGA-50-5055 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
         785         1499          246          282          267         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-50-8460 TCGA-53-7624 TCGA-53-7813 TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 
         105         1986          424          701         1178         1479 
TCGA-55-1596 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6972 TCGA-55-6980 
        1375            2          993           24         1475           67 
TCGA-55-6983 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
        1826         2151         1170           18           35          121 
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-55-7907 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 
          16           21            3           31           33          462 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8097 
         100            6          600           26            4           15 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
          33           46           66          674          216           44 
TCGA-55-8302 TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
          23           11           15          228            9            3 
TCGA-55-8513 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A490 
         146           49          106           33           42           48 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 
           1           28            5         1216         1289         2696 
TCGA-62-8402 TCGA-62-A46U TCGA-62-A471 TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 
        1445         2067         1246         1728         1189         1686 
TCGA-64-1680 TCGA-64-1681 TCGA-64-5775 TCGA-64-5778 TCGA-64-5781 TCGA-67-3770 
        1126         1968           62         1305         1559           31 
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-69-7761 TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 
         186          414          165          184           70          382 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-73-4658 TCGA-73-4662 
         100           77          129          214         1600          912 
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-73-A9RS TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 TCGA-78-7145 
         305         1970         1967         1956         1965         1973 
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-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 
         760         1948         1957         1961         1963          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-78-7537 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-78-8660 TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 
        1971         1981         1954         1965         1972          824 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
        1959           11          630         1968          591         1963 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 TCGA-86-8076 TCGA-86-8278 
         508          745         1963           13          489          476 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8281 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
         482           16         1955           19           26           35 
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-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6847 TCGA-91-6849 TCGA-91-8496 
         310           79          417          842           35          505 
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-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
         186           34         1973          477          476          830 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
          84          121          605          964         1965         1932 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
        1332          775          181           22          107          182 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M2 
        1965           87          147           15          115          197 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 TCGA-J2-8192 TCGA-J2-8194 
         271          392          459           44          154          114 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W 
         282          238          435          116            6          266 
TCGA-L9-A743 TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
         312          102          827           84         1946         1967 
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-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
        1970         1970          142         1955         1971         1490 
TCGA-S2-AA1A 
         121 

  DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE 
                            2                             1 
  DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE 
                         2199                          6443 
  DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE 
                          492                           466 
[1] "2.0 - 2199.0 (492.0)" "1.0 - 6443.0 (466.0)"
[1] "hr=" "1.3"
D37V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK  8(4P16.3) MUTATED         2       27       35        11        16
  DEL PEAK  8(4P16.3) WILD-TYPE       3       89       97        38        54
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK  8(4P16.3) MUTATED           18          4        6
  DEL PEAK  8(4P16.3) WILD-TYPE         50          7       18
D37V3, multiclass
            clus
vv           DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE
  STAGE I                              2                             3
  STAGE IA                            27                            89
  STAGE IB                            35                            97
  STAGE IIA                           11                            38
  STAGE IIB                           16                            54
  STAGE IIIA                          18                            50
  STAGE IIIB                           4                             7
  STAGE IV                             6                            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(4P16.3) MUTATED    38  65  11   3
  DEL PEAK  8(4P16.3) WILD-TYPE 109 202  31  15
D37V4, multiclass
    clus
vv   DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE
  T1                          38                           109
  T2                          65                           202
  T3                          11                            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  8(4P16.3) MUTATED    72  22    21
  DEL PEAK  8(4P16.3) WILD-TYPE 229  69    53
D37V5, multiclass
       clus
vv      DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE
  N0                             72                           229
  N1                             22                            69
  N2+N3                          21                            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  8(4P16.3) MUTATED    80   5   0   1  32
  DEL PEAK  8(4P16.3) WILD-TYPE 246  13   1   3  91
D37V6, multiclass
     clus
vv    DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE
  M0                           80                           246
  M1                            5                            13
  M1A                           0                             1
  M1B                           1                             3
  MX                           32                            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"
D37V7, binary
                               cls
clus                              0   1
  DEL PEAK  8(4P16.3) MUTATED    63  56
  DEL PEAK  8(4P16.3) WILD-TYPE 192 165
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4P16.3) MUTATED     63   56
  DEL PEAK  8(4P16.3) WILD-TYPE  192  165
        clus
vv       DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE
  FEMALE                          63                           192
  MALE                            56                           165
[1] 2 2
[1] FALSE
D37V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  DEL PEAK  8(4P16.3) MUTATED                            4
  DEL PEAK  8(4P16.3) WILD-TYPE                         11
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK  8(4P16.3) MUTATED                                  22
  DEL PEAK  8(4P16.3) WILD-TYPE                                72
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  8(4P16.3) MUTATED                                                   83
  DEL PEAK  8(4P16.3) WILD-TYPE                                                220
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK  8(4P16.3) MUTATED                                            0
  DEL PEAK  8(4P16.3) WILD-TYPE                                          5
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK  8(4P16.3) MUTATED                                               1
  DEL PEAK  8(4P16.3) WILD-TYPE                                            18
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK  8(4P16.3) MUTATED                                1
  DEL PEAK  8(4P16.3) WILD-TYPE                              1
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK  8(4P16.3) MUTATED                                    1
  DEL PEAK  8(4P16.3) WILD-TYPE                                  3
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK  8(4P16.3) MUTATED                              1
  DEL PEAK  8(4P16.3) WILD-TYPE                            1
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK  8(4P16.3) MUTATED                               2
  DEL PEAK  8(4P16.3) WILD-TYPE                            17
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK  8(4P16.3) MUTATED                                 1
  DEL PEAK  8(4P16.3) WILD-TYPE                               0
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK  8(4P16.3) MUTATED                                               2
  DEL PEAK  8(4P16.3) WILD-TYPE                                             3
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK  8(4P16.3) MUTATED                              1
  DEL PEAK  8(4P16.3) WILD-TYPE                            6
D37V9, multiclass
                                                    clus
vv                                                   DEL PEAK  8(4P16.3) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           22
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          83
  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                                2
  MUCINOUS (COLLOID) CARCINOMA                                                 1
                                                    clus
vv                                                   DEL PEAK  8(4P16.3) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                    11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             72
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           220
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 18
  LUNG CLEAR CELL ADENOCARCINOMA                                                 1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             3
  LUNG MUCINOUS ADENOCARCINOMA                                                   1
  LUNG PAPILLARY ADENOCARCINOMA                                                 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"
D37V10, binary
                               cls
clus                              0   1
  DEL PEAK  8(4P16.3) MUTATED     5 114
  DEL PEAK  8(4P16.3) WILD-TYPE  16 341
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4P16.3) MUTATED      5  114
  DEL PEAK  8(4P16.3) WILD-TYPE   16  341
     clus
vv    DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE
  NO                            5                            16
  YES                         114                           341
[1] 2 2
[1] FALSE
D37V11, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  8(4P16.3) MUTATED    79   3   2   7
  DEL PEAK  8(4P16.3) WILD-TYPE 248   9   2  14
D37V12, multiclass
    clus
vv   DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE
  R0                          79                           248
  R1                           3                             9
  R2                           2                             2
  RX                           7                            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  8(4P16.3) MUTATED                                  0     1
  DEL PEAK  8(4P16.3) WILD-TYPE                                1     5
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(4P16.3) MUTATED                          11    86
  DEL PEAK  8(4P16.3) WILD-TYPE                        24   281
D37V13, multiclass
                                  clus
vv                                 DEL PEAK  8(4P16.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                 11
  WHITE                                                     86
                                  clus
vv                                 DEL PEAK  8(4P16.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                   24
  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"
D37V14, binary
                               cls
clus                              0   1
  DEL PEAK  8(4P16.3) MUTATED     2  84
  DEL PEAK  8(4P16.3) WILD-TYPE   5 261
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4P16.3) MUTATED      2   84
  DEL PEAK  8(4P16.3) WILD-TYPE    5  261
                        clus
vv                       DEL PEAK  8(4P16.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          84
                        clus
vv                       DEL PEAK  8(4P16.3) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           261
[1] 2 2
[1] FALSE

Clustering(38) Variable = DEL PEAK  9(4Q34.3) MUTATION ANALYSIS
D38V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  9(4Q34.3) MUTATED   122  28
  DEL PEAK  9(4Q34.3) WILD-TYPE 207  59
  DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE 
                          150                           266 
  DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE 
                           28                            59 
$`DEL PEAK  9(4Q34.3) 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          705 
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-64-5778 TCGA-64-5779 TCGA-67-3771 TCGA-67-3773 
         628         1686         1305          864          610          427 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 TCGA-69-7979 TCGA-69-8255 TCGA-71-6725 
         690          414          230           89          129           61 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4670 TCGA-73-4675 TCGA-75-6214 TCGA-75-7027 
         711          912          131           40         1970         1956 
TCGA-75-7031 TCGA-78-7148 TCGA-78-7150 TCGA-78-7152 TCGA-78-7155 TCGA-78-7159 
        1965         1944         1963         1202         1957         1221 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 TCGA-86-6851 
        1937         1965         1972         1949          327         1959 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 TCGA-86-8075 
         630          422         1963          508           10          479 
TCGA-86-8279 TCGA-86-8669 TCGA-86-8672 TCGA-86-A456 TCGA-91-6828 TCGA-91-6829 
         482           34           15           10          323         1940 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6840 TCGA-91-6847 TCGA-91-7771 TCGA-91-8499 
          60          310          372          842          492           36 
TCGA-91-A4BC TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-A4VN 
          44            2          568          377          477          553 
TCGA-95-A4VP TCGA-97-7937 TCGA-97-8175 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
         605          181           87          427          459           44 
TCGA-99-8033 TCGA-J2-A4AD TCGA-L4-A4E5 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 
         170          287          578          111          102          827 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TF 
        1175           84         1967         1957         1951         1970 

$`DEL PEAK  9(4Q34.3) 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-49-AARQ 
        1700          445          890          522          354         6443 
TCGA-50-5055 TCGA-50-5068 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5942 
         785         1499         1091         2370          653          883 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6597 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 
         764          686         1015          105         1971          424 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6972 TCGA-55-6980 
           2          993           24         1239         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-55-7725 TCGA-55-7727 TCGA-55-7728 TCGA-55-7903 TCGA-55-7907 
         121           39           34           24           19           16 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8087 TCGA-55-8089 
          21            3           31            5          462          100 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8207 
           6          600           47           15           46           66 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8510 
         674          216           44           23           11          228 
TCGA-55-8511 TCGA-55-8513 TCGA-55-8614 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
           9          146          536           49           66          106 
TCGA-55-A48X TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 
          33           28            5          162         1216         1289 
TCGA-62-8402 TCGA-62-A46V TCGA-62-A471 TCGA-64-1676 TCGA-64-1678 TCGA-64-1680 
        1445         2199         1246         1728         1189         1126 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 
        1968         1959           62         1559          866           31 
TCGA-67-3772 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
         573          385          174          141          422          202 
TCGA-69-7761 TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 
         186          165          184           70          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-73-A9RS TCGA-75-7025 TCGA-78-7145 
          38          621          519          305         1967         1973 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 
        1988         1950         1093          760         1948         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-78-7537 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-80-5608 TCGA-83-5908 
        1981         1954         1964         1965         1972          824 
TCGA-86-7701 TCGA-86-7714 TCGA-86-7953 TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 
          11         1968          591          745         1963           13 
TCGA-86-8074 TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8281 TCGA-86-8358 
          24          489          476           16         1955           19 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 
          26           35           45           18          455          405 
TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6835 TCGA-91-6836 TCGA-91-6848 
          30           14           39           79          417          224 
TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
          35          505          174          218          297          127 
TCGA-93-8067 TCGA-95-7039 TCGA-95-7562 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
         186           34         1973          476          830           84 
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-97-8177 TCGA-97-8179 
          22          107          182         1965          147           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-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
         114          282          238          435          116            6 
TCGA-L9-A50W TCGA-L9-A743 TCGA-MP-A4SV TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 
         266          312         1946         1951         1954         1954 
TCGA-MP-A4T9 TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
        1980         1944         1970          142         1955         1971 
TCGA-MP-A5C7 TCGA-S2-AA1A 
        1490          121 

  DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE 
                            1                             2 
  DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE 
                         2696                          6443 
  DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE 
                        489.0                         458.5 
[1] "1.0 - 2696.0 (489.0)" "2.0 - 6443.0 (458.5)"
[1] "hr=" "1.2"
D38V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK  9(4Q34.3) MUTATED         2       42       46        19        18
  DEL PEAK  9(4Q34.3) WILD-TYPE       3       74       86        30        52
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK  9(4Q34.3) MUTATED           30          5       10
  DEL PEAK  9(4Q34.3) WILD-TYPE         38          6       14
D38V3, multiclass
            clus
vv           DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE
  STAGE I                              2                             3
  STAGE IA                            42                            74
  STAGE IB                            46                            86
  STAGE IIA                           19                            30
  STAGE IIB                           18                            52
  STAGE IIIA                          30                            38
  STAGE IIIB                           5                             6
  STAGE IV                            10                            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  9(4Q34.3) MUTATED    50 104  11   5
  DEL PEAK  9(4Q34.3) WILD-TYPE  97 163  31  13
D38V4, multiclass
    clus
vv   DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE
  T1                          50                            97
  T2                         104                           163
  T3                          11                            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  9(4Q34.3) MUTATED   106  28    34
  DEL PEAK  9(4Q34.3) WILD-TYPE 195  63    40
D38V5, multiclass
       clus
vv      DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE
  N0                            106                           195
  N1                             28                            63
  N2+N3                          34                            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  9(4Q34.3) MUTATED   123   8   0   2  37
  DEL PEAK  9(4Q34.3) WILD-TYPE 203  10   1   2  86
D38V6, multiclass
     clus
vv    DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE
  M0                          123                           203
  M1                            8                            10
  M1A                           0                             1
  M1B                           2                             2
  MX                           37                            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"
D38V7, binary
                               cls
clus                              0   1
  DEL PEAK  9(4Q34.3) MUTATED    83  89
  DEL PEAK  9(4Q34.3) WILD-TYPE 172 132
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q34.3) MUTATED     83   89
  DEL PEAK  9(4Q34.3) WILD-TYPE  172  132
        clus
vv       DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE
  FEMALE                          83                           172
  MALE                            89                           132
[1] 2 2
[1] FALSE
D38V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  DEL PEAK  9(4Q34.3) MUTATED                            5
  DEL PEAK  9(4Q34.3) WILD-TYPE                         10
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK  9(4Q34.3) MUTATED                                  37
  DEL PEAK  9(4Q34.3) WILD-TYPE                                57
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  9(4Q34.3) MUTATED                                                  111
  DEL PEAK  9(4Q34.3) WILD-TYPE                                                192
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK  9(4Q34.3) MUTATED                                            0
  DEL PEAK  9(4Q34.3) WILD-TYPE                                          5
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK  9(4Q34.3) MUTATED                                               4
  DEL PEAK  9(4Q34.3) WILD-TYPE                                            15
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK  9(4Q34.3) MUTATED                                2
  DEL PEAK  9(4Q34.3) WILD-TYPE                              0
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK  9(4Q34.3) MUTATED                                    1
  DEL PEAK  9(4Q34.3) WILD-TYPE                                  3
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK  9(4Q34.3) MUTATED                              0
  DEL PEAK  9(4Q34.3) WILD-TYPE                            2
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK  9(4Q34.3) MUTATED                               5
  DEL PEAK  9(4Q34.3) WILD-TYPE                            14
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK  9(4Q34.3) MUTATED                                 1
  DEL PEAK  9(4Q34.3) WILD-TYPE                               0
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK  9(4Q34.3) MUTATED                                               4
  DEL PEAK  9(4Q34.3) WILD-TYPE                                             1
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK  9(4Q34.3) MUTATED                              2
  DEL PEAK  9(4Q34.3) WILD-TYPE                            5
D38V9, multiclass
                                                    clus
vv                                                   DEL PEAK  9(4Q34.3) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           37
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         111
  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                                4
  MUCINOUS (COLLOID) CARCINOMA                                                 2
                                                    clus
vv                                                   DEL PEAK  9(4Q34.3) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                    10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             57
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           192
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 15
  LUNG CLEAR CELL ADENOCARCINOMA                                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             3
  LUNG MUCINOUS ADENOCARCINOMA                                                   2
  LUNG PAPILLARY ADENOCARCINOMA                                                 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"
D38V10, binary
                               cls
clus                              0   1
  DEL PEAK  9(4Q34.3) MUTATED    10 162
  DEL PEAK  9(4Q34.3) WILD-TYPE  11 293
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q34.3) MUTATED     10  162
  DEL PEAK  9(4Q34.3) WILD-TYPE   11  293
     clus
vv    DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE
  NO                           10                            11
  YES                         162                           293
[1] 2 2
[1] FALSE
D38V11, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  9(4Q34.3) MUTATED   119   4   2   8
  DEL PEAK  9(4Q34.3) WILD-TYPE 208   8   2  13
D38V12, multiclass
    clus
vv   DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE
  R0                         119                           208
  R1                           4                             8
  R2                           2                             2
  RX                           8                            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  9(4Q34.3) MUTATED                                  0     4
  DEL PEAK  9(4Q34.3) WILD-TYPE                                1     2
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(4Q34.3) MUTATED                          16   125
  DEL PEAK  9(4Q34.3) WILD-TYPE                        19   242
D38V13, multiclass
                                  clus
vv                                 DEL PEAK  9(4Q34.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 16
  WHITE                                                    125
                                  clus
vv                                 DEL PEAK  9(4Q34.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   19
  WHITE                                                      242
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V14, binary
                               cls
clus                              0   1
  DEL PEAK  9(4Q34.3) MUTATED     5 122
  DEL PEAK  9(4Q34.3) WILD-TYPE   2 223
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q34.3) MUTATED      5  122
  DEL PEAK  9(4Q34.3) WILD-TYPE    2  223
                        clus
vv                       DEL PEAK  9(4Q34.3) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         122
                        clus
vv                       DEL PEAK  9(4Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           223
[1] 2 2
[1] FALSE

Clustering(39) Variable = DEL PEAK 10(5Q12.1) MUTATION ANALYSIS
D39V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 10(5Q12.1) MUTATED   123  29
  DEL PEAK 10(5Q12.1) WILD-TYPE 206  58
  DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE 
                          152                           264 
  DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE 
                           29                            58 
$`DEL PEAK 10(5Q12.1) 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-05-4424 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          705           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-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 
           6          312          111          102          827         1175 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-MP-A4TE 
        1946         1967         1954         1957         1944         1970 
TCGA-MP-A4TK TCGA-MP-A5C7 
        1971         1490 

$`DEL PEAK 10(5Q12.1) 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-49-AARQ TCGA-50-5051 TCGA-50-5055 
         890          522          354         6443          455          785 
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-50-6597 TCGA-50-7109 TCGA-50-8460 TCGA-53-7813 
         567          883         1015          255          105          424 
TCGA-55-1595 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6971 TCGA-55-6980 
        1479            2          993           24           25           67 
TCGA-55-6983 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
        1826         2151         1170           18           35          121 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7725 TCGA-55-7728 TCGA-55-7815 
           4           95           40           39           24           54 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
          19           16           21           33          462          100 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 
           6          600           26           47           15           33 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
          46           66          674          216           44           23 
TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
          15            3          146           49          106           33 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
          29           48           28            5           47          162 
TCGA-62-8395 TCGA-62-8397 TCGA-62-A46U TCGA-62-A46V TCGA-62-A472 TCGA-64-1677 
        1216         1289         2067         2199          910          628 
TCGA-64-1680 TCGA-64-5774 TCGA-64-5775 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
        1126         1959           62          864         1559          866 
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-69-7764 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
         186          690          414          230          184           70 
TCGA-69-8253 TCGA-69-8254 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
         100           77         1600          711          912          800 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS 
          40          164           38          621          519          305 
TCGA-75-7025 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7152 
        1967         1973         1988         1950         1944         1202 
TCGA-78-7153 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7162 TCGA-78-7163 
         760         1957         1961         1963         1940         1950 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
        1934         1937         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-86-7701 TCGA-86-7714 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
          11         1968         1963          745           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-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 
          19           45           34           18          455          405 
TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 
          10           30           14           39          323           60 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
         310           79          417          842          224           35 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
         492          505          174           44          218          297 
TCGA-95-7039 TCGA-95-7562 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
          34         1973          377          830           84          121 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
         553          605          964         1965         1932         1332 
TCGA-97-7554 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8177 TCGA-97-8179 
         775           22          107         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-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG 
         459           44          154          114          282          238 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A50W TCGA-MN-A4N5 TCGA-MP-A4T2 TCGA-MP-A4T7 
         435          116          266           84         1951         1954 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-S2-AA1A 
        1980         1951         1970          142         1955          121 

  DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE 
                            1                             2 
  DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE 
                         2696                          6443 
  DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE 
                        608.5                         427.0 
[1] "1.0 - 2696.0 (608.5)" "2.0 - 6443.0 (427.0)"
[1] "hr=" "1.3"
D39V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 10(5Q12.1) MUTATED         2       39       49        19        27
  DEL PEAK 10(5Q12.1) WILD-TYPE       3       77       83        30        43
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 10(5Q12.1) MUTATED           20          4        9
  DEL PEAK 10(5Q12.1) WILD-TYPE         48          7       15
D39V3, multiclass
            clus
vv           DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE
  STAGE I                              2                             3
  STAGE IA                            39                            77
  STAGE IB                            49                            83
  STAGE IIA                           19                            30
  STAGE IIB                           27                            43
  STAGE IIIA                          20                            48
  STAGE IIIB                           4                             7
  STAGE IV                             9                            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(5Q12.1) MUTATED    53  96  12   6
  DEL PEAK 10(5Q12.1) WILD-TYPE  94 171  30  12
D39V4, multiclass
    clus
vv   DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE
  T1                          53                            94
  T2                          96                           171
  T3                          12                            30
  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 10(5Q12.1) MUTATED   102  40    22
  DEL PEAK 10(5Q12.1) WILD-TYPE 199  51    52
D39V5, multiclass
       clus
vv      DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE
  N0                            102                           199
  N1                             40                            51
  N2+N3                          22                            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 10(5Q12.1) MUTATED   122   6   0   2  39
  DEL PEAK 10(5Q12.1) WILD-TYPE 204  12   1   2  84
D39V6, multiclass
     clus
vv    DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE
  M0                          122                           204
  M1                            6                            12
  M1A                           0                             1
  M1B                           2                             2
  MX                           39                            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"
D39V7, binary
                               cls
clus                              0   1
  DEL PEAK 10(5Q12.1) MUTATED    86  83
  DEL PEAK 10(5Q12.1) WILD-TYPE 169 138
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(5Q12.1) MUTATED     86   83
  DEL PEAK 10(5Q12.1) WILD-TYPE  169  138
        clus
vv       DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE
  FEMALE                          86                           169
  MALE                            83                           138
[1] 2 2
[1] FALSE
D39V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 10(5Q12.1) MUTATED                            5
  DEL PEAK 10(5Q12.1) WILD-TYPE                         10
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 10(5Q12.1) MUTATED                                  33
  DEL PEAK 10(5Q12.1) WILD-TYPE                                61
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 10(5Q12.1) MUTATED                                                  117
  DEL PEAK 10(5Q12.1) WILD-TYPE                                                186
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 10(5Q12.1) MUTATED                                            0
  DEL PEAK 10(5Q12.1) WILD-TYPE                                          5
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 10(5Q12.1) MUTATED                                               2
  DEL PEAK 10(5Q12.1) WILD-TYPE                                            17
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 10(5Q12.1) MUTATED                                0
  DEL PEAK 10(5Q12.1) WILD-TYPE                              2
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 10(5Q12.1) MUTATED                                    2
  DEL PEAK 10(5Q12.1) WILD-TYPE                                  2
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 10(5Q12.1) MUTATED                              1
  DEL PEAK 10(5Q12.1) WILD-TYPE                            1
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 10(5Q12.1) MUTATED                               4
  DEL PEAK 10(5Q12.1) WILD-TYPE                            15
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 10(5Q12.1) MUTATED                                 0
  DEL PEAK 10(5Q12.1) WILD-TYPE                               1
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 10(5Q12.1) MUTATED                                               4
  DEL PEAK 10(5Q12.1) WILD-TYPE                                             1
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 10(5Q12.1) MUTATED                              1
  DEL PEAK 10(5Q12.1) WILD-TYPE                            6
D39V9, multiclass
                                                    clus
vv                                                   DEL PEAK 10(5Q12.1) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           33
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         117
  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 10(5Q12.1) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                    10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             61
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           186
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     5
  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                                  1
  MUCINOUS (COLLOID) CARCINOMA                                                   6
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V10, binary
                               cls
clus                              0   1
  DEL PEAK 10(5Q12.1) MUTATED     6 163
  DEL PEAK 10(5Q12.1) WILD-TYPE  15 292
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(5Q12.1) MUTATED      6  163
  DEL PEAK 10(5Q12.1) WILD-TYPE   15  292
     clus
vv    DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE
  NO                            6                            15
  YES                         163                           292
[1] 2 2
[1] FALSE
D39V11, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 10(5Q12.1) MUTATED   124   3   1  10
  DEL PEAK 10(5Q12.1) WILD-TYPE 203   9   3  11
D39V12, multiclass
    clus
vv   DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE
  R0                         124                           203
  R1                           3                             9
  R2                           1                             3
  RX                          10                            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(5Q12.1) MUTATED                                  1     3
  DEL PEAK 10(5Q12.1) WILD-TYPE                                0     3
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(5Q12.1) MUTATED                          15   121
  DEL PEAK 10(5Q12.1) WILD-TYPE                        20   246
D39V13, multiclass
                                  clus
vv                                 DEL PEAK 10(5Q12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 15
  WHITE                                                    121
                                  clus
vv                                 DEL PEAK 10(5Q12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        3
  BLACK OR AFRICAN AMERICAN                                   20
  WHITE                                                      246
[1] 4 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 10(5Q12.1) MUTATED     6 117
  DEL PEAK 10(5Q12.1) WILD-TYPE   1 228
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(5Q12.1) MUTATED      6  117
  DEL PEAK 10(5Q12.1) WILD-TYPE    1  228
                        clus
vv                       DEL PEAK 10(5Q12.1) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                         117
                        clus
vv                       DEL PEAK 10(5Q12.1) WILD-TYPE
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                           228
[1] 2 2
[1] FALSE

Clustering(40) Variable = DEL PEAK 11(5Q31.1) MUTATION ANALYSIS
D40V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 11(5Q31.1) MUTATED   144  35
  DEL PEAK 11(5Q31.1) WILD-TYPE 185  52
  DEL PEAK 11(5Q31.1) MUTATED DEL PEAK 11(5Q31.1) WILD-TYPE 
                          179                           237 
  DEL PEAK 11(5Q31.1) MUTATED DEL PEAK 11(5Q31.1) WILD-TYPE 
                           35                            52 
$`DEL PEAK 11(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-49-AARQ TCGA-50-5045 TCGA-50-5049 TCGA-50-5066 TCGA-50-5068 TCGA-50-5941 
        6443         2174         2146          944         1499          567 
TCGA-50-5944 TCGA-50-5946 TCGA-50-7109 TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ 
         764          686          255         1986         1971          280 
TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6969 TCGA-55-6972 
         701         1178         1375           87         1239         1475 
TCGA-55-6985 TCGA-55-7281 TCGA-55-7570 TCGA-55-7576 TCGA-55-7724 TCGA-55-7726 
        1233           18            6           40          705           39 
TCGA-55-7727 TCGA-55-7907 TCGA-55-7910 TCGA-55-7914 TCGA-55-7994 TCGA-55-8094 
          34           16          197            3           31            4 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 TCGA-55-8511 
          23           29           11            8          228            9 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y 
         202          536           15           48           66           42 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DG TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 
        1952            1          162         1216         1970         2696 
TCGA-62-8402 TCGA-62-A46V TCGA-62-A471 TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 
        1445         2199         1246         1728         1189         1686 
TCGA-64-1681 TCGA-64-5778 TCGA-64-5779 TCGA-67-3771 TCGA-67-3772 TCGA-69-7764 
        1968         1305          864          610          573          414 
TCGA-69-7765 TCGA-69-7979 TCGA-69-7980 TCGA-69-8255 TCGA-71-6725 TCGA-73-4668 
         165           89          382          129           61          467 
TCGA-73-4670 TCGA-73-A9RS TCGA-75-6214 TCGA-75-7027 TCGA-78-7146 TCGA-78-7149 
         131          305         1970         1956         1988         1093 
TCGA-78-7150 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7167 TCGA-78-7220 
        1963         1221          678          215         1937         1965 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-8640 TCGA-80-5608 TCGA-83-5908 
        1972         1949         1944         1949         1972          824 
TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-7955 TCGA-86-8056 
        1959          630          422          591          508         1963 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8279 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
          13           24          482           19           26           35 
TCGA-86-8672 TCGA-91-6829 TCGA-91-6831 TCGA-91-6840 TCGA-91-8499 TCGA-93-7348 
          15         1940          310          372           36          127 
TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
         186           34            2         1973          568          377 
TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VP TCGA-97-7937 TCGA-97-8172 
         477          476          121          605          181          182 
TCGA-97-8175 TCGA-99-8025 TCGA-J2-A4AD TCGA-L4-A4E5 TCGA-L9-A444 TCGA-L9-A50W 
          87          427          287          578            6          266 
TCGA-L9-A7SV TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4T4 TCGA-MP-A4T7 
         111          827         1175         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 11(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          462          100            6 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 
         600           26           47           15           33           46 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8508 TCGA-55-8512 
          66          674          216           44           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-62-8397 TCGA-62-A46U TCGA-62-A472 
          28            5           47         1289         2067          910 
TCGA-64-1677 TCGA-64-1680 TCGA-64-5774 TCGA-64-5775 TCGA-64-5781 TCGA-64-5815 
         628         1126         1959           62         1559          866 
TCGA-67-3770 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
          31          427          385          174          141          422 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
         202          186          690          230          184           70 
TCGA-69-8253 TCGA-69-8254 TCGA-69-A59K TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
         100           77          214         1600          711          912 
TCGA-73-4666 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
         800           40          164           38          621          519 
TCGA-75-7025 TCGA-75-7031 TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 TCGA-78-7152 
        1967         1965         1973         1950         1944         1202 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7162 
         760         1948         1957         1961         1963         1940 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        1950         1934          327          881         1952          994 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 TCGA-86-7701 
        1971         1981         1954         1964         1965           11 
TCGA-86-7714 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 TCGA-86-8075 TCGA-86-8076 
        1968         1963          745           10          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-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 
         455          405           10           30           14           39 
TCGA-91-6828 TCGA-91-6830 TCGA-91-6835 TCGA-91-6836 TCGA-91-6847 TCGA-91-6848 
         323           60           79          417          842          224 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD 
          35          492          505          174           44          218 
TCGA-93-7347 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VN TCGA-97-7546 TCGA-97-7547 
         297          830           84          553          964         1965 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 
        1932         1332          775           22          107         1965 
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-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
         392          459           44          170          154          114 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A743 TCGA-L9-A8F4 
         282          238          435          116          312          102 
TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TF 
          84         1967         1951         1980         1951         1970 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-S2-AA1A 
         142         1955          121 

  DEL PEAK 11(5Q31.1) MUTATED DEL PEAK 11(5Q31.1) WILD-TYPE 
                            1                             2 
  DEL PEAK 11(5Q31.1) MUTATED DEL PEAK 11(5Q31.1) WILD-TYPE 
                         6443                          2370 
  DEL PEAK 11(5Q31.1) MUTATED DEL PEAK 11(5Q31.1) WILD-TYPE 
                          607                           422 
[1] "1.0 - 6443.0 (607.0)" "2.0 - 2370.0 (422.0)"
[1] "hr=" "1.6"
D40V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 11(5Q31.1) MUTATED         4       42       57        21        31
  DEL PEAK 11(5Q31.1) WILD-TYPE       1       74       75        28        39
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 11(5Q31.1) MUTATED           28          4       11
  DEL PEAK 11(5Q31.1) WILD-TYPE         40          7       13
D40V3, multiclass
            clus
vv           DEL PEAK 11(5Q31.1) MUTATED DEL PEAK 11(5Q31.1) WILD-TYPE
  STAGE I                              4                             1
  STAGE IA                            42                            74
  STAGE IB                            57                            75
  STAGE IIA                           21                            28
  STAGE IIB                           31                            39
  STAGE IIIA                          28                            40
  STAGE IIIB                           4                             7
  STAGE IV                            11                            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(5Q31.1) MUTATED    60 114  16   7
  DEL PEAK 11(5Q31.1) WILD-TYPE  87 153  26  11
D40V4, multiclass
    clus
vv   DEL PEAK 11(5Q31.1) MUTATED DEL PEAK 11(5Q31.1) WILD-TYPE
  T1                          60                            87
  T2                         114                           153
  T3                          16                            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
  DEL PEAK 11(5Q31.1) MUTATED   123  42    29
  DEL PEAK 11(5Q31.1) WILD-TYPE 178  49    45
D40V5, multiclass
       clus
vv      DEL PEAK 11(5Q31.1) MUTATED DEL PEAK 11(5Q31.1) WILD-TYPE
  N0                            123                           178
  N1                             42                            49
  N2+N3                          29                            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 11(5Q31.1) MUTATED   137   8   0   2  50
  DEL PEAK 11(5Q31.1) WILD-TYPE 189  10   1   2  73
D40V6, multiclass
     clus
vv    DEL PEAK 11(5Q31.1) MUTATED DEL PEAK 11(5Q31.1) WILD-TYPE
  M0                          137                           189
  M1                            8                            10
  M1A                           0                             1
  M1B                           2                             2
  MX                           50                            73
[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 11(5Q31.1) MUTATED    99  99
  DEL PEAK 11(5Q31.1) WILD-TYPE 156 122
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(5Q31.1) MUTATED     99   99
  DEL PEAK 11(5Q31.1) WILD-TYPE  156  122
        clus
vv       DEL PEAK 11(5Q31.1) MUTATED DEL PEAK 11(5Q31.1) WILD-TYPE
  FEMALE                          99                           156
  MALE                            99                           122
[1] 2 2
[1] FALSE
D40V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 11(5Q31.1) MUTATED                            7
  DEL PEAK 11(5Q31.1) WILD-TYPE                          8
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 11(5Q31.1) MUTATED                                  44
  DEL PEAK 11(5Q31.1) WILD-TYPE                                50
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 11(5Q31.1) MUTATED                                                  130
  DEL PEAK 11(5Q31.1) WILD-TYPE                                                173
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 11(5Q31.1) MUTATED                                            0
  DEL PEAK 11(5Q31.1) WILD-TYPE                                          5
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 11(5Q31.1) MUTATED                                               3
  DEL PEAK 11(5Q31.1) WILD-TYPE                                            16
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 11(5Q31.1) MUTATED                                1
  DEL PEAK 11(5Q31.1) WILD-TYPE                              1
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 11(5Q31.1) MUTATED                                    2
  DEL PEAK 11(5Q31.1) WILD-TYPE                                  2
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 11(5Q31.1) MUTATED                              1
  DEL PEAK 11(5Q31.1) WILD-TYPE                            1
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 11(5Q31.1) MUTATED                               6
  DEL PEAK 11(5Q31.1) WILD-TYPE                            13
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 11(5Q31.1) MUTATED                                 0
  DEL PEAK 11(5Q31.1) WILD-TYPE                               1
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 11(5Q31.1) MUTATED                                               3
  DEL PEAK 11(5Q31.1) WILD-TYPE                                             2
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 11(5Q31.1) MUTATED                              1
  DEL PEAK 11(5Q31.1) WILD-TYPE                            6
D40V9, multiclass
                                                    clus
vv                                                   DEL PEAK 11(5Q31.1) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           44
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         130
  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 11(5Q31.1) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             50
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           173
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     5
  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                                  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"
D40V10, binary
                               cls
clus                              0   1
  DEL PEAK 11(5Q31.1) MUTATED     9 189
  DEL PEAK 11(5Q31.1) WILD-TYPE  12 266
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(5Q31.1) MUTATED      9  189
  DEL PEAK 11(5Q31.1) WILD-TYPE   12  266
     clus
vv    DEL PEAK 11(5Q31.1) MUTATED DEL PEAK 11(5Q31.1) WILD-TYPE
  NO                            9                            12
  YES                         189                           266
[1] 2 2
[1] FALSE
D40V11, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 11(5Q31.1) MUTATED   138   3   1  11
  DEL PEAK 11(5Q31.1) WILD-TYPE 189   9   3  10
D40V12, multiclass
    clus
vv   DEL PEAK 11(5Q31.1) MUTATED DEL PEAK 11(5Q31.1) WILD-TYPE
  R0                         138                           189
  R1                           3                             9
  R2                           1                             3
  RX                          11                            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 11(5Q31.1) MUTATED                                  1     3
  DEL PEAK 11(5Q31.1) WILD-TYPE                                0     3
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(5Q31.1) MUTATED                          19   144
  DEL PEAK 11(5Q31.1) WILD-TYPE                        16   223
D40V13, multiclass
                                  clus
vv                                 DEL PEAK 11(5Q31.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 19
  WHITE                                                    144
                                  clus
vv                                 DEL PEAK 11(5Q31.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        3
  BLACK OR AFRICAN AMERICAN                                   16
  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"
D40V14, binary
                               cls
clus                              0   1
  DEL PEAK 11(5Q31.1) MUTATED     5 137
  DEL PEAK 11(5Q31.1) WILD-TYPE   2 208
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(5Q31.1) MUTATED      5  137
  DEL PEAK 11(5Q31.1) WILD-TYPE    2  208
                        clus
vv                       DEL PEAK 11(5Q31.1) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         137
                        clus
vv                       DEL PEAK 11(5Q31.1) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           208
[1] 2 2
[1] FALSE

Clustering(41) Variable = DEL PEAK 12(6Q11.1) MUTATION ANALYSIS
D41V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 12(6Q11.1) MUTATED    82  30
  DEL PEAK 12(6Q11.1) WILD-TYPE 247  57
  DEL PEAK 12(6Q11.1) MUTATED DEL PEAK 12(6Q11.1) WILD-TYPE 
                          112                           304 
  DEL PEAK 12(6Q11.1) MUTATED DEL PEAK 12(6Q11.1) WILD-TYPE 
                           30                            57 
$`DEL PEAK 12(6Q11.1) MUTATED`
TCGA-05-4390 TCGA-05-4405 TCGA-05-4415 TCGA-35-3615 TCGA-35-4123 TCGA-38-4631 
        1126          610         1997           14          182          354 
TCGA-44-2656 TCGA-44-2659 TCGA-44-2666 TCGA-44-2668 TCGA-44-5644 TCGA-44-6147 
        1429         1367           97          246          863          845 
TCGA-44-6775 TCGA-44-6778 TCGA-44-6779 TCGA-44-7667 TCGA-44-A47F TCGA-44-A4SU 
         705         1864         1978          557          337           76 
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-50-5935 TCGA-50-5941 
         455          944         1499         1091          653          567 
TCGA-50-5942 TCGA-50-5946 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-6543 TCGA-55-6971 
         883          686         1971          280            2           25 
TCGA-55-6972 TCGA-55-6983 TCGA-55-7283 TCGA-55-7724 TCGA-55-7815 TCGA-55-7914 
        1475         1826           35          705           54            3 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8207 TCGA-55-8302 TCGA-55-8506 
         100            6          600           66           23           11 
TCGA-55-8508 TCGA-55-8511 TCGA-55-8512 TCGA-55-A48X TCGA-55-A490 TCGA-55-A493 
          15            9            3           33           48           28 
TCGA-62-8398 TCGA-62-8402 TCGA-62-A46U TCGA-62-A472 TCGA-64-1677 TCGA-64-5775 
        1970         1445         2067          910          628           62 
TCGA-64-5781 TCGA-67-3771 TCGA-67-6216 TCGA-69-7974 TCGA-69-8253 TCGA-69-8254 
        1559          610          141          184          100           77 
TCGA-69-A59K TCGA-73-4659 TCGA-73-4666 TCGA-73-4675 TCGA-75-6214 TCGA-75-7025 
         214          711          800           40         1970         1967 
TCGA-78-7146 TCGA-78-7152 TCGA-78-7153 TCGA-78-7158 TCGA-78-7220 TCGA-78-7535 
        1988         1202          760         1963         1965         1972 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 TCGA-80-5608 TCGA-83-5908 TCGA-86-7701 
        1949         1944          881         1972          824           11 
TCGA-86-7714 TCGA-86-7953 TCGA-86-8074 TCGA-86-8280 TCGA-86-8359 TCGA-86-A456 
        1968          591           24           16           26           10 
TCGA-91-6831 TCGA-93-7347 TCGA-93-7348 TCGA-95-7567 TCGA-95-7944 TCGA-95-8494 
         310          297          127          568          377           84 
TCGA-95-A4VP TCGA-97-7547 TCGA-97-7554 TCGA-97-8177 TCGA-97-8547 TCGA-99-7458 
         605         1965          775          147          148          392 
TCGA-99-8025 TCGA-J2-8192 TCGA-L9-A443 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4SV 
         427          154          116          827         1175         1946 
TCGA-MP-A4T2 TCGA-MP-A4TC TCGA-MP-A4TF TCGA-MP-A5C7 
        1951         1944         1970         1490 

$`DEL PEAK 12(6Q11.1) 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-05-4410 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
         578         1958          455          912          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-05-5428 TCGA-05-5429 TCGA-05-5715 
         457          151          882          670           30           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-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F 
         864         1073         1357          448         1971          133 
TCGA-44-2655 TCGA-44-2657 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-3396 
        1324          400          741         1280         1301         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-44-6148 TCGA-44-6774 TCGA-44-6776 
         723          328          302          704          658         1938 
TCGA-44-6777 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7669 
        1942          444          592          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-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 
         486          466          287          351          415         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-49-AARQ TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5072 
         369         6443         2174         2146          785          246 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5944 TCGA-50-6597 TCGA-50-7109 
         282          267         2370          764         1015          255 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7813 TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 
         105         1986          424          701         1178         1479 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6980 
        1375           87          993           24         1239           67 
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-55-7576 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
           4           95           40           39           39           34 
TCGA-55-7728 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7994 
          24           19           16          197           21           31 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
           5           33          462           26            4           47 
TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
          15           33           46          674          216           44 
TCGA-55-8505 TCGA-55-8507 TCGA-55-8510 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
          29            8          228          146          202          536 
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-A494 TCGA-55-A4DF TCGA-55-A4DG 
          29         1952            1            5           47          162 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 TCGA-62-A46V TCGA-62-A471 TCGA-64-1676 
        1216         1289         2696         2199         1246         1728 
TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 
        1189         1686         1126         1968         1959         1305 
TCGA-64-5779 TCGA-64-5815 TCGA-67-3770 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 
         864          866           31          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-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS TCGA-75-7027 TCGA-75-7031 
          38          621          519          305         1956         1965 
TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7154 
        1973         1950         1944         1093         1963         1948 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
        1957         1961         1221          678          215         1940 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7539 TCGA-78-7542 TCGA-78-7633 
        1950         1934         1937          327         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-86-6851 TCGA-86-7711 TCGA-86-7713 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
        1959          630          422         1963          508          745 
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-86-8281 TCGA-86-8358 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
         482         1955           19           35           45           34 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4D0 TCGA-86-A4P7 
          18           15          455          405           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-91-6849 TCGA-91-7771 TCGA-91-8496 
         372          842          224           35          492          505 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-8067 TCGA-95-7039 
         174           36           44          218          186           34 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-A4VK 
           2         1973          477          476          830          121 
TCGA-95-A4VN TCGA-97-7546 TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 TCGA-97-7941 
         553          964         1932         1332          181           22 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8179 TCGA-97-8552 
         107          182         1965           87           15          115 
TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8194 
         197          271          459           44          170          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-L9-A50W TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N5 TCGA-MP-A4SW 
         266          312          111          102           84         1967 
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-S2-AA1A 
         142         1955         1971          121 

  DEL PEAK 12(6Q11.1) MUTATED DEL PEAK 12(6Q11.1) WILD-TYPE 
                            2                             1 
  DEL PEAK 12(6Q11.1) MUTATED DEL PEAK 12(6Q11.1) WILD-TYPE 
                         2067                          6443 
  DEL PEAK 12(6Q11.1) MUTATED DEL PEAK 12(6Q11.1) WILD-TYPE 
                        602.5                         456.0 
[1] "2.0 - 2067.0 (602.5)" "1.0 - 6443.0 (456.0)"
[1] "hr=" "1.3"
D41V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 12(6Q11.1) MUTATED         0       24       37        14        15
  DEL PEAK 12(6Q11.1) WILD-TYPE       5       92       95        35        55
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 12(6Q11.1) MUTATED           32          3        5
  DEL PEAK 12(6Q11.1) WILD-TYPE         36          8       19
D41V3, multiclass
            clus
vv           DEL PEAK 12(6Q11.1) MUTATED DEL PEAK 12(6Q11.1) WILD-TYPE
  STAGE I                              0                             5
  STAGE IA                            24                            92
  STAGE IB                            37                            95
  STAGE IIA                           14                            35
  STAGE IIB                           15                            55
  STAGE IIIA                          32                            36
  STAGE IIIB                           3                             8
  STAGE IV                             5                            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 12(6Q11.1) MUTATED    38  76  12   5
  DEL PEAK 12(6Q11.1) WILD-TYPE 109 191  30  13
D41V4, multiclass
    clus
vv   DEL PEAK 12(6Q11.1) MUTATED DEL PEAK 12(6Q11.1) WILD-TYPE
  T1                          38                           109
  T2                          76                           191
  T3                          12                            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 12(6Q11.1) MUTATED    72  26    31
  DEL PEAK 12(6Q11.1) WILD-TYPE 229  65    43
D41V5, multiclass
       clus
vv      DEL PEAK 12(6Q11.1) MUTATED DEL PEAK 12(6Q11.1) WILD-TYPE
  N0                             72                           229
  N1                             26                            65
  N2+N3                          31                            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 12(6Q11.1) MUTATED    90   4   0   1  34
  DEL PEAK 12(6Q11.1) WILD-TYPE 236  14   1   3  89
D41V6, multiclass
     clus
vv    DEL PEAK 12(6Q11.1) MUTATED DEL PEAK 12(6Q11.1) WILD-TYPE
  M0                           90                           236
  M1                            4                            14
  M1A                           0                             1
  M1B                           1                             3
  MX                           34                            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"
D41V7, binary
                               cls
clus                              0   1
  DEL PEAK 12(6Q11.1) MUTATED    75  56
  DEL PEAK 12(6Q11.1) WILD-TYPE 180 165
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(6Q11.1) MUTATED     75   56
  DEL PEAK 12(6Q11.1) WILD-TYPE  180  165
        clus
vv       DEL PEAK 12(6Q11.1) MUTATED DEL PEAK 12(6Q11.1) WILD-TYPE
  FEMALE                          75                           180
  MALE                            56                           165
[1] 2 2
[1] FALSE
D41V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 12(6Q11.1) MUTATED                            3
  DEL PEAK 12(6Q11.1) WILD-TYPE                         12
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 12(6Q11.1) MUTATED                                  28
  DEL PEAK 12(6Q11.1) WILD-TYPE                                66
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 12(6Q11.1) MUTATED                                                   86
  DEL PEAK 12(6Q11.1) WILD-TYPE                                                217
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 12(6Q11.1) MUTATED                                            2
  DEL PEAK 12(6Q11.1) WILD-TYPE                                          3
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 12(6Q11.1) MUTATED                                               4
  DEL PEAK 12(6Q11.1) WILD-TYPE                                            15
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 12(6Q11.1) MUTATED                                0
  DEL PEAK 12(6Q11.1) WILD-TYPE                              2
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 12(6Q11.1) MUTATED                                    1
  DEL PEAK 12(6Q11.1) WILD-TYPE                                  3
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 12(6Q11.1) MUTATED                              0
  DEL PEAK 12(6Q11.1) WILD-TYPE                            2
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 12(6Q11.1) MUTATED                               5
  DEL PEAK 12(6Q11.1) WILD-TYPE                            14
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 12(6Q11.1) MUTATED                                 0
  DEL PEAK 12(6Q11.1) WILD-TYPE                               1
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 12(6Q11.1) MUTATED                                               0
  DEL PEAK 12(6Q11.1) WILD-TYPE                                             5
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 12(6Q11.1) MUTATED                              2
  DEL PEAK 12(6Q11.1) WILD-TYPE                            5
D41V9, multiclass
                                                    clus
vv                                                   DEL PEAK 12(6Q11.1) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           28
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          86
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                   2
  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                                0
  MUCINOUS (COLLOID) CARCINOMA                                                 2
                                                    clus
vv                                                   DEL PEAK 12(6Q11.1) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                    12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             66
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           217
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 15
  LUNG CLEAR CELL ADENOCARCINOMA                                                 2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             3
  LUNG MUCINOUS ADENOCARCINOMA                                                   2
  LUNG PAPILLARY ADENOCARCINOMA                                                 14
  LUNG SIGNET RING ADENOCARCINOMA                                                1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                  5
  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"
D41V10, binary
                               cls
clus                              0   1
  DEL PEAK 12(6Q11.1) MUTATED     7 124
  DEL PEAK 12(6Q11.1) WILD-TYPE  14 331
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(6Q11.1) MUTATED      7  124
  DEL PEAK 12(6Q11.1) WILD-TYPE   14  331
     clus
vv    DEL PEAK 12(6Q11.1) MUTATED DEL PEAK 12(6Q11.1) WILD-TYPE
  NO                            7                            14
  YES                         124                           331
[1] 2 2
[1] FALSE
D41V11, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 12(6Q11.1) MUTATED    91   1   1   6
  DEL PEAK 12(6Q11.1) WILD-TYPE 236  11   3  15
D41V12, multiclass
    clus
vv   DEL PEAK 12(6Q11.1) MUTATED DEL PEAK 12(6Q11.1) WILD-TYPE
  R0                          91                           236
  R1                           1                            11
  R2                           1                             3
  RX                           6                            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 12(6Q11.1) MUTATED                                  0     1
  DEL PEAK 12(6Q11.1) WILD-TYPE                                1     5
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(6Q11.1) MUTATED                          10   104
  DEL PEAK 12(6Q11.1) WILD-TYPE                        25   263
D41V13, multiclass
                                  clus
vv                                 DEL PEAK 12(6Q11.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                 10
  WHITE                                                    104
                                  clus
vv                                 DEL PEAK 12(6Q11.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                   25
  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"
D41V14, binary
                               cls
clus                              0   1
  DEL PEAK 12(6Q11.1) MUTATED     3  92
  DEL PEAK 12(6Q11.1) WILD-TYPE   4 253
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(6Q11.1) MUTATED      3   92
  DEL PEAK 12(6Q11.1) WILD-TYPE    4  253
                        clus
vv                       DEL PEAK 12(6Q11.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          92
                        clus
vv                       DEL PEAK 12(6Q11.1) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           253
[1] 2 2
[1] FALSE

Clustering(42) Variable = DEL PEAK 13(6Q22.31) MUTATION ANALYSIS
D42V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 13(6Q22.31) MUTATED   158  53
  DEL PEAK 13(6Q22.31) WILD-TYPE 171  34
  DEL PEAK 13(6Q22.31) MUTATED DEL PEAK 13(6Q22.31) WILD-TYPE 
                           211                            205 
  DEL PEAK 13(6Q22.31) MUTATED DEL PEAK 13(6Q22.31) WILD-TYPE 
                            53                             34 
$`DEL PEAK 13(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          705 
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          600            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-73-A9RS TCGA-75-6214 TCGA-75-7025 
          40          621          519          305         1970         1967 
TCGA-75-7027 TCGA-78-7146 TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7156 
        1956         1988         1093         1202          760         1961 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7161 TCGA-78-7162 TCGA-78-7167 TCGA-78-7535 
        1963         1221          215         1940         1937         1972 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8655 
        1949         1944          881         1952          994         1981 
TCGA-80-5607 TCGA-83-5908 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
        1965          824           11          630          422         1968 
TCGA-86-7953 TCGA-86-7955 TCGA-86-8054 TCGA-86-8075 TCGA-86-8278 TCGA-86-8279 
         591          508          745          479          476          482 
TCGA-86-8280 TCGA-86-8281 TCGA-86-8358 TCGA-86-8359 TCGA-86-8672 TCGA-86-8674 
          16         1955           19           26           15          405 
TCGA-86-A456 TCGA-91-6831 TCGA-91-7771 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
          10          310          492          218          297          127 
TCGA-93-8067 TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 TCGA-95-7948 TCGA-95-8494 
         186            2          568          377          476           84 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7547 TCGA-97-7554 TCGA-97-7937 TCGA-97-8174 
         553          605         1965          775          181         1965 
TCGA-97-8547 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8033 
         148          197          271          392          427          170 
TCGA-J2-8192 TCGA-J2-8194 TCGA-L4-A4E5 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W 
         154          114          578          116            6          266 
TCGA-L9-A7SV TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
         111          827         1175           84         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 13(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-49-AARQ TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 
         445          369         6443         2174         2146          785 
TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5944 TCGA-50-6597 
         944          246          282          267          764         1015 
TCGA-50-7109 TCGA-50-8460 TCGA-55-1594 TCGA-55-5899 TCGA-55-6712 TCGA-55-6969 
         255          105         1178           87           24         1239 
TCGA-55-6980 TCGA-55-6987 TCGA-55-7281 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
          67         1170           18          121            6            4 
TCGA-55-7574 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7907 TCGA-55-7910 
          95           39           34           24           16          197 
TCGA-55-7995 TCGA-55-8087 TCGA-55-8092 TCGA-55-8096 TCGA-55-8205 TCGA-55-8206 
           5          462           26           47           33           46 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8507 TCGA-55-8510 
         674          216           44           29            8          228 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
         146          202          536           49           66          106 
TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A4DF TCGA-55-A4DG 
          29         1952            1           28           47          162 
TCGA-62-8397 TCGA-62-8399 TCGA-62-A471 TCGA-64-1676 TCGA-64-1679 TCGA-64-1681 
        1289         2696         1246         1728         1686         1968 
TCGA-64-5778 TCGA-67-3770 TCGA-67-3772 TCGA-67-3774 TCGA-67-6215 TCGA-67-6217 
        1305           31          573          385          174          422 
TCGA-69-7761 TCGA-69-7765 TCGA-69-7980 TCGA-69-8255 TCGA-71-6725 TCGA-73-4662 
         186          165          382          129           61          912 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-75-7031 TCGA-78-7145 
         467          131          164           38         1965         1973 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7150 TCGA-78-7154 TCGA-78-7155 TCGA-78-7160 
        1950         1944         1963         1948         1957          678 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7220 TCGA-78-7539 TCGA-78-8640 TCGA-78-8648 
        1950         1934         1965          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-86-8585 TCGA-86-8668 
        1963           13           24          489           35           45 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 
          34           18          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-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
         842          224           35          505          174           36 
TCGA-91-A4BC TCGA-95-7039 TCGA-95-7562 TCGA-95-7947 TCGA-95-8039 TCGA-95-A4VK 
          44           34         1973          477          830          121 
TCGA-97-7546 TCGA-97-7552 TCGA-97-7553 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
         964         1932         1332           22          107          182 
TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-99-8028 TCGA-99-8032 
          87          147           15          115          459           44 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A743 TCGA-L9-A8F4 
         287          282          238          435          312          102 
TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TH 
        1954         1954         1957         1980         1951          142 
TCGA-S2-AA1A 
         121 

  DEL PEAK 13(6Q22.31) MUTATED DEL PEAK 13(6Q22.31) WILD-TYPE 
                             2                              1 
  DEL PEAK 13(6Q22.31) MUTATED DEL PEAK 13(6Q22.31) WILD-TYPE 
                          2370                           6443 
  DEL PEAK 13(6Q22.31) MUTATED DEL PEAK 13(6Q22.31) WILD-TYPE 
                           605                            400 
[1] "2.0 - 2370.0 (605.0)" "1.0 - 6443.0 (400.0)"
[1] "hr=" "1.3"
D42V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 13(6Q22.31) MUTATED         1       49       67        28        32
  DEL PEAK 13(6Q22.31) WILD-TYPE       4       67       65        21        38
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 13(6Q22.31) MUTATED           39          7       13
  DEL PEAK 13(6Q22.31) WILD-TYPE         29          4       11
D42V3, multiclass
            clus
vv           DEL PEAK 13(6Q22.31) MUTATED DEL PEAK 13(6Q22.31) WILD-TYPE
  STAGE I                               1                              4
  STAGE IA                             49                             67
  STAGE IB                             67                             65
  STAGE IIA                            28                             21
  STAGE IIB                            32                             38
  STAGE IIIA                           39                             29
  STAGE IIIB                            7                              4
  STAGE IV                             13                             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 13(6Q22.31) MUTATED    66 137  22  10
  DEL PEAK 13(6Q22.31) WILD-TYPE  81 130  20   8
D42V4, multiclass
    clus
vv   DEL PEAK 13(6Q22.31) MUTATED DEL PEAK 13(6Q22.31) WILD-TYPE
  T1                           66                             81
  T2                          137                            130
  T3                           22                             20
  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 13(6Q22.31) MUTATED   143  48    40
  DEL PEAK 13(6Q22.31) WILD-TYPE 158  43    34
D42V5, multiclass
       clus
vv      DEL PEAK 13(6Q22.31) MUTATED DEL PEAK 13(6Q22.31) WILD-TYPE
  N0                             143                            158
  N1                              48                             43
  N2+N3                           40                             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
  DEL PEAK 13(6Q22.31) MUTATED   162  11   0   2  59
  DEL PEAK 13(6Q22.31) WILD-TYPE 164   7   1   2  64
D42V6, multiclass
     clus
vv    DEL PEAK 13(6Q22.31) MUTATED DEL PEAK 13(6Q22.31) WILD-TYPE
  M0                           162                            164
  M1                            11                              7
  M1A                            0                              1
  M1B                            2                              2
  MX                            59                             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"
D42V7, binary
                                cls
clus                               0   1
  DEL PEAK 13(6Q22.31) MUTATED   119 118
  DEL PEAK 13(6Q22.31) WILD-TYPE 136 103
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 13(6Q22.31) MUTATED    119  118
  DEL PEAK 13(6Q22.31) WILD-TYPE  136  103
        clus
vv       DEL PEAK 13(6Q22.31) MUTATED DEL PEAK 13(6Q22.31) WILD-TYPE
  FEMALE                          119                            136
  MALE                            118                            103
[1] 2 2
[1] FALSE
D42V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 13(6Q22.31) MUTATED                            8
  DEL PEAK 13(6Q22.31) WILD-TYPE                          7
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 13(6Q22.31) MUTATED                                  56
  DEL PEAK 13(6Q22.31) WILD-TYPE                                38
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 13(6Q22.31) MUTATED                                                  145
  DEL PEAK 13(6Q22.31) WILD-TYPE                                                158
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 13(6Q22.31) MUTATED                                            2
  DEL PEAK 13(6Q22.31) WILD-TYPE                                          3
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 13(6Q22.31) MUTATED                                               8
  DEL PEAK 13(6Q22.31) WILD-TYPE                                            11
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 13(6Q22.31) MUTATED                                1
  DEL PEAK 13(6Q22.31) WILD-TYPE                              1
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 13(6Q22.31) MUTATED                                    2
  DEL PEAK 13(6Q22.31) WILD-TYPE                                  2
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 13(6Q22.31) MUTATED                              0
  DEL PEAK 13(6Q22.31) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 13(6Q22.31) MUTATED                              10
  DEL PEAK 13(6Q22.31) WILD-TYPE                             9
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 13(6Q22.31) MUTATED                                 1
  DEL PEAK 13(6Q22.31) WILD-TYPE                               0
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 13(6Q22.31) MUTATED                                               2
  DEL PEAK 13(6Q22.31) WILD-TYPE                                             3
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 13(6Q22.31) MUTATED                              2
  DEL PEAK 13(6Q22.31) WILD-TYPE                            5
D42V9, multiclass
                                                    clus
vv                                                   DEL PEAK 13(6Q22.31) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            56
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          145
  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                                 2
  MUCINOUS (COLLOID) CARCINOMA                                                  2
                                                    clus
vv                                                   DEL PEAK 13(6Q22.31) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              38
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            158
  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                                                   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"
D42V10, binary
                                cls
clus                               0   1
  DEL PEAK 13(6Q22.31) MUTATED    11 226
  DEL PEAK 13(6Q22.31) WILD-TYPE  10 229
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 13(6Q22.31) MUTATED     11  226
  DEL PEAK 13(6Q22.31) WILD-TYPE   10  229
     clus
vv    DEL PEAK 13(6Q22.31) MUTATED DEL PEAK 13(6Q22.31) WILD-TYPE
  NO                            11                             10
  YES                          226                            229
[1] 2 2
[1] FALSE
D42V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 13(6Q22.31) MUTATED   170   5   1  10
  DEL PEAK 13(6Q22.31) WILD-TYPE 157   7   3  11
D42V12, multiclass
    clus
vv   DEL PEAK 13(6Q22.31) MUTATED DEL PEAK 13(6Q22.31) WILD-TYPE
  R0                          170                            157
  R1                            5                              7
  R2                            1                              3
  RX                           10                             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 13(6Q22.31) MUTATED                                  0     4
  DEL PEAK 13(6Q22.31) WILD-TYPE                                1     2
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(6Q22.31) MUTATED                          16   186
  DEL PEAK 13(6Q22.31) WILD-TYPE                        19   181
D42V13, multiclass
                                  clus
vv                                 DEL PEAK 13(6Q22.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  16
  WHITE                                                     186
                                  clus
vv                                 DEL PEAK 13(6Q22.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         2
  BLACK OR AFRICAN AMERICAN                                    19
  WHITE                                                       181
[1] 4 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 13(6Q22.31) MUTATED     6 167
  DEL PEAK 13(6Q22.31) WILD-TYPE   1 178
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 13(6Q22.31) MUTATED      6  167
  DEL PEAK 13(6Q22.31) WILD-TYPE    1  178
                        clus
vv                       DEL PEAK 13(6Q22.31) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          167
                        clus
vv                       DEL PEAK 13(6Q22.31) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                            178
[1] 2 2
[1] FALSE

Clustering(43) Variable = DEL PEAK 14(6Q26) MUTATION ANALYSIS
D43V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 14(6Q26) MUTATED   162  53
  DEL PEAK 14(6Q26) WILD-TYPE 167  34
  DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE 
                        215                         201 
  DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE 
                         53                          34 
$`DEL PEAK 14(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          705 
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          600           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-73-A9RS TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7146 TCGA-78-7149 
         305         1970         1967         1956         1988         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-78-7162 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        1940         1937         1965         1972         1949         1944 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8655 TCGA-80-5607 TCGA-83-5908 
         881         1952          994         1981         1965          824 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7955 
          11          630          422         1968          591          508 
TCGA-86-8054 TCGA-86-8075 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8281 
         745          479          476          482           16         1955 
TCGA-86-8359 TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 TCGA-91-6831 
          26           18           15          405           10          310 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
          35          492           36          218          297          127 
TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 TCGA-95-7948 TCGA-95-8494 TCGA-95-A4VN 
           2          568          377          476           84          553 
TCGA-95-A4VP TCGA-97-7547 TCGA-97-7554 TCGA-97-7937 TCGA-97-8174 TCGA-97-8547 
         605         1965          775          181         1965          148 
TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-8025 TCGA-99-8028 TCGA-99-8033 TCGA-J2-8192 
         197          271          427          459          170          154 
TCGA-J2-8194 TCGA-L4-A4E5 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A7SV 
         114          578          116            6          266          111 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4TC 
        1175           84         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 14(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-49-AARQ TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 
         445          369         6443         2174         2146          785 
TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5944 TCGA-50-6597 
         944          246          282          267          764         1015 
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-55-6986 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-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7907 TCGA-55-7910 
          95           39           34           24           16          197 
TCGA-55-8087 TCGA-55-8096 TCGA-55-8205 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 
         462           47           33           46          674          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-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48Z 
         536           48           49           66          106           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-62-8397 TCGA-62-8399 TCGA-62-A471 TCGA-64-1679 TCGA-64-1681 TCGA-64-5778 
        1289         2696         1246         1686         1968         1305 
TCGA-67-3770 TCGA-67-3772 TCGA-67-3774 TCGA-67-6215 TCGA-67-6217 TCGA-69-7761 
          31          573          385          174          422          186 
TCGA-69-7765 TCGA-69-7980 TCGA-69-8255 TCGA-73-4662 TCGA-73-4668 TCGA-73-4676 
         165          382          129          912          467          164 
TCGA-73-4677 TCGA-75-7031 TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 TCGA-78-7150 
          38         1965         1973         1950         1944         1963 
TCGA-78-7155 TCGA-78-7160 TCGA-78-7161 TCGA-78-7163 TCGA-78-7166 TCGA-78-7539 
        1957          678          215         1950         1934          327 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8660 TCGA-78-8662 TCGA-80-5608 TCGA-86-6851 
        1949         1971         1954         1964         1972         1959 
TCGA-86-7954 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8076 
        1963           10         1963           13           24          489 
TCGA-86-8358 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8673 TCGA-86-A4D0 
          19           35           45           34          455           30 
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-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-8496 TCGA-91-8497 
         417          372          842          224          505          174 
TCGA-91-A4BC TCGA-93-8067 TCGA-95-7039 TCGA-95-7562 TCGA-95-7947 TCGA-95-8039 
          44          186           34         1973          477          830 
TCGA-95-A4VK TCGA-97-7546 TCGA-97-7552 TCGA-97-7553 TCGA-97-7941 TCGA-97-8171 
         121          964         1932         1332           22          107 
TCGA-97-8172 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-99-7458 
         182           87          147           15          115          392 
TCGA-99-8032 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A743 
          44          287          282          238          435          312 
TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
         102          827         1954         1954         1957         1980 
TCGA-MP-A4TA TCGA-MP-A4TH TCGA-S2-AA1A 
        1951          142          121 

  DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE 
                          2                           1 
  DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE 
                       2370                        6443 
  DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE 
                        600                         400 
[1] "2.0 - 2370.0 (600.0)" "1.0 - 6443.0 (400.0)"
[1] "hr=" "1.4"
D43V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 14(6Q26) MUTATED         2       53       64        26        33
  DEL PEAK 14(6Q26) WILD-TYPE       3       63       68        23        37
                             vv
clus                          STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 14(6Q26) MUTATED           39          6       15
  DEL PEAK 14(6Q26) WILD-TYPE         29          5        9
D43V3, multiclass
            clus
vv           DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE
  STAGE I                            2                           3
  STAGE IA                          53                          63
  STAGE IB                          64                          68
  STAGE IIA                         26                          23
  STAGE IIB                         33                          37
  STAGE IIIA                        39                          29
  STAGE IIIB                         6                           5
  STAGE IV                          15                           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 14(6Q26) MUTATED    70 135  23   9
  DEL PEAK 14(6Q26) WILD-TYPE  77 132  19   9
D43V4, multiclass
    clus
vv   DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE
  T1                        70                          77
  T2                       135                         132
  T3                        23                          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 14(6Q26) MUTATED   144  48    41
  DEL PEAK 14(6Q26) WILD-TYPE 157  43    33
D43V5, multiclass
       clus
vv      DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE
  N0                          144                         157
  N1                           48                          43
  N2+N3                        41                          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 14(6Q26) MUTATED   161  13   0   2  60
  DEL PEAK 14(6Q26) WILD-TYPE 165   5   1   2  63
D43V6, multiclass
     clus
vv    DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE
  M0                        161                         165
  M1                         13                           5
  M1A                         0                           1
  M1B                         2                           2
  MX                         60                          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"
D43V7, binary
                             cls
clus                            0   1
  DEL PEAK 14(6Q26) MUTATED   122 117
  DEL PEAK 14(6Q26) WILD-TYPE 133 104
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 14(6Q26) MUTATED    122  117
  DEL PEAK 14(6Q26) WILD-TYPE  133  104
        clus
vv       DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE
  FEMALE                       122                         133
  MALE                         117                         104
[1] 2 2
[1] FALSE
D43V8, continuous
                             vv
clus                          LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 14(6Q26) MUTATED                            8
  DEL PEAK 14(6Q26) WILD-TYPE                          7
                             vv
clus                          LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 14(6Q26) MUTATED                                  55
  DEL PEAK 14(6Q26) WILD-TYPE                                39
                             vv
clus                          LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 14(6Q26) MUTATED                                                  148
  DEL PEAK 14(6Q26) WILD-TYPE                                                155
                             vv
clus                          LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 14(6Q26) MUTATED                                            2
  DEL PEAK 14(6Q26) WILD-TYPE                                          3
                             vv
clus                          LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 14(6Q26) MUTATED                                               6
  DEL PEAK 14(6Q26) WILD-TYPE                                            13
                             vv
clus                          LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 14(6Q26) MUTATED                                1
  DEL PEAK 14(6Q26) WILD-TYPE                              1
                             vv
clus                          LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 14(6Q26) MUTATED                                    2
  DEL PEAK 14(6Q26) WILD-TYPE                                  2
                             vv
clus                          LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 14(6Q26) MUTATED                              0
  DEL PEAK 14(6Q26) WILD-TYPE                            2
                             vv
clus                          LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 14(6Q26) MUTATED                              12
  DEL PEAK 14(6Q26) WILD-TYPE                             7
                             vv
clus                          LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 14(6Q26) MUTATED                                 1
  DEL PEAK 14(6Q26) WILD-TYPE                               0
                             vv
clus                          LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 14(6Q26) MUTATED                                               2
  DEL PEAK 14(6Q26) WILD-TYPE                                             3
                             vv
clus                          MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 14(6Q26) MUTATED                              2
  DEL PEAK 14(6Q26) WILD-TYPE                            5
D43V9, multiclass
                                                    clus
vv                                                   DEL PEAK 14(6Q26) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                 8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                         55
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                       148
  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                              2
  MUCINOUS (COLLOID) CARCINOMA                                               2
                                                    clus
vv                                                   DEL PEAK 14(6Q26) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                   7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           39
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         155
  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                                                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"
D43V10, binary
                             cls
clus                            0   1
  DEL PEAK 14(6Q26) MUTATED    12 227
  DEL PEAK 14(6Q26) WILD-TYPE   9 228
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 14(6Q26) MUTATED     12  227
  DEL PEAK 14(6Q26) WILD-TYPE    9  228
     clus
vv    DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE
  NO                         12                           9
  YES                       227                         228
[1] 2 2
[1] FALSE
D43V11, continuous
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 14(6Q26) MUTATED   172   4   2   9
  DEL PEAK 14(6Q26) WILD-TYPE 155   8   2  12
D43V12, multiclass
    clus
vv   DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE
  R0                       172                         155
  R1                         4                           8
  R2                         2                           2
  RX                         9                          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 14(6Q26) MUTATED                                  0     4
  DEL PEAK 14(6Q26) WILD-TYPE                                1     2
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(6Q26) MUTATED                          17   187
  DEL PEAK 14(6Q26) WILD-TYPE                        18   180
D43V13, multiclass
                                  clus
vv                                 DEL PEAK 14(6Q26) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    4
  BLACK OR AFRICAN AMERICAN                               17
  WHITE                                                  187
                                  clus
vv                                 DEL PEAK 14(6Q26) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 18
  WHITE                                                    180
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V14, binary
                             cls
clus                            0   1
  DEL PEAK 14(6Q26) MUTATED     6 171
  DEL PEAK 14(6Q26) WILD-TYPE   1 174
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 14(6Q26) MUTATED      6  171
  DEL PEAK 14(6Q26) WILD-TYPE    1  174
                        clus
vv                       DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE
  HISPANIC OR LATINO                             6                           1
  NOT HISPANIC OR LATINO                       171                         174
[1] 2 2
[1] FALSE

Clustering(44) Variable = DEL PEAK 15(8P23.2) MUTATION ANALYSIS
D44V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 15(8P23.2) MUTATED   159  44
  DEL PEAK 15(8P23.2) WILD-TYPE 170  43
  DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE 
                          203                           213 
  DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE 
                           44                            43 
$`DEL PEAK 15(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-73-A9RS TCGA-75-6214 
         467          131          621          519          305         1970 
TCGA-75-7025 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7155 TCGA-78-7159 
        1967         1963         1202          760         1957         1221 
TCGA-78-7167 TCGA-78-7536 TCGA-78-7542 TCGA-78-8640 TCGA-78-8660 TCGA-78-8662 
        1937         1949         1952         1949         1954         1964 
TCGA-86-6851 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 
        1959          422          591         1963          745           10 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 TCGA-86-8280 TCGA-86-8585 TCGA-86-8668 
          24          479          482           16           35           45 
TCGA-86-8669 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-91-6836 TCGA-91-6847 
          34           10           30           14          417          842 
TCGA-91-6848 TCGA-91-8499 TCGA-91-A4BD TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 
         224           36          218          186           34            2 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        1973          568          377          477          476          830 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-7546 TCGA-97-7554 TCGA-97-7937 
          84          121          553          964          775          181 
TCGA-97-8547 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8032 TCGA-J2-8192 TCGA-J2-8194 
         148          271          392           44          154          114 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A7SV 
         287          282          578            6          266          111 
TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T4 
         102         1175           84         1946         1967         1954 
TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TF 
        1954         1980         1951         1944         1970 

$`DEL PEAK 15(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-49-AARQ TCGA-50-5051 TCGA-50-5055 TCGA-50-5935 TCGA-50-5942 TCGA-50-5944 
        6443          455          785          653          883          764 
TCGA-50-5946 TCGA-50-8460 TCGA-53-7813 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
         686          105          424            2          993           24 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6983 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 
          25         1475         1826         2151         1170           18 
TCGA-55-7284 TCGA-55-7724 TCGA-55-7725 TCGA-55-7728 TCGA-55-7815 TCGA-55-7907 
         121          705           39           24           54           16 
TCGA-55-7910 TCGA-55-7911 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
         197           21          462          100            6          600 
TCGA-55-8094 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8505 TCGA-55-8507 
           4           46          674          216           29            8 
TCGA-55-8508 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8615 
          15            9            3          146          202           15 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Z TCGA-55-A492 
          49           66          106           33           29            1 
TCGA-55-A494 TCGA-55-A4DF TCGA-62-8398 TCGA-62-8399 TCGA-62-A46V TCGA-62-A471 
           5           47         1970         2696         2199         1246 
TCGA-64-1680 TCGA-64-5774 TCGA-64-5779 TCGA-64-5781 TCGA-67-3773 TCGA-67-3774 
        1126         1959          864         1559          427          385 
TCGA-67-6215 TCGA-67-6216 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
         174          141          186          690          414          165 
TCGA-69-7973 TCGA-69-8253 TCGA-69-8254 TCGA-73-4658 TCGA-73-4659 TCGA-73-4666 
         230          100           77         1600          711          800 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-75-7027 TCGA-75-7031 TCGA-78-7145 
          40          164           38         1956         1965         1973 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7154 TCGA-78-7156 
        1988         1950         1944         1093         1948         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-78-7220 TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7633 
        1965         1972         1944          327          881          994 
TCGA-78-8648 TCGA-78-8655 TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 TCGA-86-7701 
        1971         1981         1965         1972          824           11 
TCGA-86-7711 TCGA-86-7714 TCGA-86-7955 TCGA-86-8056 TCGA-86-8073 TCGA-86-8076 
         630         1968          508         1963           13          489 
TCGA-86-8278 TCGA-86-8281 TCGA-86-8358 TCGA-86-8359 TCGA-86-8671 TCGA-86-8672 
         476         1955           19           26           18           15 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
         455          405           39          323         1940           60 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
         310           79          372           35          492          505 
TCGA-91-8497 TCGA-91-A4BC TCGA-93-7347 TCGA-93-7348 TCGA-95-A4VP TCGA-97-7547 
         174           44          297          127          605         1965 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        1932         1332           22          107          182         1965 
TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M2 TCGA-99-8025 
          87          147           15          115          197          427 
TCGA-99-8028 TCGA-99-8033 TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A743 
         459          170          238          435          116          312 
TCGA-MN-A4N1 TCGA-MP-A4T2 TCGA-MP-A4T8 TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TI 
         827         1951         1957         1970          142         1955 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-S2-AA1A 
        1971         1490          121 

  DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE 
                            2                             1 
  DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE 
                         2370                          6443 
  DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE 
                          486                           457 
[1] "2.0 - 2370.0 (486.0)" "1.0 - 6443.0 (457.0)"
[1] "hr=" "1.2"
D44V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 15(8P23.2) MUTATED         3       55       66        27        39
  DEL PEAK 15(8P23.2) WILD-TYPE       2       61       66        22        31
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 15(8P23.2) MUTATED           32          4       10
  DEL PEAK 15(8P23.2) WILD-TYPE         36          7       14
D44V3, multiclass
            clus
vv           DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE
  STAGE I                              3                             2
  STAGE IA                            55                            61
  STAGE IB                            66                            66
  STAGE IIA                           27                            22
  STAGE IIB                           39                            31
  STAGE IIIA                          32                            36
  STAGE IIIB                           4                             7
  STAGE IV                            10                            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 15(8P23.2) MUTATED    73 136  20   6
  DEL PEAK 15(8P23.2) WILD-TYPE  74 131  22  12
D44V4, multiclass
    clus
vv   DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE
  T1                          73                            74
  T2                         136                           131
  T3                          20                            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 15(8P23.2) MUTATED   150  45    36
  DEL PEAK 15(8P23.2) WILD-TYPE 151  46    38
D44V5, multiclass
       clus
vv      DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE
  N0                            150                           151
  N1                             45                            46
  N2+N3                          36                            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 15(8P23.2) MUTATED   164   9   0   1  60
  DEL PEAK 15(8P23.2) WILD-TYPE 162   9   1   3  63
D44V6, multiclass
     clus
vv    DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE
  M0                          164                           162
  M1                            9                             9
  M1A                           0                             1
  M1B                           1                             3
  MX                           60                            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"
D44V7, binary
                               cls
clus                              0   1
  DEL PEAK 15(8P23.2) MUTATED   135 101
  DEL PEAK 15(8P23.2) WILD-TYPE 120 120
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8P23.2) MUTATED    135  101
  DEL PEAK 15(8P23.2) WILD-TYPE  120  120
        clus
vv       DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE
  FEMALE                         135                           120
  MALE                           101                           120
[1] 2 2
[1] FALSE
D44V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 15(8P23.2) MUTATED                            7
  DEL PEAK 15(8P23.2) WILD-TYPE                          8
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 15(8P23.2) MUTATED                                  41
  DEL PEAK 15(8P23.2) WILD-TYPE                                53
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 15(8P23.2) MUTATED                                                  161
  DEL PEAK 15(8P23.2) WILD-TYPE                                                142
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 15(8P23.2) MUTATED                                            1
  DEL PEAK 15(8P23.2) WILD-TYPE                                          4
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 15(8P23.2) MUTATED                                               8
  DEL PEAK 15(8P23.2) WILD-TYPE                                            11
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 15(8P23.2) MUTATED                                2
  DEL PEAK 15(8P23.2) WILD-TYPE                              0
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 15(8P23.2) MUTATED                                    4
  DEL PEAK 15(8P23.2) WILD-TYPE                                  0
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 15(8P23.2) MUTATED                              0
  DEL PEAK 15(8P23.2) WILD-TYPE                            2
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 15(8P23.2) MUTATED                               7
  DEL PEAK 15(8P23.2) WILD-TYPE                            12
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 15(8P23.2) MUTATED                                 1
  DEL PEAK 15(8P23.2) WILD-TYPE                               0
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 15(8P23.2) MUTATED                                               4
  DEL PEAK 15(8P23.2) WILD-TYPE                                             1
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 15(8P23.2) MUTATED                              0
  DEL PEAK 15(8P23.2) WILD-TYPE                            7
D44V9, multiclass
                                                    clus
vv                                                   DEL PEAK 15(8P23.2) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           41
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         161
  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                                4
  MUCINOUS (COLLOID) CARCINOMA                                                 0
                                                    clus
vv                                                   DEL PEAK 15(8P23.2) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             53
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           142
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 11
  LUNG CLEAR CELL ADENOCARCINOMA                                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             0
  LUNG MUCINOUS ADENOCARCINOMA                                                   2
  LUNG PAPILLARY ADENOCARCINOMA                                                 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"
D44V10, binary
                               cls
clus                              0   1
  DEL PEAK 15(8P23.2) MUTATED    11 225
  DEL PEAK 15(8P23.2) WILD-TYPE  10 230
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8P23.2) MUTATED     11  225
  DEL PEAK 15(8P23.2) WILD-TYPE   10  230
     clus
vv    DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE
  NO                           11                            10
  YES                         225                           230
[1] 2 2
[1] FALSE
D44V11, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 15(8P23.2) MUTATED   155   6   2  14
  DEL PEAK 15(8P23.2) WILD-TYPE 172   6   2   7
D44V12, multiclass
    clus
vv   DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE
  R0                         155                           172
  R1                           6                             6
  R2                           2                             2
  RX                          14                             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 15(8P23.2) MUTATED                                  1     5
  DEL PEAK 15(8P23.2) WILD-TYPE                                0     1
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(8P23.2) MUTATED                          17   182
  DEL PEAK 15(8P23.2) WILD-TYPE                        18   185
D44V13, multiclass
                                  clus
vv                                 DEL PEAK 15(8P23.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      5
  BLACK OR AFRICAN AMERICAN                                 17
  WHITE                                                    182
                                  clus
vv                                 DEL PEAK 15(8P23.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                   18
  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"
D44V14, binary
                               cls
clus                              0   1
  DEL PEAK 15(8P23.2) MUTATED     5 178
  DEL PEAK 15(8P23.2) WILD-TYPE   2 167
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8P23.2) MUTATED      5  178
  DEL PEAK 15(8P23.2) WILD-TYPE    2  167
                        clus
vv                       DEL PEAK 15(8P23.2) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         178
                        clus
vv                       DEL PEAK 15(8P23.2) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           167
[1] 2 2
[1] FALSE

Clustering(45) Variable = DEL PEAK 16(8P11.21) MUTATION ANALYSIS
D45V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 16(8P11.21) MUTATED    82  20
  DEL PEAK 16(8P11.21) WILD-TYPE 247  67
  DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE 
                           102                            314 
  DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE 
                            20                             67 
$`DEL PEAK 16(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-44-7662 TCGA-44-7672 TCGA-44-8120 TCGA-44-A479 
         705         1942          218          719          260          486 
TCGA-44-A4SU TCGA-49-4501 TCGA-49-4505 TCGA-49-4507 TCGA-49-6742 TCGA-49-6743 
          76         1421          428          268          445          369 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-AARQ TCGA-50-5049 TCGA-50-5932 
         890          522          354         6443         2146         1091 
TCGA-50-5933 TCGA-50-6597 TCGA-53-7813 TCGA-55-1595 TCGA-55-1596 TCGA-55-6972 
        2370         1015          424         1479         1375         1475 
TCGA-55-6985 TCGA-55-7283 TCGA-55-7573 TCGA-55-7726 TCGA-55-7994 TCGA-55-8097 
        1233           35            4           39           31           15 
TCGA-55-8302 TCGA-55-8506 TCGA-55-8510 TCGA-55-8615 TCGA-55-A490 TCGA-55-A4DG 
          23           11          228           15           48          162 
TCGA-62-8402 TCGA-62-A46U TCGA-62-A472 TCGA-64-1678 TCGA-64-1679 TCGA-67-3770 
        1445         2067          910         1189         1686           31 
TCGA-67-6217 TCGA-69-7978 TCGA-69-7980 TCGA-69-A59K TCGA-71-6725 TCGA-73-4662 
         422           70          382          214           61          912 
TCGA-73-4668 TCGA-73-4670 TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS TCGA-75-7025 
         467          131          621          519          305         1967 
TCGA-78-7146 TCGA-78-7161 TCGA-78-8640 TCGA-86-7711 TCGA-86-7953 TCGA-86-8054 
        1988          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-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
         492           34         1973          568          377          477 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-97-7546 TCGA-97-8547 TCGA-97-A4M7 
         830           84          121          964          148          271 
TCGA-99-8025 TCGA-J2-8192 TCGA-L4-A4E5 TCGA-L9-A50W TCGA-L9-A8F4 TCGA-MN-A4N4 
         427          154          578          266          102         1175 
TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TC 
        1967         1954         1954         1957         1980         1944 

$`DEL PEAK 16(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-44-7667 
        1864         1978          444          592          366          557 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-8117 TCGA-44-8119 TCGA-44-A47A 
        1970          882          535          385           99          466 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4494 
         287          337          351          415         1932         1081 
TCGA-49-4506 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-50-5045 TCGA-50-5051 
         999          896          157         1700         2174          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-50-5935 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-7109 
         653          567          883          764          686          255 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 
         105         1986         1971          280          701         1178 
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-55-6980 TCGA-55-6983 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7284 
          67         1826         2151         1170           18          121 
TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7727 
           6           95           40          705           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-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
           3            5           33          462          100            6 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8205 TCGA-55-8206 
         600           26            4           47           33           46 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8507 
          66          674          216           44           29            8 
TCGA-55-8508 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
          15            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-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-A46V TCGA-62-A471 
        1216         1289         1970         2696         2199         1246 
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-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
        1305          864         1559          866          610          573 
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-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 
         690          414          165          230          184           89 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-73-4658 TCGA-73-4659 TCGA-73-4666 
         100           77          129         1600          711          800 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-75-6214 TCGA-75-7027 TCGA-75-7031 
          40          164           38         1970         1956         1965 
TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        1973         1950         1944         1093         1963         1202 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
         760         1948         1957         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-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
        1972         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-86-7701 TCGA-86-7713 TCGA-86-7714 
        1972          824         1959           11          422         1968 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 
        1963          508           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-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4D0 
          34           18           15          455          405           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-91-8496 
          79          417          372          224           35          505 
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-95-7043 TCGA-95-7948 TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7547 
         186            2          476          553          605         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-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8194 
         197          392          459           44          170          114 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
         287          282          238          435          116            6 
TCGA-L9-A743 TCGA-L9-A7SV TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4T2 
         312          111          827           84         1946         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 TCGA-S2-AA1A 
        1490          121 

  DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE 
                             4                              1 
  DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE 
                          6443                           2696 
  DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE 
                         481.5                          471.0 
[1] "4.0 - 6443.0 (481.5)" "1.0 - 2696.0 (471.0)"
[1] "hr=" "1.2"
D45V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 16(8P11.21) MUTATED         3       24       28        13        23
  DEL PEAK 16(8P11.21) WILD-TYPE       2       92      104        36        47
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 16(8P11.21) MUTATED           18          3        6
  DEL PEAK 16(8P11.21) WILD-TYPE         50          8       18
D45V3, multiclass
            clus
vv           DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE
  STAGE I                               3                              2
  STAGE IA                             24                             92
  STAGE IB                             28                            104
  STAGE IIA                            13                             36
  STAGE IIB                            23                             47
  STAGE IIIA                           18                             50
  STAGE IIIB                            3                              8
  STAGE IV                              6                             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 16(8P11.21) MUTATED    32  67  16   3
  DEL PEAK 16(8P11.21) WILD-TYPE 115 200  26  15
D45V4, multiclass
    clus
vv   DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE
  T1                           32                            115
  T2                           67                            200
  T3                           16                             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 16(8P11.21) MUTATED    70  25    20
  DEL PEAK 16(8P11.21) WILD-TYPE 231  66    54
D45V5, multiclass
       clus
vv      DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE
  N0                              70                            231
  N1                              25                             66
  N2+N3                           20                             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 16(8P11.21) MUTATED    77   5   0   1  33
  DEL PEAK 16(8P11.21) WILD-TYPE 249  13   1   3  90
D45V6, multiclass
     clus
vv    DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE
  M0                            77                            249
  M1                             5                             13
  M1A                            0                              1
  M1B                            1                              3
  MX                            33                             90
[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 16(8P11.21) MUTATED    73  45
  DEL PEAK 16(8P11.21) WILD-TYPE 182 176
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(8P11.21) MUTATED     73   45
  DEL PEAK 16(8P11.21) WILD-TYPE  182  176
        clus
vv       DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE
  FEMALE                           73                            182
  MALE                             45                            176
[1] 2 2
[1] FALSE
D45V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 16(8P11.21) MUTATED                            3
  DEL PEAK 16(8P11.21) WILD-TYPE                         12
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 16(8P11.21) MUTATED                                  22
  DEL PEAK 16(8P11.21) WILD-TYPE                                72
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 16(8P11.21) MUTATED                                                   78
  DEL PEAK 16(8P11.21) WILD-TYPE                                                225
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 16(8P11.21) MUTATED                                            1
  DEL PEAK 16(8P11.21) WILD-TYPE                                          4
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 16(8P11.21) MUTATED                                               5
  DEL PEAK 16(8P11.21) WILD-TYPE                                            14
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 16(8P11.21) MUTATED                                2
  DEL PEAK 16(8P11.21) WILD-TYPE                              0
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 16(8P11.21) MUTATED                                    3
  DEL PEAK 16(8P11.21) WILD-TYPE                                  1
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 16(8P11.21) MUTATED                              0
  DEL PEAK 16(8P11.21) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 16(8P11.21) MUTATED                               3
  DEL PEAK 16(8P11.21) WILD-TYPE                            16
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 16(8P11.21) MUTATED                                 0
  DEL PEAK 16(8P11.21) WILD-TYPE                               1
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 16(8P11.21) MUTATED                                               0
  DEL PEAK 16(8P11.21) WILD-TYPE                                             5
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 16(8P11.21) MUTATED                              1
  DEL PEAK 16(8P11.21) WILD-TYPE                            6
D45V9, multiclass
                                                    clus
vv                                                   DEL PEAK 16(8P11.21) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            22
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           78
  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                                                  1
                                                    clus
vv                                                   DEL PEAK 16(8P11.21) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              72
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            225
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  14
  LUNG CLEAR CELL ADENOCARCINOMA                                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              1
  LUNG MUCINOUS ADENOCARCINOMA                                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                                  16
  LUNG SIGNET RING ADENOCARCINOMA                                                 1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                   5
  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 16(8P11.21) MUTATED     4 114
  DEL PEAK 16(8P11.21) WILD-TYPE  17 341
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(8P11.21) MUTATED      4  114
  DEL PEAK 16(8P11.21) WILD-TYPE   17  341
     clus
vv    DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE
  NO                             4                             17
  YES                          114                            341
[1] 2 2
[1] FALSE
D45V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 16(8P11.21) MUTATED    73   4   1   9
  DEL PEAK 16(8P11.21) WILD-TYPE 254   8   3  12
D45V12, multiclass
    clus
vv   DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE
  R0                           73                            254
  R1                            4                              8
  R2                            1                              3
  RX                            9                             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 16(8P11.21) MUTATED                                  1     4
  DEL PEAK 16(8P11.21) WILD-TYPE                                0     2
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(8P11.21) MUTATED                          10    90
  DEL PEAK 16(8P11.21) WILD-TYPE                        25   277
D45V13, multiclass
                                  clus
vv                                 DEL PEAK 16(8P11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  10
  WHITE                                                      90
                                  clus
vv                                 DEL PEAK 16(8P11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         2
  BLACK OR AFRICAN AMERICAN                                    25
  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"
D45V14, binary
                                cls
clus                               0   1
  DEL PEAK 16(8P11.21) MUTATED     2  92
  DEL PEAK 16(8P11.21) WILD-TYPE   5 253
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(8P11.21) MUTATED      2   92
  DEL PEAK 16(8P11.21) WILD-TYPE    5  253
                        clus
vv                       DEL PEAK 16(8P11.21) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           92
                        clus
vv                       DEL PEAK 16(8P11.21) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            253
[1] 2 2
[1] FALSE

Clustering(46) Variable = DEL PEAK 17(9P23) MUTATION ANALYSIS
D46V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 17(9P23) MUTATED   173  59
  DEL PEAK 17(9P23) WILD-TYPE 156  28
  DEL PEAK 17(9P23) MUTATED DEL PEAK 17(9P23) WILD-TYPE 
                        232                         184 
  DEL PEAK 17(9P23) MUTATED DEL PEAK 17(9P23) WILD-TYPE 
                         59                          28 
$`DEL PEAK 17(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          705           39           16 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8097 
         100            6          600           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-73-A9RS 
         800          467          131           40          519          305 
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-78-7150 TCGA-78-7156 TCGA-78-7160 TCGA-78-7161 
        1944         1093         1963         1961          678          215 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        1934         1937         1965          881         1952          994 
TCGA-78-8640 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-86-6851 TCGA-86-7711 
        1949         1981         1954         1964         1959          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-86-8279 TCGA-86-8280 TCGA-86-8358 
        1963           24          479          482           16           19 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8672 TCGA-86-A456 TCGA-91-6829 TCGA-91-6830 
          35           45           15           10         1940           60 
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-91-8499 TCGA-93-7348 TCGA-93-8067 TCGA-95-7562 TCGA-95-7567 
         174           36          127          186         1973          568 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VP TCGA-97-7937 TCGA-97-7941 
         830           84          121          605          181           22 
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-L9-A50W TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 
         266          312          111          102          827         1175 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
          84         1946         1967         1954         1957         1980 
TCGA-MP-A4TA TCGA-MP-A4TE TCGA-MP-A4TK TCGA-MP-A5C7 
        1951         1970         1971         1490 

$`DEL PEAK 17(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-49-AARQ 
         999          157          890          522          354         6443 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5066 TCGA-50-5941 TCGA-50-5942 
        2174         2146          455          944          567          883 
TCGA-53-7624 TCGA-55-1595 TCGA-55-6543 TCGA-55-6969 TCGA-55-6972 TCGA-55-6983 
        1986         1479            2         1239         1475         1826 
TCGA-55-6987 TCGA-55-7284 TCGA-55-7574 TCGA-55-7725 TCGA-55-7727 TCGA-55-7728 
        1170          121           95           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-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8096 TCGA-55-8205 TCGA-55-8208 
           5           33          462           47           33          674 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8508 TCGA-55-8511 TCGA-55-8513 
         216           44           23           15            9          146 
TCGA-55-8514 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48Y 
         202           48           49           66          106           42 
TCGA-55-A48Z TCGA-55-A491 TCGA-55-A494 TCGA-55-A4DF TCGA-62-A46U TCGA-64-1676 
          29         1952            5           47         2067         1728 
TCGA-64-1677 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-67-3773 
         628         1959           62         1305          864          427 
TCGA-67-6215 TCGA-69-7765 TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
         174          165          230           70           89          382 
TCGA-69-8253 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4676 
         100          214           61         1600          711          164 
TCGA-73-4677 TCGA-73-7498 TCGA-75-6214 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
          38          621         1970         1202          760         1948 
TCGA-78-7155 TCGA-78-7158 TCGA-78-7159 TCGA-78-7162 TCGA-78-7163 TCGA-78-7535 
        1957         1963         1221         1940         1950         1972 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-8648 TCGA-80-5607 TCGA-80-5608 
        1949         1944          327         1971         1965         1972 
TCGA-83-5908 TCGA-86-7701 TCGA-86-7714 TCGA-86-8073 TCGA-86-8076 TCGA-86-8278 
         824           11         1968           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-91-6831 TCGA-91-7771 
          30           14           39          323          310          492 
TCGA-91-8496 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-95-7039 TCGA-95-7043 
         505           44          218          297           34            2 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VN TCGA-97-7546 TCGA-97-7547 
         377          477          476          553          964         1965 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-8171 TCGA-97-8172 TCGA-97-A4M2 
        1932         1332          775          107          182          197 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-J2-8194 TCGA-J2-A4AE TCGA-L4-A4E5 
         392          427          459          114          282          578 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4TC 
         435          116            6         1951         1954         1944 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-S2-AA1A 
        1970          142         1955          121 

  DEL PEAK 17(9P23) MUTATED DEL PEAK 17(9P23) WILD-TYPE 
                          1                           2 
  DEL PEAK 17(9P23) MUTATED DEL PEAK 17(9P23) WILD-TYPE 
                       2696                        6443 
  DEL PEAK 17(9P23) MUTATED DEL PEAK 17(9P23) WILD-TYPE 
                      535.5                       455.0 
[1] "1.0 - 2696.0 (535.5)" "2.0 - 6443.0 (455.0)"
[1] "hr=" "1.5"
D46V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 17(9P23) MUTATED         2       59       68        31        41
  DEL PEAK 17(9P23) WILD-TYPE       3       57       64        18        29
                             vv
clus                          STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 17(9P23) MUTATED           39          7       14
  DEL PEAK 17(9P23) WILD-TYPE         29          4       10
D46V3, multiclass
            clus
vv           DEL PEAK 17(9P23) MUTATED DEL PEAK 17(9P23) WILD-TYPE
  STAGE I                            2                           3
  STAGE IA                          59                          57
  STAGE IB                          68                          64
  STAGE IIA                         31                          18
  STAGE IIB                         41                          29
  STAGE IIIA                        39                          29
  STAGE IIIB                         7                           4
  STAGE IV                          14                          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 17(9P23) MUTATED    79 149  22  11
  DEL PEAK 17(9P23) WILD-TYPE  68 118  20   7
D46V4, multiclass
    clus
vv   DEL PEAK 17(9P23) MUTATED DEL PEAK 17(9P23) WILD-TYPE
  T1                        79                          68
  T2                       149                         118
  T3                        22                          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 17(9P23) MUTATED   153  63    41
  DEL PEAK 17(9P23) WILD-TYPE 148  28    33
D46V5, multiclass
       clus
vv      DEL PEAK 17(9P23) MUTATED DEL PEAK 17(9P23) WILD-TYPE
  N0                          153                         148
  N1                           63                          28
  N2+N3                        41                          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 17(9P23) MUTATED   181  12   0   2  64
  DEL PEAK 17(9P23) WILD-TYPE 145   6   1   2  59
D46V6, multiclass
     clus
vv    DEL PEAK 17(9P23) MUTATED DEL PEAK 17(9P23) WILD-TYPE
  M0                        181                         145
  M1                         12                           6
  M1A                         0                           1
  M1B                         2                           2
  MX                         64                          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"
D46V7, binary
                             cls
clus                            0   1
  DEL PEAK 17(9P23) MUTATED   133 129
  DEL PEAK 17(9P23) WILD-TYPE 122  92
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 17(9P23) MUTATED    133  129
  DEL PEAK 17(9P23) WILD-TYPE  122   92
        clus
vv       DEL PEAK 17(9P23) MUTATED DEL PEAK 17(9P23) WILD-TYPE
  FEMALE                       133                         122
  MALE                         129                          92
[1] 2 2
[1] FALSE
D46V8, continuous
                             vv
clus                          LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 17(9P23) MUTATED                           10
  DEL PEAK 17(9P23) WILD-TYPE                          5
                             vv
clus                          LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 17(9P23) MUTATED                                  54
  DEL PEAK 17(9P23) WILD-TYPE                                40
                             vv
clus                          LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 17(9P23) MUTATED                                                  167
  DEL PEAK 17(9P23) WILD-TYPE                                                136
                             vv
clus                          LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 17(9P23) MUTATED                                            2
  DEL PEAK 17(9P23) WILD-TYPE                                          3
                             vv
clus                          LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 17(9P23) MUTATED                                              11
  DEL PEAK 17(9P23) WILD-TYPE                                             8
                             vv
clus                          LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 17(9P23) MUTATED                                1
  DEL PEAK 17(9P23) WILD-TYPE                              1
                             vv
clus                          LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 17(9P23) MUTATED                                    4
  DEL PEAK 17(9P23) WILD-TYPE                                  0
                             vv
clus                          LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 17(9P23) MUTATED                              1
  DEL PEAK 17(9P23) WILD-TYPE                            1
                             vv
clus                          LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 17(9P23) MUTATED                               7
  DEL PEAK 17(9P23) WILD-TYPE                            12
                             vv
clus                          LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 17(9P23) MUTATED                                 0
  DEL PEAK 17(9P23) WILD-TYPE                               1
                             vv
clus                          LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 17(9P23) MUTATED                                               3
  DEL PEAK 17(9P23) WILD-TYPE                                             2
                             vv
clus                          MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 17(9P23) MUTATED                              2
  DEL PEAK 17(9P23) WILD-TYPE                            5
D46V9, multiclass
                                                    clus
vv                                                   DEL PEAK 17(9P23) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                         54
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                       167
  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 17(9P23) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                   5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           40
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         136
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                   3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                8
  LUNG CLEAR CELL ADENOCARCINOMA                                               1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                           0
  LUNG MUCINOUS ADENOCARCINOMA                                                 1
  LUNG PAPILLARY ADENOCARCINOMA                                               12
  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"
D46V10, binary
                             cls
clus                            0   1
  DEL PEAK 17(9P23) MUTATED    12 250
  DEL PEAK 17(9P23) WILD-TYPE   9 205
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 17(9P23) MUTATED     12  250
  DEL PEAK 17(9P23) WILD-TYPE    9  205
     clus
vv    DEL PEAK 17(9P23) MUTATED DEL PEAK 17(9P23) WILD-TYPE
  NO                         12                           9
  YES                       250                         205
[1] 2 2
[1] FALSE
D46V11, continuous
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 17(9P23) MUTATED   177   5   2  16
  DEL PEAK 17(9P23) WILD-TYPE 150   7   2   5
D46V12, multiclass
    clus
vv   DEL PEAK 17(9P23) MUTATED DEL PEAK 17(9P23) WILD-TYPE
  R0                       177                         150
  R1                         5                           7
  R2                         2                           2
  RX                        16                           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 17(9P23) MUTATED                                  1     3
  DEL PEAK 17(9P23) WILD-TYPE                                0     3
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(9P23) MUTATED                          18   202
  DEL PEAK 17(9P23) WILD-TYPE                        17   165
D46V13, multiclass
                                  clus
vv                                 DEL PEAK 17(9P23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                    3
  BLACK OR AFRICAN AMERICAN                               18
  WHITE                                                  202
                                  clus
vv                                 DEL PEAK 17(9P23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 17
  WHITE                                                    165
[1] 4 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 17(9P23) MUTATED     4 184
  DEL PEAK 17(9P23) WILD-TYPE   3 161
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 17(9P23) MUTATED      4  184
  DEL PEAK 17(9P23) WILD-TYPE    3  161
                        clus
vv                       DEL PEAK 17(9P23) MUTATED DEL PEAK 17(9P23) WILD-TYPE
  HISPANIC OR LATINO                             4                           3
  NOT HISPANIC OR LATINO                       184                         161
[1] 2 2
[1] FALSE

Clustering(47) Variable = DEL PEAK 18(9P21.3) MUTATION ANALYSIS
D47V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 18(9P21.3) MUTATED   178  60
  DEL PEAK 18(9P21.3) WILD-TYPE 151  27
  DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE 
                          238                           178 
  DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE 
                           60                            27 
$`DEL PEAK 18(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          705           39           16            3 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8097 
         100            6          600           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-73-A9RS TCGA-75-6214 
         467          131           40          519          305         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-78-7150 TCGA-78-7156 TCGA-78-7160 TCGA-78-7161 
        1944         1093         1963         1961          678          215 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        1934         1937         1965          881         1952          994 
TCGA-78-8640 TCGA-78-8655 TCGA-78-8660 TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 
        1949         1981         1954         1959          630          422 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 
        1963          508          745           10         1963           24 
TCGA-86-8075 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8585 TCGA-86-8668 
         479          482           16           19           35           45 
TCGA-86-8672 TCGA-86-A456 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
          15           10         1940           60          310           79 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8497 TCGA-91-8499 
         372          842          224           35          174           36 
TCGA-93-7348 TCGA-93-8067 TCGA-95-7562 TCGA-95-7567 TCGA-95-8039 TCGA-95-8494 
         127          186         1973          568          830           84 
TCGA-95-A4VK TCGA-95-A4VP TCGA-97-7547 TCGA-97-7552 TCGA-97-7937 TCGA-97-8174 
         121          605         1965         1932          181         1965 
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-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L9-A50W 
          44          170          154          287          238          266 
TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
         312          111          102          827         1175           84 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
        1946         1967         1954         1957         1980         1951 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TK TCGA-MP-A5C7 
        1970         1970         1971         1490 

$`DEL PEAK 18(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-49-AARQ TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
         890          354         6443         2174         2146          455 
TCGA-50-5066 TCGA-50-5941 TCGA-50-5942 TCGA-53-A4EZ TCGA-55-1595 TCGA-55-6543 
         944          567          883          280         1479            2 
TCGA-55-6969 TCGA-55-6972 TCGA-55-6983 TCGA-55-7574 TCGA-55-7725 TCGA-55-7727 
        1239         1475         1826           95           39           34 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7994 
          24           54           19          197           21           31 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8096 TCGA-55-8205 TCGA-55-8208 
           5           33          462           47           33          674 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8508 TCGA-55-8511 TCGA-55-8513 
         216           44           23           15            9          146 
TCGA-55-8514 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
         202           15           48           49           66          106 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 TCGA-55-A494 TCGA-55-A4DF TCGA-62-A46U 
          42           29         1952            5           47         2067 
TCGA-64-1677 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-67-3773 
         628         1959           62         1305          864          427 
TCGA-67-6215 TCGA-69-7765 TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 
         174          165          230           70           89          100 
TCGA-69-8254 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4666 
          77          214           61         1600          711          800 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
         164           38          621         1202          760         1948 
TCGA-78-7155 TCGA-78-7158 TCGA-78-7159 TCGA-78-7162 TCGA-78-7163 TCGA-78-7535 
        1957         1963         1221         1940         1950         1972 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-8648 TCGA-78-8662 TCGA-80-5607 
        1949         1944          327         1971         1964         1965 
TCGA-80-5608 TCGA-83-5908 TCGA-86-7701 TCGA-86-7714 TCGA-86-7953 TCGA-86-8073 
        1972          824           11         1968          591           13 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8281 TCGA-86-8359 TCGA-86-8669 TCGA-86-8671 
         489          476         1955           26           34           18 
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-91-6836 TCGA-91-7771 TCGA-91-8496 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
         417          492          505           44          218          297 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VN 
          34            2          377          477          476          553 
TCGA-97-7546 TCGA-97-7553 TCGA-97-7554 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
         964         1332          775           22          107          182 
TCGA-97-A4M2 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-J2-8194 TCGA-J2-A4AE 
         197          392          427          459          114          282 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MP-A4T2 TCGA-MP-A4T4 
         578          435          116            6         1951         1954 
TCGA-MP-A4TC TCGA-MP-A4TH TCGA-MP-A4TI TCGA-S2-AA1A 
        1944          142         1955          121 

  DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE 
                            1                             2 
  DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE 
                         2696                          6443 
  DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE 
                        575.5                         427.0 
[1] "1.0 - 2696.0 (575.5)" "2.0 - 6443.0 (427.0)"
[1] "hr=" "1.2"
D47V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 18(9P21.3) MUTATED         3       59       69        33        45
  DEL PEAK 18(9P21.3) WILD-TYPE       2       57       63        16        25
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 18(9P21.3) MUTATED           41          6       14
  DEL PEAK 18(9P21.3) WILD-TYPE         27          5       10
D47V3, multiclass
            clus
vv           DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE
  STAGE I                              3                             2
  STAGE IA                            59                            57
  STAGE IB                            69                            63
  STAGE IIA                           33                            16
  STAGE IIB                           45                            25
  STAGE IIIA                          41                            27
  STAGE IIIB                           6                             5
  STAGE IV                            14                            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 18(9P21.3) MUTATED    80 156  23  10
  DEL PEAK 18(9P21.3) WILD-TYPE  67 111  19   8
D47V4, multiclass
    clus
vv   DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE
  T1                          80                            67
  T2                         156                           111
  T3                          23                            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 18(9P21.3) MUTATED   158  65    43
  DEL PEAK 18(9P21.3) WILD-TYPE 143  26    31
D47V5, multiclass
       clus
vv      DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE
  N0                            158                           143
  N1                             65                            26
  N2+N3                          43                            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
  DEL PEAK 18(9P21.3) MUTATED   189  12   0   2  65
  DEL PEAK 18(9P21.3) WILD-TYPE 137   6   1   2  58
D47V6, multiclass
     clus
vv    DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE
  M0                          189                           137
  M1                           12                             6
  M1A                           0                             1
  M1B                           2                             2
  MX                           65                            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"
D47V7, binary
                               cls
clus                              0   1
  DEL PEAK 18(9P21.3) MUTATED   132 138
  DEL PEAK 18(9P21.3) WILD-TYPE 123  83
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(9P21.3) MUTATED    132  138
  DEL PEAK 18(9P21.3) WILD-TYPE  123   83
        clus
vv       DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE
  FEMALE                         132                           123
  MALE                           138                            83
[1] 2 2
[1] FALSE
D47V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 18(9P21.3) MUTATED                            8
  DEL PEAK 18(9P21.3) WILD-TYPE                          7
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 18(9P21.3) MUTATED                                  54
  DEL PEAK 18(9P21.3) WILD-TYPE                                40
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 18(9P21.3) MUTATED                                                  174
  DEL PEAK 18(9P21.3) WILD-TYPE                                                129
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 18(9P21.3) MUTATED                                            3
  DEL PEAK 18(9P21.3) WILD-TYPE                                          2
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 18(9P21.3) MUTATED                                              12
  DEL PEAK 18(9P21.3) WILD-TYPE                                             7
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 18(9P21.3) MUTATED                                1
  DEL PEAK 18(9P21.3) WILD-TYPE                              1
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 18(9P21.3) MUTATED                                    4
  DEL PEAK 18(9P21.3) WILD-TYPE                                  0
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 18(9P21.3) MUTATED                              1
  DEL PEAK 18(9P21.3) WILD-TYPE                            1
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 18(9P21.3) MUTATED                               7
  DEL PEAK 18(9P21.3) WILD-TYPE                            12
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 18(9P21.3) MUTATED                                 0
  DEL PEAK 18(9P21.3) WILD-TYPE                               1
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 18(9P21.3) MUTATED                                               4
  DEL PEAK 18(9P21.3) WILD-TYPE                                             1
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 18(9P21.3) MUTATED                              2
  DEL PEAK 18(9P21.3) WILD-TYPE                            5
D47V9, multiclass
                                                    clus
vv                                                   DEL PEAK 18(9P21.3) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           54
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         174
  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 18(9P21.3) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             40
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           129
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  7
  LUNG CLEAR CELL ADENOCARCINOMA                                                 1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             0
  LUNG MUCINOUS ADENOCARCINOMA                                                   1
  LUNG PAPILLARY ADENOCARCINOMA                                                 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"
D47V10, binary
                               cls
clus                              0   1
  DEL PEAK 18(9P21.3) MUTATED    11 259
  DEL PEAK 18(9P21.3) WILD-TYPE  10 196
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(9P21.3) MUTATED     11  259
  DEL PEAK 18(9P21.3) WILD-TYPE   10  196
     clus
vv    DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE
  NO                           11                            10
  YES                         259                           196
[1] 2 2
[1] FALSE
D47V11, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 18(9P21.3) MUTATED   184   5   2  14
  DEL PEAK 18(9P21.3) WILD-TYPE 143   7   2   7
D47V12, multiclass
    clus
vv   DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE
  R0                         184                           143
  R1                           5                             7
  R2                           2                             2
  RX                          14                             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 18(9P21.3) MUTATED                                  1     3
  DEL PEAK 18(9P21.3) WILD-TYPE                                0     3
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(9P21.3) MUTATED                          18   207
  DEL PEAK 18(9P21.3) WILD-TYPE                        17   160
D47V13, multiclass
                                  clus
vv                                 DEL PEAK 18(9P21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 18
  WHITE                                                    207
                                  clus
vv                                 DEL PEAK 18(9P21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        3
  BLACK OR AFRICAN AMERICAN                                   17
  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"
D47V14, binary
                               cls
clus                              0   1
  DEL PEAK 18(9P21.3) MUTATED     4 188
  DEL PEAK 18(9P21.3) WILD-TYPE   3 157
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(9P21.3) MUTATED      4  188
  DEL PEAK 18(9P21.3) WILD-TYPE    3  157
                        clus
vv                       DEL PEAK 18(9P21.3) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         188
                        clus
vv                       DEL PEAK 18(9P21.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           157
[1] 2 2
[1] FALSE

Clustering(48) Variable = DEL PEAK 19(9Q21.11) MUTATION ANALYSIS
D48V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 19(9Q21.11) MUTATED   161  47
  DEL PEAK 19(9Q21.11) WILD-TYPE 168  40
  DEL PEAK 19(9Q21.11) MUTATED DEL PEAK 19(9Q21.11) WILD-TYPE 
                           208                            208 
  DEL PEAK 19(9Q21.11) MUTATED DEL PEAK 19(9Q21.11) WILD-TYPE 
                            47                             40 
$`DEL PEAK 19(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          705           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          600            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-73-A9RS 
         214          711          467          131           40          305 
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-78-7150 TCGA-78-7161 TCGA-78-7167 TCGA-78-7536 TCGA-78-7633 
        1093         1963          215         1937         1949          994 
TCGA-78-8640 TCGA-78-8660 TCGA-80-5608 TCGA-86-7711 TCGA-86-7713 TCGA-86-7954 
        1949         1954         1972          630          422         1963 
TCGA-86-7955 TCGA-86-8055 TCGA-86-8075 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
         508           10          479          482           16           19 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8672 TCGA-86-A456 TCGA-91-6829 
          35           45           34           15           10         1940 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
          60          310           79          372          842          224 
TCGA-91-7771 TCGA-91-8499 TCGA-93-7348 TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 
         492           36          127           34            2          568 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7937 TCGA-97-8174 
         476          830           84          605          181         1965 
TCGA-97-8177 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M7 TCGA-99-8032 TCGA-99-8033 
         147          148          115          271           44          170 
TCGA-J2-8192 TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 
         154          287          238          111          102          827 
TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
        1175         1946         1967         1954         1957         1980 
TCGA-MP-A4TA TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A5C7 
        1951         1970         1970         1490 

$`DEL PEAK 19(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-49-AARQ TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
         522          354         6443         2174         2146          455 
TCGA-50-5066 TCGA-50-5930 TCGA-50-5941 TCGA-50-5942 TCGA-50-5946 TCGA-53-7626 
         944          282          567          883          686         1971 
TCGA-53-A4EZ TCGA-55-1595 TCGA-55-6543 TCGA-55-6969 TCGA-55-6972 TCGA-55-6983 
         280         1479            2         1239         1475         1826 
TCGA-55-6987 TCGA-55-7281 TCGA-55-7284 TCGA-55-7574 TCGA-55-7576 TCGA-55-7725 
        1170           18          121           95           40           39 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7910 TCGA-55-7995 
          34           24           54           19          197            5 
TCGA-55-8087 TCGA-55-8092 TCGA-55-8096 TCGA-55-8205 TCGA-55-8208 TCGA-55-8299 
         462           26           47           33          674          216 
TCGA-55-8302 TCGA-55-8506 TCGA-55-8511 TCGA-55-8513 TCGA-55-8616 TCGA-55-8619 
          23           11            9          146           48           49 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
          66          106           42           29           48         1952 
TCGA-62-8395 TCGA-62-A46U TCGA-62-A471 TCGA-62-A472 TCGA-64-1677 TCGA-64-1680 
        1216         2067         1246          910          628         1126 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 TCGA-67-3773 TCGA-67-6215 
          62         1305         1559          866          427          174 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 
         414          165           70           89          100           77 
TCGA-71-6725 TCGA-73-4658 TCGA-73-4662 TCGA-73-4666 TCGA-73-4676 TCGA-73-4677 
          61         1600          912          800          164           38 
TCGA-73-7498 TCGA-73-7499 TCGA-75-6214 TCGA-75-7031 TCGA-78-7152 TCGA-78-7153 
         621          519         1970         1965         1202          760 
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-78-7220 TCGA-78-7535 TCGA-78-7537 
        1940         1950         1934         1965         1972         1944 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 
         327          881         1952         1971         1981         1964 
TCGA-80-5607 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-7714 TCGA-86-7953 
        1965          824         1959           11         1968          591 
TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8076 TCGA-86-8278 
         745         1963           13           24          489          476 
TCGA-86-8281 TCGA-86-8359 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4D0 
        1955           26           18          455          405           30 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6836 TCGA-91-6849 TCGA-91-8496 
          14           39          323          417           35          505 
TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-8067 TCGA-95-7562 
         174           44          218          297          186         1973 
TCGA-95-7944 TCGA-95-7947 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-7546 TCGA-97-7547 
         377          477          121          553          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-97-8175 TCGA-97-8179 TCGA-97-A4M2 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
          87           15          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-L9-A50W TCGA-L9-A743 TCGA-MN-A4N5 TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4TC 
         266          312           84         1951         1954         1944 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-S2-AA1A 
         142         1955         1971          121 

  DEL PEAK 19(9Q21.11) MUTATED DEL PEAK 19(9Q21.11) WILD-TYPE 
                             1                              2 
  DEL PEAK 19(9Q21.11) MUTATED DEL PEAK 19(9Q21.11) WILD-TYPE 
                          2696                           6443 
  DEL PEAK 19(9Q21.11) MUTATED DEL PEAK 19(9Q21.11) WILD-TYPE 
                         480.5                          464.0 
[1] "1.0 - 2696.0 (480.5)" "2.0 - 6443.0 (464.0)"
[1] "hr=" "1.1"
D48V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 19(9Q21.11) MUTATED         3       57       68        26        35
  DEL PEAK 19(9Q21.11) WILD-TYPE       2       59       64        23        35
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 19(9Q21.11) MUTATED           36          4       10
  DEL PEAK 19(9Q21.11) WILD-TYPE         32          7       14
D48V3, multiclass
            clus
vv           DEL PEAK 19(9Q21.11) MUTATED DEL PEAK 19(9Q21.11) WILD-TYPE
  STAGE I                               3                              2
  STAGE IA                             57                             59
  STAGE IB                             68                             64
  STAGE IIA                            26                             23
  STAGE IIB                            35                             35
  STAGE IIIA                           36                             32
  STAGE IIIB                            4                              7
  STAGE IV                             10                             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 19(9Q21.11) MUTATED    74 137  21   5
  DEL PEAK 19(9Q21.11) WILD-TYPE  73 130  21  13
D48V4, multiclass
    clus
vv   DEL PEAK 19(9Q21.11) MUTATED DEL PEAK 19(9Q21.11) WILD-TYPE
  T1                           74                             73
  T2                          137                            130
  T3                           21                             21
  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 19(9Q21.11) MUTATED   150  48    36
  DEL PEAK 19(9Q21.11) WILD-TYPE 151  43    38
D48V5, multiclass
       clus
vv      DEL PEAK 19(9Q21.11) MUTATED DEL PEAK 19(9Q21.11) WILD-TYPE
  N0                             150                            151
  N1                              48                             43
  N2+N3                           36                             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 19(9Q21.11) MUTATED   161   8   0   2  66
  DEL PEAK 19(9Q21.11) WILD-TYPE 165  10   1   2  57
D48V6, multiclass
     clus
vv    DEL PEAK 19(9Q21.11) MUTATED DEL PEAK 19(9Q21.11) WILD-TYPE
  M0                           161                            165
  M1                             8                             10
  M1A                            0                              1
  M1B                            2                              2
  MX                            66                             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"
D48V7, binary
                                cls
clus                               0   1
  DEL PEAK 19(9Q21.11) MUTATED   125 114
  DEL PEAK 19(9Q21.11) WILD-TYPE 130 107
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(9Q21.11) MUTATED    125  114
  DEL PEAK 19(9Q21.11) WILD-TYPE  130  107
        clus
vv       DEL PEAK 19(9Q21.11) MUTATED DEL PEAK 19(9Q21.11) WILD-TYPE
  FEMALE                          125                            130
  MALE                            114                            107
[1] 2 2
[1] FALSE
D48V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 19(9Q21.11) MUTATED                            8
  DEL PEAK 19(9Q21.11) WILD-TYPE                          7
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 19(9Q21.11) MUTATED                                  38
  DEL PEAK 19(9Q21.11) WILD-TYPE                                56
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 19(9Q21.11) MUTATED                                                  162
  DEL PEAK 19(9Q21.11) WILD-TYPE                                                141
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 19(9Q21.11) MUTATED                                            1
  DEL PEAK 19(9Q21.11) WILD-TYPE                                          4
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 19(9Q21.11) MUTATED                                              10
  DEL PEAK 19(9Q21.11) WILD-TYPE                                             9
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 19(9Q21.11) MUTATED                                1
  DEL PEAK 19(9Q21.11) WILD-TYPE                              1
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 19(9Q21.11) MUTATED                                    4
  DEL PEAK 19(9Q21.11) WILD-TYPE                                  0
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 19(9Q21.11) MUTATED                              0
  DEL PEAK 19(9Q21.11) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 19(9Q21.11) MUTATED                               8
  DEL PEAK 19(9Q21.11) WILD-TYPE                            11
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 19(9Q21.11) MUTATED                                 1
  DEL PEAK 19(9Q21.11) WILD-TYPE                               0
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 19(9Q21.11) MUTATED                                               3
  DEL PEAK 19(9Q21.11) WILD-TYPE                                             2
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 19(9Q21.11) MUTATED                              3
  DEL PEAK 19(9Q21.11) WILD-TYPE                            4
D48V9, multiclass
                                                    clus
vv                                                   DEL PEAK 19(9Q21.11) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            38
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          162
  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 19(9Q21.11) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              56
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            141
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                   9
  LUNG CLEAR CELL ADENOCARCINOMA                                                  1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              0
  LUNG MUCINOUS ADENOCARCINOMA                                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                                  11
  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"
D48V10, binary
                                cls
clus                               0   1
  DEL PEAK 19(9Q21.11) MUTATED     8 231
  DEL PEAK 19(9Q21.11) WILD-TYPE  13 224
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(9Q21.11) MUTATED      8  231
  DEL PEAK 19(9Q21.11) WILD-TYPE   13  224
     clus
vv    DEL PEAK 19(9Q21.11) MUTATED DEL PEAK 19(9Q21.11) WILD-TYPE
  NO                             8                             13
  YES                          231                            224
[1] 2 2
[1] FALSE
D48V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 19(9Q21.11) MUTATED   162   6   2   9
  DEL PEAK 19(9Q21.11) WILD-TYPE 165   6   2  12
D48V12, multiclass
    clus
vv   DEL PEAK 19(9Q21.11) MUTATED DEL PEAK 19(9Q21.11) WILD-TYPE
  R0                          162                            165
  R1                            6                              6
  R2                            2                              2
  RX                            9                             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(9Q21.11) MUTATED                                  1     2
  DEL PEAK 19(9Q21.11) WILD-TYPE                                0     4
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 19(9Q21.11) MUTATED                          17   189
  DEL PEAK 19(9Q21.11) WILD-TYPE                        18   178
D48V13, multiclass
                                  clus
vv                                 DEL PEAK 19(9Q21.11) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  17
  WHITE                                                     189
                                  clus
vv                                 DEL PEAK 19(9Q21.11) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    18
  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 19(9Q21.11) MUTATED     4 176
  DEL PEAK 19(9Q21.11) WILD-TYPE   3 169
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(9Q21.11) MUTATED      4  176
  DEL PEAK 19(9Q21.11) WILD-TYPE    3  169
                        clus
vv                       DEL PEAK 19(9Q21.11) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          176
                        clus
vv                       DEL PEAK 19(9Q21.11) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            169
[1] 2 2
[1] FALSE

Clustering(49) Variable = DEL PEAK 20(10P15.3) MUTATION ANALYSIS
D49V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 20(10P15.3) MUTATED    71  30
  DEL PEAK 20(10P15.3) WILD-TYPE 258  57
  DEL PEAK 20(10P15.3) MUTATED DEL PEAK 20(10P15.3) WILD-TYPE 
                           101                            315 
  DEL PEAK 20(10P15.3) MUTATED DEL PEAK 20(10P15.3) WILD-TYPE 
                            30                             57 
$`DEL PEAK 20(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-49-AARQ TCGA-50-5931 TCGA-50-6597 TCGA-53-7624 TCGA-53-7626 
         445         6443          267         1015         1986         1971 
TCGA-55-6642 TCGA-55-6980 TCGA-55-6986 TCGA-55-7281 TCGA-55-7283 TCGA-55-7726 
         993           67         2151           18           35           39 
TCGA-55-7994 TCGA-55-8091 TCGA-55-8094 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
          31          600            4           29           11            8 
TCGA-55-8514 TCGA-55-8614 TCGA-55-A48X TCGA-55-A490 TCGA-55-A4DF TCGA-62-8402 
         202          536           33           48           47         1445 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5779 TCGA-67-3771 
        1686         1968         1959           62          864          610 
TCGA-67-3772 TCGA-69-7973 TCGA-69-7974 TCGA-69-A59K TCGA-73-4659 TCGA-73-4666 
         573          230          184          214          711          800 
TCGA-73-4675 TCGA-78-7150 TCGA-78-7155 TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 
          40         1963         1957         1937         1965         1949 
TCGA-78-7540 TCGA-78-8640 TCGA-78-8655 TCGA-83-5908 TCGA-86-6851 TCGA-86-7954 
         881         1949         1981          824         1959         1963 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8074 TCGA-86-8075 TCGA-86-8278 TCGA-86-8280 
         745           10           24          479          476           16 
TCGA-86-8359 TCGA-86-8669 TCGA-91-6828 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 
          26           34          323          310           79          372 
TCGA-91-6848 TCGA-93-7348 TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 
         224          127            2         1973          477          476 
TCGA-95-8494 TCGA-97-7546 TCGA-97-8547 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-A4AD 
          84          964          148          271          154          287 
TCGA-J2-A4AG TCGA-MP-A4T2 TCGA-MP-A4T9 TCGA-MP-A4TK TCGA-MP-A5C7 
         238         1951         1980         1971         1490 

$`DEL PEAK 20(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          705           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          462          100            6           26           47 
TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
          15           33           46           66          674          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-55-8615 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-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
          42           29         1952            1           28            5 
TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-A46U 
         162         1216         1289         1970         2696         2067 
TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 
        2199         1246          910         1728          628         1189 
TCGA-64-1680 TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3773 
        1126         1305         1559          866           31          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-69-7978 TCGA-69-7979 TCGA-69-7980 
         690          414          165           70           89          382 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-71-6725 TCGA-73-4658 TCGA-73-4662 
         100           77          129           61         1600          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-73-A9RS TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 TCGA-78-7145 
         305         1970         1967         1956         1965         1973 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 
        1988         1950         1944         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-78-7535 TCGA-78-7537 TCGA-78-7539 
        1940         1950         1934         1972         1944          327 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 
        1952          994         1971         1954         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-86-7955 TCGA-86-8056 TCGA-86-8073 TCGA-86-8076 TCGA-86-8279 TCGA-86-8281 
         508         1963           13          489          482         1955 
TCGA-86-8358 TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
          19           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-91-6830 TCGA-91-6836 TCGA-91-6847 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
          60          417          842           35          492          505 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-8067 
         174           36           44          218          297          186 
TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-A4VK TCGA-95-A4VN 
          34          568          377          830          121          553 
TCGA-95-A4VP TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
         605         1965         1932         1332          775          181 
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-99-7458 TCGA-99-8025 TCGA-99-8028 
          15          115          197          392          427          459 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8194 TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 
          44          170          114          282          578          435 
TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 
         116            6          266          312          111          102 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T4 
         827         1175           84         1946         1967         1954 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TF 
        1954         1957         1951         1944         1970         1970 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-S2-AA1A 
         142         1955          121 

  DEL PEAK 20(10P15.3) MUTATED DEL PEAK 20(10P15.3) WILD-TYPE 
                             2                              1 
  DEL PEAK 20(10P15.3) MUTATED DEL PEAK 20(10P15.3) WILD-TYPE 
                          6443                           2696 
  DEL PEAK 20(10P15.3) MUTATED DEL PEAK 20(10P15.3) WILD-TYPE 
                           477                            466 
[1] "2.0 - 6443.0 (477.0)" "1.0 - 2696.0 (466.0)"
[1] "hr=" "1.2"
D49V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 20(10P15.3) MUTATED         1       27       28        15        15
  DEL PEAK 20(10P15.3) WILD-TYPE       4       89      104        34        55
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 20(10P15.3) MUTATED           24          1        6
  DEL PEAK 20(10P15.3) WILD-TYPE         44         10       18
D49V3, multiclass
            clus
vv           DEL PEAK 20(10P15.3) MUTATED DEL PEAK 20(10P15.3) WILD-TYPE
  STAGE I                               1                              4
  STAGE IA                             27                             89
  STAGE IB                             28                            104
  STAGE IIA                            15                             34
  STAGE IIB                            15                             55
  STAGE IIIA                           24                             44
  STAGE IIIB                            1                             10
  STAGE IV                              6                             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 20(10P15.3) MUTATED    40  64  10   2
  DEL PEAK 20(10P15.3) WILD-TYPE 107 203  32  16
D49V4, multiclass
    clus
vv   DEL PEAK 20(10P15.3) MUTATED DEL PEAK 20(10P15.3) WILD-TYPE
  T1                           40                            107
  T2                           64                            203
  T3                           10                             32
  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 20(10P15.3) MUTATED    67  25    23
  DEL PEAK 20(10P15.3) WILD-TYPE 234  66    51
D49V5, multiclass
       clus
vv      DEL PEAK 20(10P15.3) MUTATED DEL PEAK 20(10P15.3) WILD-TYPE
  N0                              67                            234
  N1                              25                             66
  N2+N3                           23                             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 20(10P15.3) MUTATED    75   5   0   1  34
  DEL PEAK 20(10P15.3) WILD-TYPE 251  13   1   3  89
D49V6, multiclass
     clus
vv    DEL PEAK 20(10P15.3) MUTATED DEL PEAK 20(10P15.3) WILD-TYPE
  M0                            75                            251
  M1                             5                             13
  M1A                            0                              1
  M1B                            1                              3
  MX                            34                             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"
D49V7, binary
                                cls
clus                               0   1
  DEL PEAK 20(10P15.3) MUTATED    77  40
  DEL PEAK 20(10P15.3) WILD-TYPE 178 181
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(10P15.3) MUTATED     77   40
  DEL PEAK 20(10P15.3) WILD-TYPE  178  181
        clus
vv       DEL PEAK 20(10P15.3) MUTATED DEL PEAK 20(10P15.3) WILD-TYPE
  FEMALE                           77                            178
  MALE                             40                            181
[1] 2 2
[1] FALSE
D49V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 20(10P15.3) MUTATED                            3
  DEL PEAK 20(10P15.3) WILD-TYPE                         12
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 20(10P15.3) MUTATED                                  16
  DEL PEAK 20(10P15.3) WILD-TYPE                                78
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 20(10P15.3) MUTATED                                                   86
  DEL PEAK 20(10P15.3) WILD-TYPE                                                217
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 20(10P15.3) MUTATED                                            1
  DEL PEAK 20(10P15.3) WILD-TYPE                                          4
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 20(10P15.3) MUTATED                                               5
  DEL PEAK 20(10P15.3) WILD-TYPE                                            14
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 20(10P15.3) MUTATED                                0
  DEL PEAK 20(10P15.3) WILD-TYPE                              2
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 20(10P15.3) MUTATED                                    2
  DEL PEAK 20(10P15.3) WILD-TYPE                                  2
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 20(10P15.3) MUTATED                              0
  DEL PEAK 20(10P15.3) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 20(10P15.3) MUTATED                               2
  DEL PEAK 20(10P15.3) WILD-TYPE                            17
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 20(10P15.3) MUTATED                                 1
  DEL PEAK 20(10P15.3) WILD-TYPE                               0
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 20(10P15.3) MUTATED                                               0
  DEL PEAK 20(10P15.3) WILD-TYPE                                             5
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 20(10P15.3) MUTATED                              1
  DEL PEAK 20(10P15.3) WILD-TYPE                            6
D49V9, multiclass
                                                    clus
vv                                                   DEL PEAK 20(10P15.3) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            16
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           86
  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 20(10P15.3) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              78
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            217
  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                                                  17
  LUNG SIGNET RING ADENOCARCINOMA                                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                   5
  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"
D49V10, binary
                                cls
clus                               0   1
  DEL PEAK 20(10P15.3) MUTATED     5 112
  DEL PEAK 20(10P15.3) WILD-TYPE  16 343
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(10P15.3) MUTATED      5  112
  DEL PEAK 20(10P15.3) WILD-TYPE   16  343
     clus
vv    DEL PEAK 20(10P15.3) MUTATED DEL PEAK 20(10P15.3) WILD-TYPE
  NO                             5                             16
  YES                          112                            343
[1] 2 2
[1] FALSE
D49V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 20(10P15.3) MUTATED    84   3   1   5
  DEL PEAK 20(10P15.3) WILD-TYPE 243   9   3  16
D49V12, multiclass
    clus
vv   DEL PEAK 20(10P15.3) MUTATED DEL PEAK 20(10P15.3) WILD-TYPE
  R0                           84                            243
  R1                            3                              9
  R2                            1                              3
  RX                            5                             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(10P15.3) MUTATED                                  0     0
  DEL PEAK 20(10P15.3) WILD-TYPE                                1     6
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(10P15.3) MUTATED                           8    98
  DEL PEAK 20(10P15.3) WILD-TYPE                        27   269
D49V13, multiclass
                                  clus
vv                                 DEL PEAK 20(10P15.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   8
  WHITE                                                      98
                                  clus
vv                                 DEL PEAK 20(10P15.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         6
  BLACK OR AFRICAN AMERICAN                                    27
  WHITE                                                       269
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V14, binary
                                cls
clus                               0   1
  DEL PEAK 20(10P15.3) MUTATED     3  90
  DEL PEAK 20(10P15.3) WILD-TYPE   4 255
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(10P15.3) MUTATED      3   90
  DEL PEAK 20(10P15.3) WILD-TYPE    4  255
                        clus
vv                       DEL PEAK 20(10P15.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           90
                        clus
vv                       DEL PEAK 20(10P15.3) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            255
[1] 2 2
[1] FALSE

Clustering(50) Variable = DEL PEAK 21(10Q26.3) MUTATION ANALYSIS
D50V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 21(10Q26.3) MUTATED    93  27
  DEL PEAK 21(10Q26.3) WILD-TYPE 236  60
  DEL PEAK 21(10Q26.3) MUTATED DEL PEAK 21(10Q26.3) WILD-TYPE 
                           120                            296 
  DEL PEAK 21(10Q26.3) MUTATED DEL PEAK 21(10Q26.3) WILD-TYPE 
                            27                             60 
$`DEL PEAK 21(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-49-AARQ TCGA-50-5049 TCGA-50-5931 TCGA-50-5941 
         428          445         6443         2146          267          567 
TCGA-50-5944 TCGA-50-6597 TCGA-50-7109 TCGA-55-1592 TCGA-55-5899 TCGA-55-6971 
         764         1015          255          701           87           25 
TCGA-55-6980 TCGA-55-6986 TCGA-55-7281 TCGA-55-7994 TCGA-55-8091 TCGA-55-8092 
          67         2151           18           31          600           26 
TCGA-55-8094 TCGA-55-8206 TCGA-55-8207 TCGA-55-8505 TCGA-55-8508 TCGA-55-8514 
           4           46           66           29           15          202 
TCGA-55-8614 TCGA-55-A48X TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8402 TCGA-62-A46U 
         536           33           47          162         1445         2067 
TCGA-64-1676 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 TCGA-67-3770 
        1728         1686         1968         1959         1305           31 
TCGA-67-3772 TCGA-69-7978 TCGA-69-7979 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
         573           70           89          129          214           61 
TCGA-73-4666 TCGA-73-4668 TCGA-73-A9RS TCGA-75-7031 TCGA-78-7147 TCGA-78-7154 
         800          467          305         1965         1950         1948 
TCGA-78-7155 TCGA-78-7220 TCGA-78-7535 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 
        1957         1965         1972          881         1952         1949 
TCGA-78-8655 TCGA-78-8660 TCGA-83-5908 TCGA-86-6851 TCGA-86-7954 TCGA-86-7955 
        1981         1954          824         1959         1963          508 
TCGA-86-8055 TCGA-86-8074 TCGA-86-8075 TCGA-86-8278 TCGA-86-8280 TCGA-86-8358 
          10           24          479          476           16           19 
TCGA-86-8359 TCGA-86-8669 TCGA-91-6828 TCGA-91-6829 TCGA-91-6835 TCGA-91-6836 
          26           34          323         1940           79          417 
TCGA-91-6840 TCGA-91-6848 TCGA-91-8499 TCGA-93-7348 TCGA-95-7043 TCGA-95-7562 
         372          224           36          127            2         1973 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-97-7546 TCGA-97-7554 TCGA-97-8175 
         377          477          476          964          775           87 
TCGA-97-8547 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L9-A443 
         148          271          154          287          238          116 
TCGA-MN-A4N5 TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T9 TCGA-MP-A4TF TCGA-MP-A4TK 
          84         1951         1954         1980         1970         1971 

$`DEL PEAK 21(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          705           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          462          100 
TCGA-55-8090 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8208 TCGA-55-8299 
           6           47           15           33          674          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-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
           3          146           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-62-8399 
          28            5         1216         1289         1970         2696 
TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 TCGA-64-1677 TCGA-64-1678 TCGA-64-1680 
        2199         1246          910          628         1189         1126 
TCGA-64-5775 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3773 
          62          864         1559          866          610          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-69-7980 
         690          414          165          230          184          382 
TCGA-69-8253 TCGA-69-8254 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4670 
         100           77         1600          711          912          131 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-75-6214 
          40          164           38          621          519         1970 
TCGA-75-7025 TCGA-75-7027 TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 
        1967         1956         1973         1988         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-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
         678          215         1940         1950         1934         1937 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7633 TCGA-78-8648 TCGA-78-8662 
        1949         1944          327          994         1971         1964 
TCGA-80-5607 TCGA-80-5608 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
        1965         1972           11          630          422         1968 
TCGA-86-7953 TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 TCGA-86-8076 TCGA-86-8279 
         591          745         1963           13          489          482 
TCGA-86-8281 TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1955           35           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-91-6831 TCGA-91-6847 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
         310          842           35          492          505          174 
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-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7547 
         830           84          121          553          605         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-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M2 TCGA-99-7458 
        1965          147           15          115          197          392 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8194 TCGA-J2-A4AE 
         427          459           44          170          114          282 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A743 TCGA-L9-A7SV 
         578          435            6          266          312          111 
TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T7 
         102          827         1175         1946         1967         1954 
TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TI 
        1957         1951         1944         1970          142         1955 
TCGA-MP-A5C7 TCGA-S2-AA1A 
        1490          121 

  DEL PEAK 21(10Q26.3) MUTATED DEL PEAK 21(10Q26.3) WILD-TYPE 
                             2                              1 
  DEL PEAK 21(10Q26.3) MUTATED DEL PEAK 21(10Q26.3) WILD-TYPE 
                          6443                           2696 
  DEL PEAK 21(10Q26.3) MUTATED DEL PEAK 21(10Q26.3) WILD-TYPE 
                         478.0                          460.5 
[1] "2.0 - 6443.0 (478.0)" "1.0 - 2696.0 (460.5)"
[1] "hr=" "1.2"
D50V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 21(10Q26.3) MUTATED         2       39       40        13        22
  DEL PEAK 21(10Q26.3) WILD-TYPE       3       77       92        36        48
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 21(10Q26.3) MUTATED           17          2        5
  DEL PEAK 21(10Q26.3) WILD-TYPE         51          9       19
D50V3, multiclass
            clus
vv           DEL PEAK 21(10Q26.3) MUTATED DEL PEAK 21(10Q26.3) WILD-TYPE
  STAGE I                               2                              3
  STAGE IA                             39                             77
  STAGE IB                             40                             92
  STAGE IIA                            13                             36
  STAGE IIB                            22                             48
  STAGE IIIA                           17                             51
  STAGE IIIB                            2                              9
  STAGE IV                              5                             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 21(10Q26.3) MUTATED    48  79  10   2
  DEL PEAK 21(10Q26.3) WILD-TYPE  99 188  32  16
D50V4, multiclass
    clus
vv   DEL PEAK 21(10Q26.3) MUTATED DEL PEAK 21(10Q26.3) WILD-TYPE
  T1                           48                             99
  T2                           79                            188
  T3                           10                             32
  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 21(10Q26.3) MUTATED    90  28    20
  DEL PEAK 21(10Q26.3) WILD-TYPE 211  63    54
D50V5, multiclass
       clus
vv      DEL PEAK 21(10Q26.3) MUTATED DEL PEAK 21(10Q26.3) WILD-TYPE
  N0                              90                            211
  N1                              28                             63
  N2+N3                           20                             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 21(10Q26.3) MUTATED   100   4   0   1  35
  DEL PEAK 21(10Q26.3) WILD-TYPE 226  14   1   3  88
D50V6, multiclass
     clus
vv    DEL PEAK 21(10Q26.3) MUTATED DEL PEAK 21(10Q26.3) WILD-TYPE
  M0                           100                            226
  M1                             4                             14
  M1A                            0                              1
  M1B                            1                              3
  MX                            35                             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"
D50V7, binary
                                cls
clus                               0   1
  DEL PEAK 21(10Q26.3) MUTATED    81  59
  DEL PEAK 21(10Q26.3) WILD-TYPE 174 162
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(10Q26.3) MUTATED     81   59
  DEL PEAK 21(10Q26.3) WILD-TYPE  174  162
        clus
vv       DEL PEAK 21(10Q26.3) MUTATED DEL PEAK 21(10Q26.3) WILD-TYPE
  FEMALE                           81                            174
  MALE                             59                            162
[1] 2 2
[1] FALSE
D50V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 21(10Q26.3) MUTATED                            4
  DEL PEAK 21(10Q26.3) WILD-TYPE                         11
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 21(10Q26.3) MUTATED                                  24
  DEL PEAK 21(10Q26.3) WILD-TYPE                                70
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 21(10Q26.3) MUTATED                                                   95
  DEL PEAK 21(10Q26.3) WILD-TYPE                                                208
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 21(10Q26.3) MUTATED                                            1
  DEL PEAK 21(10Q26.3) WILD-TYPE                                          4
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 21(10Q26.3) MUTATED                                               6
  DEL PEAK 21(10Q26.3) WILD-TYPE                                            13
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 21(10Q26.3) MUTATED                                0
  DEL PEAK 21(10Q26.3) WILD-TYPE                              2
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 21(10Q26.3) MUTATED                                    3
  DEL PEAK 21(10Q26.3) WILD-TYPE                                  1
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 21(10Q26.3) MUTATED                              0
  DEL PEAK 21(10Q26.3) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 21(10Q26.3) MUTATED                               2
  DEL PEAK 21(10Q26.3) WILD-TYPE                            17
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 21(10Q26.3) MUTATED                                 1
  DEL PEAK 21(10Q26.3) WILD-TYPE                               0
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 21(10Q26.3) MUTATED                                               2
  DEL PEAK 21(10Q26.3) WILD-TYPE                                             3
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 21(10Q26.3) MUTATED                              2
  DEL PEAK 21(10Q26.3) WILD-TYPE                            5
D50V9, multiclass
                                                    clus
vv                                                   DEL PEAK 21(10Q26.3) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            24
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           95
  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 21(10Q26.3) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              70
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            208
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  13
  LUNG CLEAR CELL ADENOCARCINOMA                                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              1
  LUNG MUCINOUS ADENOCARCINOMA                                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                                  17
  LUNG SIGNET RING ADENOCARCINOMA                                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                   3
  MUCINOUS (COLLOID) CARCINOMA                                                    5
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V10, binary
                                cls
clus                               0   1
  DEL PEAK 21(10Q26.3) MUTATED     3 137
  DEL PEAK 21(10Q26.3) WILD-TYPE  18 318
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(10Q26.3) MUTATED      3  137
  DEL PEAK 21(10Q26.3) WILD-TYPE   18  318
     clus
vv    DEL PEAK 21(10Q26.3) MUTATED DEL PEAK 21(10Q26.3) WILD-TYPE
  NO                             3                             18
  YES                          137                            318
[1] 2 2
[1] FALSE
D50V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 21(10Q26.3) MUTATED   106   1   1   8
  DEL PEAK 21(10Q26.3) WILD-TYPE 221  11   3  13
D50V12, multiclass
    clus
vv   DEL PEAK 21(10Q26.3) MUTATED DEL PEAK 21(10Q26.3) WILD-TYPE
  R0                          106                            221
  R1                            1                             11
  R2                            1                              3
  RX                            8                             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 21(10Q26.3) MUTATED                                  1     1
  DEL PEAK 21(10Q26.3) WILD-TYPE                                0     5
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(10Q26.3) MUTATED                           7   108
  DEL PEAK 21(10Q26.3) WILD-TYPE                        28   259
D50V13, multiclass
                                  clus
vv                                 DEL PEAK 21(10Q26.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   7
  WHITE                                                     108
                                  clus
vv                                 DEL PEAK 21(10Q26.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         5
  BLACK OR AFRICAN AMERICAN                                    28
  WHITE                                                       259
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V14, binary
                                cls
clus                               0   1
  DEL PEAK 21(10Q26.3) MUTATED     3  97
  DEL PEAK 21(10Q26.3) WILD-TYPE   4 248
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(10Q26.3) MUTATED      3   97
  DEL PEAK 21(10Q26.3) WILD-TYPE    4  248
                        clus
vv                       DEL PEAK 21(10Q26.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           97
                        clus
vv                       DEL PEAK 21(10Q26.3) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            248
[1] 2 2
[1] FALSE

Clustering(51) Variable = DEL PEAK 22(11P15.5) MUTATION ANALYSIS
D51V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 22(11P15.5) MUTATED    91  28
  DEL PEAK 22(11P15.5) WILD-TYPE 238  59
  DEL PEAK 22(11P15.5) MUTATED DEL PEAK 22(11P15.5) WILD-TYPE 
                           119                            297 
  DEL PEAK 22(11P15.5) MUTATED DEL PEAK 22(11P15.5) WILD-TYPE 
                            28                             59 
$`DEL PEAK 22(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-73-A9RS 
         214          711          131           40          519          305 
TCGA-75-7025 TCGA-78-7145 TCGA-78-7147 TCGA-78-7154 TCGA-78-7160 TCGA-78-7535 
        1967         1973         1950         1948          678         1972 
TCGA-78-8640 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-7955 
        1949           11          630          422          591          508 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8669 TCGA-86-8673 TCGA-91-6836 TCGA-91-6840 
          16           19           34          455          417          372 
TCGA-91-6847 TCGA-95-7039 TCGA-95-7043 TCGA-95-8039 TCGA-95-8494 TCGA-97-7553 
         842           34            2          830           84         1332 
TCGA-97-8174 TCGA-99-8025 TCGA-99-8028 TCGA-99-8033 TCGA-J2-A4AD TCGA-L4-A4E5 
        1965          427          459          170          287          578 
TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4T2 TCGA-MP-A4T4 
         111          102          827         1175         1951         1954 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TK 
        1957         1980         1970         1970         1971 

$`DEL PEAK 22(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-49-AARQ TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
         354         6443         2174         2146          455          785 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5932 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 
         944         1499         1091          653          567          883 
TCGA-50-5944 TCGA-50-6597 TCGA-50-7109 TCGA-53-7813 TCGA-55-1592 TCGA-55-1594 
         764         1015          255          424          701         1178 
TCGA-55-6543 TCGA-55-6712 TCGA-55-6969 TCGA-55-6971 TCGA-55-6980 TCGA-55-6983 
           2           24         1239           25           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-55-7574 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 TCGA-55-7907 
          95          705           39           39           24           16 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 
         197           21            3           33          462            6 
TCGA-55-8091 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 
         600            4           47           15           33           46 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 
          66          674          216           44           29           11 
TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8615 TCGA-55-8616 
          15            3          146          202           15           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-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-62-8395 
        1952            1           28            5           47         1216 
TCGA-62-8402 TCGA-62-A46U TCGA-62-A46V TCGA-64-1678 TCGA-64-1680 TCGA-64-1681 
        1445         2067         2199         1189         1126         1968 
TCGA-64-5775 TCGA-64-5779 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 
          62          864          573          427          385          174 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 
         141          422          202          186          414          165 
TCGA-69-7973 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
         230           70          382          100           77          129 
TCGA-71-6725 TCGA-73-4658 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4676 
          61         1600          912          800          467          164 
TCGA-73-4677 TCGA-73-7498 TCGA-75-6214 TCGA-75-7027 TCGA-75-7031 TCGA-78-7146 
          38          621         1970         1956         1965         1988 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7155 
        1944         1093         1963         1202          760         1957 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        1961         1963         1221          215         1940         1950 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
        1934         1937         1965         1949         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-78-8662 TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 TCGA-86-7714 
        1964         1965         1972          824         1959         1968 
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-86-8281 TCGA-86-8359 
         479          489          476          482         1955           26 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 
          35           45           18           15          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-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
         310           79          224           35          492          505 
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-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
         186         1973          568          377          477          476 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
         121          553          605          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-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 
         147           15          148          115          197          271 
TCGA-99-7458 TCGA-99-8032 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG 
         392           44          154          114          282          238 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A743 TCGA-MN-A4N5 
         435          116            6          266          312           84 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T7 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TH 
        1946         1967         1954         1951         1944          142 
TCGA-MP-A4TI TCGA-MP-A5C7 TCGA-S2-AA1A 
        1955         1490          121 

  DEL PEAK 22(11P15.5) MUTATED DEL PEAK 22(11P15.5) WILD-TYPE 
                             2                              1 
  DEL PEAK 22(11P15.5) MUTATED DEL PEAK 22(11P15.5) WILD-TYPE 
                          2696                           6443 
  DEL PEAK 22(11P15.5) MUTATED DEL PEAK 22(11P15.5) WILD-TYPE 
                           578                            455 
[1] "2.0 - 2696.0 (578.0)" "1.0 - 6443.0 (455.0)"
[1] "hr=" "1"  
D51V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 22(11P15.5) MUTATED         1       28       36        14        24
  DEL PEAK 22(11P15.5) WILD-TYPE       4       88       96        35        46
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 22(11P15.5) MUTATED           21          1        9
  DEL PEAK 22(11P15.5) WILD-TYPE         47         10       15
D51V3, multiclass
            clus
vv           DEL PEAK 22(11P15.5) MUTATED DEL PEAK 22(11P15.5) WILD-TYPE
  STAGE I                               1                              4
  STAGE IA                             28                             88
  STAGE IB                             36                             96
  STAGE IIA                            14                             35
  STAGE IIB                            24                             46
  STAGE IIIA                           21                             47
  STAGE IIIB                            1                             10
  STAGE IV                              9                             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 22(11P15.5) MUTATED    36  76  16   4
  DEL PEAK 22(11P15.5) WILD-TYPE 111 191  26  14
D51V4, multiclass
    clus
vv   DEL PEAK 22(11P15.5) MUTATED DEL PEAK 22(11P15.5) WILD-TYPE
  T1                           36                            111
  T2                           76                            191
  T3                           16                             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
  DEL PEAK 22(11P15.5) MUTATED    84  28    21
  DEL PEAK 22(11P15.5) WILD-TYPE 217  63    53
D51V5, multiclass
       clus
vv      DEL PEAK 22(11P15.5) MUTATED DEL PEAK 22(11P15.5) WILD-TYPE
  N0                              84                            217
  N1                              28                             63
  N2+N3                           21                             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 22(11P15.5) MUTATED    89   9   0   0  35
  DEL PEAK 22(11P15.5) WILD-TYPE 237   9   1   4  88
D51V6, multiclass
     clus
vv    DEL PEAK 22(11P15.5) MUTATED DEL PEAK 22(11P15.5) WILD-TYPE
  M0                            89                            237
  M1                             9                              9
  M1A                            0                              1
  M1B                            0                              4
  MX                            35                             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"
D51V7, binary
                                cls
clus                               0   1
  DEL PEAK 22(11P15.5) MUTATED    58  76
  DEL PEAK 22(11P15.5) WILD-TYPE 197 145
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(11P15.5) MUTATED     58   76
  DEL PEAK 22(11P15.5) WILD-TYPE  197  145
        clus
vv       DEL PEAK 22(11P15.5) MUTATED DEL PEAK 22(11P15.5) WILD-TYPE
  FEMALE                           58                            197
  MALE                             76                            145
[1] 2 2
[1] FALSE
D51V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 22(11P15.5) MUTATED                            3
  DEL PEAK 22(11P15.5) WILD-TYPE                         12
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 22(11P15.5) MUTATED                                  25
  DEL PEAK 22(11P15.5) WILD-TYPE                                69
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 22(11P15.5) MUTATED                                                   94
  DEL PEAK 22(11P15.5) WILD-TYPE                                                209
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 22(11P15.5) MUTATED                                            0
  DEL PEAK 22(11P15.5) WILD-TYPE                                          5
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 22(11P15.5) MUTATED                                               4
  DEL PEAK 22(11P15.5) WILD-TYPE                                            15
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 22(11P15.5) MUTATED                                2
  DEL PEAK 22(11P15.5) WILD-TYPE                              0
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 22(11P15.5) MUTATED                                    0
  DEL PEAK 22(11P15.5) WILD-TYPE                                  4
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 22(11P15.5) MUTATED                              0
  DEL PEAK 22(11P15.5) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 22(11P15.5) MUTATED                               5
  DEL PEAK 22(11P15.5) WILD-TYPE                            14
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 22(11P15.5) MUTATED                                 0
  DEL PEAK 22(11P15.5) WILD-TYPE                               1
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 22(11P15.5) MUTATED                                               0
  DEL PEAK 22(11P15.5) WILD-TYPE                                             5
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 22(11P15.5) MUTATED                              1
  DEL PEAK 22(11P15.5) WILD-TYPE                            6
D51V9, multiclass
                                                    clus
vv                                                   DEL PEAK 22(11P15.5) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            25
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           94
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 4
  LUNG CLEAR CELL ADENOCARCINOMA                                                2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            0
  LUNG MUCINOUS ADENOCARCINOMA                                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                                 5
  LUNG SIGNET RING ADENOCARCINOMA                                               0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 0
  MUCINOUS (COLLOID) CARCINOMA                                                  1
                                                    clus
vv                                                   DEL PEAK 22(11P15.5) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              69
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            209
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      5
  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                                   5
  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"
D51V10, binary
                                cls
clus                               0   1
  DEL PEAK 22(11P15.5) MUTATED     5 129
  DEL PEAK 22(11P15.5) WILD-TYPE  16 326
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(11P15.5) MUTATED      5  129
  DEL PEAK 22(11P15.5) WILD-TYPE   16  326
     clus
vv    DEL PEAK 22(11P15.5) MUTATED DEL PEAK 22(11P15.5) WILD-TYPE
  NO                             5                             16
  YES                          129                            326
[1] 2 2
[1] FALSE
D51V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 22(11P15.5) MUTATED    89   2   1   9
  DEL PEAK 22(11P15.5) WILD-TYPE 238  10   3  12
D51V12, multiclass
    clus
vv   DEL PEAK 22(11P15.5) MUTATED DEL PEAK 22(11P15.5) WILD-TYPE
  R0                           89                            238
  R1                            2                             10
  R2                            1                              3
  RX                            9                             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 22(11P15.5) MUTATED                                  0     2
  DEL PEAK 22(11P15.5) WILD-TYPE                                1     4
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 22(11P15.5) MUTATED                          14   104
  DEL PEAK 22(11P15.5) WILD-TYPE                        21   263
D51V13, multiclass
                                  clus
vv                                 DEL PEAK 22(11P15.5) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  14
  WHITE                                                     104
                                  clus
vv                                 DEL PEAK 22(11P15.5) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    21
  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"
D51V14, binary
                                cls
clus                               0   1
  DEL PEAK 22(11P15.5) MUTATED     3 105
  DEL PEAK 22(11P15.5) WILD-TYPE   4 240
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(11P15.5) MUTATED      3  105
  DEL PEAK 22(11P15.5) WILD-TYPE    4  240
                        clus
vv                       DEL PEAK 22(11P15.5) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          105
                        clus
vv                       DEL PEAK 22(11P15.5) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            240
[1] 2 2
[1] FALSE

Clustering(52) Variable = DEL PEAK 23(11Q23.2) MUTATION ANALYSIS
D52V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 23(11Q23.2) MUTATED    81  19
  DEL PEAK 23(11Q23.2) WILD-TYPE 248  68
  DEL PEAK 23(11Q23.2) MUTATED DEL PEAK 23(11Q23.2) WILD-TYPE 
                           100                            316 
  DEL PEAK 23(11Q23.2) MUTATED DEL PEAK 23(11Q23.2) WILD-TYPE 
                            19                             68 
$`DEL PEAK 23(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-73-A9RS TCGA-75-6214 
         414          912           40          519          305         1970 
TCGA-75-7025 TCGA-78-7145 TCGA-78-7148 TCGA-78-7159 TCGA-78-7160 TCGA-78-7220 
        1967         1973         1944         1221          678         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-95-8039 TCGA-95-8494 
         417           35          186            2          830           84 
TCGA-95-A4VN TCGA-97-8174 TCGA-99-8033 TCGA-L4-A4E5 TCGA-L9-A443 TCGA-MN-A4N1 
         553         1965          170          578          116          827 
TCGA-MN-A4N5 TCGA-MP-A4T2 TCGA-MP-A4TE TCGA-MP-A4TF 
          84         1951         1970         1970 

$`DEL PEAK 23(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-49-AARQ TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
         369          522         6443         2174         2146          455 
TCGA-50-5055 TCGA-50-5068 TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
         785         1499          282         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-53-7624 TCGA-53-7813 TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 
         105         1986          424          701         1178         1375 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6980 TCGA-55-6983 
           2          993           24         1239           67         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-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
           4           95           40          705           39           39 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-8087 
          16          197           21            3           31          462 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 
         100            6          600           26           47           15 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
          33           46           66          674          216           44 
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-55-8616 TCGA-55-8619 
           3          146          202          536           48           49 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 
          66          106           33           42           29         1952 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8398 TCGA-62-8399 
           1           28            5          162         1970         2696 
TCGA-62-8402 TCGA-62-A46V TCGA-62-A471 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
        1445         2199         1246         1728          628         1686 
TCGA-64-1680 TCGA-64-5775 TCGA-64-5779 TCGA-64-5781 TCGA-67-3770 TCGA-67-3771 
        1126           62          864         1559           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-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
         202          186          165          230          184           70 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
          89          382          100           77          129          214 
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-75-7027 TCGA-75-7031 TCGA-78-7146 
         164           38          621         1956         1965         1988 
TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
        1950         1093         1963         1202          760         1948 
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-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
        1934         1937         1972         1949         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-78-8662 TCGA-80-5607 TCGA-83-5908 TCGA-86-6851 TCGA-86-7711 TCGA-86-7714 
        1964         1965          824         1959          630         1968 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 
        1963          508           10         1963           13          479 
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-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 
          35           45           18           15          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-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
         372          842          224          492          505          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-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK 
        1973          568          377          477          476          121 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
         605          964         1965         1932         1332          775 
TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 TCGA-97-8177 
         181           22          107          182           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-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
         427          459           44          154          114          287 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A743 
         282          238          435            6          266          312 
TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T4 
         111          102         1175         1946         1967         1954 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TH 
        1954         1957         1980         1951         1944          142 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-S2-AA1A 
        1955         1971         1490          121 

  DEL PEAK 23(11Q23.2) MUTATED DEL PEAK 23(11Q23.2) WILD-TYPE 
                             2                              1 
  DEL PEAK 23(11Q23.2) MUTATED DEL PEAK 23(11Q23.2) WILD-TYPE 
                          2067                           6443 
  DEL PEAK 23(11Q23.2) MUTATED DEL PEAK 23(11Q23.2) WILD-TYPE 
                         584.5                          457.0 
[1] "2.0 - 2067.0 (584.5)" "1.0 - 6443.0 (457.0)"
[1] "hr=" "1.2"
D52V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 23(11Q23.2) MUTATED         1       27       26        15        18
  DEL PEAK 23(11Q23.2) WILD-TYPE       4       89      106        34        52
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 23(11Q23.2) MUTATED           14          3        7
  DEL PEAK 23(11Q23.2) WILD-TYPE         54          8       17
D52V3, multiclass
            clus
vv           DEL PEAK 23(11Q23.2) MUTATED DEL PEAK 23(11Q23.2) WILD-TYPE
  STAGE I                               1                              4
  STAGE IA                             27                             89
  STAGE IB                             26                            106
  STAGE IIA                            15                             34
  STAGE IIB                            18                             52
  STAGE IIIA                           14                             54
  STAGE IIIB                            3                              8
  STAGE IV                              7                             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 23(11Q23.2) MUTATED    32  62  10   5
  DEL PEAK 23(11Q23.2) WILD-TYPE 115 205  32  13
D52V4, multiclass
    clus
vv   DEL PEAK 23(11Q23.2) MUTATED DEL PEAK 23(11Q23.2) WILD-TYPE
  T1                           32                            115
  T2                           62                            205
  T3                           10                             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
  DEL PEAK 23(11Q23.2) MUTATED    67  25    17
  DEL PEAK 23(11Q23.2) WILD-TYPE 234  66    57
D52V5, multiclass
       clus
vv      DEL PEAK 23(11Q23.2) MUTATED DEL PEAK 23(11Q23.2) WILD-TYPE
  N0                              67                            234
  N1                              25                             66
  N2+N3                           17                             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
  DEL PEAK 23(11Q23.2) MUTATED    82   6   0   1  22
  DEL PEAK 23(11Q23.2) WILD-TYPE 244  12   1   3 101
D52V6, multiclass
     clus
vv    DEL PEAK 23(11Q23.2) MUTATED DEL PEAK 23(11Q23.2) WILD-TYPE
  M0                            82                            244
  M1                             6                             12
  M1A                            0                              1
  M1B                            1                              3
  MX                            22                            101
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V7, binary
                                cls
clus                               0   1
  DEL PEAK 23(11Q23.2) MUTATED    49  62
  DEL PEAK 23(11Q23.2) WILD-TYPE 206 159
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(11Q23.2) MUTATED     49   62
  DEL PEAK 23(11Q23.2) WILD-TYPE  206  159
        clus
vv       DEL PEAK 23(11Q23.2) MUTATED DEL PEAK 23(11Q23.2) WILD-TYPE
  FEMALE                           49                            206
  MALE                             62                            159
[1] 2 2
[1] FALSE
D52V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 23(11Q23.2) MUTATED                            4
  DEL PEAK 23(11Q23.2) WILD-TYPE                         11
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 23(11Q23.2) MUTATED                                  26
  DEL PEAK 23(11Q23.2) WILD-TYPE                                68
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 23(11Q23.2) MUTATED                                                   69
  DEL PEAK 23(11Q23.2) WILD-TYPE                                                234
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 23(11Q23.2) MUTATED                                            0
  DEL PEAK 23(11Q23.2) WILD-TYPE                                          5
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 23(11Q23.2) MUTATED                                               3
  DEL PEAK 23(11Q23.2) WILD-TYPE                                            16
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 23(11Q23.2) MUTATED                                1
  DEL PEAK 23(11Q23.2) WILD-TYPE                              1
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 23(11Q23.2) MUTATED                                    0
  DEL PEAK 23(11Q23.2) WILD-TYPE                                  4
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 23(11Q23.2) MUTATED                              0
  DEL PEAK 23(11Q23.2) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 23(11Q23.2) MUTATED                               5
  DEL PEAK 23(11Q23.2) WILD-TYPE                            14
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 23(11Q23.2) MUTATED                                 0
  DEL PEAK 23(11Q23.2) WILD-TYPE                               1
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 23(11Q23.2) MUTATED                                               1
  DEL PEAK 23(11Q23.2) WILD-TYPE                                             4
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 23(11Q23.2) MUTATED                              2
  DEL PEAK 23(11Q23.2) WILD-TYPE                            5
D52V9, multiclass
                                                    clus
vv                                                   DEL PEAK 23(11Q23.2) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            26
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           69
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 3
  LUNG CLEAR CELL ADENOCARCINOMA                                                1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            0
  LUNG MUCINOUS ADENOCARCINOMA                                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                                 5
  LUNG SIGNET RING ADENOCARCINOMA                                               0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 1
  MUCINOUS (COLLOID) CARCINOMA                                                  2
                                                    clus
vv                                                   DEL PEAK 23(11Q23.2) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              68
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            234
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      5
  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"
D52V10, binary
                                cls
clus                               0   1
  DEL PEAK 23(11Q23.2) MUTATED     3 108
  DEL PEAK 23(11Q23.2) WILD-TYPE  18 347
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(11Q23.2) MUTATED      3  108
  DEL PEAK 23(11Q23.2) WILD-TYPE   18  347
     clus
vv    DEL PEAK 23(11Q23.2) MUTATED DEL PEAK 23(11Q23.2) WILD-TYPE
  NO                             3                             18
  YES                          108                            347
[1] 2 2
[1] FALSE
D52V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 23(11Q23.2) MUTATED    84   2   0   7
  DEL PEAK 23(11Q23.2) WILD-TYPE 243  10   4  14
D52V12, multiclass
    clus
vv   DEL PEAK 23(11Q23.2) MUTATED DEL PEAK 23(11Q23.2) WILD-TYPE
  R0                           84                            243
  R1                            2                             10
  R2                            0                              4
  RX                            7                             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 23(11Q23.2) MUTATED                                  0     2
  DEL PEAK 23(11Q23.2) WILD-TYPE                                1     4
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 23(11Q23.2) MUTATED                           8    83
  DEL PEAK 23(11Q23.2) WILD-TYPE                        27   284
D52V13, multiclass
                                  clus
vv                                 DEL PEAK 23(11Q23.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   8
  WHITE                                                      83
                                  clus
vv                                 DEL PEAK 23(11Q23.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    27
  WHITE                                                       284
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V14, binary
                                cls
clus                               0   1
  DEL PEAK 23(11Q23.2) MUTATED     1  82
  DEL PEAK 23(11Q23.2) WILD-TYPE   6 263
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(11Q23.2) MUTATED      1   82
  DEL PEAK 23(11Q23.2) WILD-TYPE    6  263
                        clus
vv                       DEL PEAK 23(11Q23.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           82
                        clus
vv                       DEL PEAK 23(11Q23.2) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            263
[1] 2 2
[1] FALSE

Clustering(53) Variable = DEL PEAK 24(11Q25) MUTATION ANALYSIS
D53V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 24(11Q25) MUTATED    71  23
  DEL PEAK 24(11Q25) WILD-TYPE 258  64
  DEL PEAK 24(11Q25) MUTATED DEL PEAK 24(11Q25) WILD-TYPE 
                          94                          322 
  DEL PEAK 24(11Q25) MUTATED DEL PEAK 24(11Q25) WILD-TYPE 
                          23                           64 
$`DEL PEAK 24(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-62-8395 TCGA-62-8397 TCGA-62-A46U TCGA-62-A472 
          23           15         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-78-7154 TCGA-78-7159 TCGA-78-7160 TCGA-78-7220 
        1973         1944         1948         1221          678         1965 
TCGA-78-7539 TCGA-78-7542 TCGA-78-8640 TCGA-78-8662 TCGA-86-7701 TCGA-86-7713 
         327         1952         1949         1964           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-95-8039 TCGA-95-8494 TCGA-95-A4VN TCGA-97-8174 
         186            2          830           84          553         1965 
TCGA-L4-A4E5 TCGA-L9-A443 TCGA-L9-A7SV TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4T2 
         578          116          111          827           84         1951 
TCGA-MP-A4T8 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TI 
        1957         1970         1970         1955 

$`DEL PEAK 24(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-49-AARQ TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5068 
        6443         2174         2146          455          785         1499 
TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 
         282         1091         2370          653          567          883 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 TCGA-53-7624 
         764          686         1015          255          105         1986 
TCGA-53-7813 TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 TCGA-55-6543 TCGA-55-6642 
         424          701         1178         1375            2          993 
TCGA-55-6712 TCGA-55-6969 TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 
          24         1239           67         1826         1233         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-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
         705           39           39           16          197           21 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
           3           31            5          462          100            6 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 
         600           26           47           15           33           46 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 
          66          674          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-A490 TCGA-55-A491 TCGA-55-A492 
          33           42           29           48         1952            1 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8398 TCGA-62-8399 
          28            5           47          162         1970         2696 
TCGA-62-8402 TCGA-62-A46V TCGA-62-A471 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
        1445         2199         1246         1728          628         1686 
TCGA-64-1680 TCGA-64-5775 TCGA-64-5779 TCGA-64-5781 TCGA-67-3770 TCGA-67-3771 
        1126           62          864         1559           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-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
         202          186          165          230          184           70 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
          89          382          100           77          129          214 
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-A9RS TCGA-75-7027 TCGA-75-7031 
         164           38          621          305         1956         1965 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
        1988         1950         1093         1963         1202          760 
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-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 
        1934         1937         1972         1949         1944          881 
TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-80-5607 TCGA-80-5608 
         994         1971         1981         1954         1965         1972 
TCGA-83-5908 TCGA-86-6851 TCGA-86-7711 TCGA-86-7714 TCGA-86-7954 TCGA-86-7955 
         824         1959          630         1968         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-86-8671 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-91-6847 TCGA-91-6848 TCGA-91-7771 
          79          417          372          842          224          492 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
         505          174           36           44          218          297 
TCGA-93-7348 TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
         127           34         1973          568          377          477 
TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
         476          121          605          964         1965         1932 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
        1332          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-99-8025 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-A4E6 
         154          114          287          282          238          435 
TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A743 TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4SV 
           6          266          312          102         1175         1946 
TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
        1967         1954         1954         1980         1951         1944 
TCGA-MP-A4TH TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-S2-AA1A 
         142         1971         1490          121 

  DEL PEAK 24(11Q25) MUTATED DEL PEAK 24(11Q25) WILD-TYPE 
                           2                            1 
  DEL PEAK 24(11Q25) MUTATED DEL PEAK 24(11Q25) WILD-TYPE 
                        2067                         6443 
  DEL PEAK 24(11Q25) MUTATED DEL PEAK 24(11Q25) WILD-TYPE 
                       737.5                        444.5 
[1] "2.0 - 2067.0 (737.5)" "1.0 - 6443.0 (444.5)"
[1] "hr=" "1"  
D53V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 24(11Q25) MUTATED         1       22       26        16        18
  DEL PEAK 24(11Q25) WILD-TYPE       4       94      106        33        52
                              vv
clus                           STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 24(11Q25) MUTATED           16          2        6
  DEL PEAK 24(11Q25) WILD-TYPE         52          9       18
D53V3, multiclass
            clus
vv           DEL PEAK 24(11Q25) MUTATED DEL PEAK 24(11Q25) WILD-TYPE
  STAGE I                             1                            4
  STAGE IA                           22                           94
  STAGE IB                           26                          106
  STAGE IIA                          16                           33
  STAGE IIB                          18                           52
  STAGE IIIA                         16                           52
  STAGE IIIB                          2                            9
  STAGE IV                            6                           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 24(11Q25) MUTATED    27  65  10   4
  DEL PEAK 24(11Q25) WILD-TYPE 120 202  32  14
D53V4, multiclass
    clus
vv   DEL PEAK 24(11Q25) MUTATED DEL PEAK 24(11Q25) WILD-TYPE
  T1                         27                          120
  T2                         65                          202
  T3                         10                           32
  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 24(11Q25) MUTATED    60  28    18
  DEL PEAK 24(11Q25) WILD-TYPE 241  63    56
D53V5, multiclass
       clus
vv      DEL PEAK 24(11Q25) MUTATED DEL PEAK 24(11Q25) WILD-TYPE
  N0                            60                          241
  N1                            28                           63
  N2+N3                         18                           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
  DEL PEAK 24(11Q25) MUTATED    81   5   0   1  20
  DEL PEAK 24(11Q25) WILD-TYPE 245  13   1   3 103
D53V6, multiclass
     clus
vv    DEL PEAK 24(11Q25) MUTATED DEL PEAK 24(11Q25) WILD-TYPE
  M0                          81                          245
  M1                           5                           13
  M1A                          0                            1
  M1B                          1                            3
  MX                          20                          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"
D53V7, binary
                              cls
clus                             0   1
  DEL PEAK 24(11Q25) MUTATED    46  61
  DEL PEAK 24(11Q25) WILD-TYPE 209 160
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 24(11Q25) MUTATED     46   61
  DEL PEAK 24(11Q25) WILD-TYPE  209  160
        clus
vv       DEL PEAK 24(11Q25) MUTATED DEL PEAK 24(11Q25) WILD-TYPE
  FEMALE                         46                          209
  MALE                           61                          160
[1] 2 2
[1] FALSE
D53V8, continuous
                              vv
clus                           LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 24(11Q25) MUTATED                            4
  DEL PEAK 24(11Q25) WILD-TYPE                         11
                              vv
clus                           LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 24(11Q25) MUTATED                                  24
  DEL PEAK 24(11Q25) WILD-TYPE                                70
                              vv
clus                           LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 24(11Q25) MUTATED                                                   67
  DEL PEAK 24(11Q25) WILD-TYPE                                                236
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 24(11Q25) MUTATED                                            0
  DEL PEAK 24(11Q25) WILD-TYPE                                          5
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 24(11Q25) MUTATED                                               2
  DEL PEAK 24(11Q25) WILD-TYPE                                            17
                              vv
clus                           LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 24(11Q25) MUTATED                                1
  DEL PEAK 24(11Q25) WILD-TYPE                              1
                              vv
clus                           LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 24(11Q25) MUTATED                                    0
  DEL PEAK 24(11Q25) WILD-TYPE                                  4
                              vv
clus                           LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 24(11Q25) MUTATED                              0
  DEL PEAK 24(11Q25) WILD-TYPE                            2
                              vv
clus                           LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 24(11Q25) MUTATED                               5
  DEL PEAK 24(11Q25) WILD-TYPE                            14
                              vv
clus                           LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 24(11Q25) MUTATED                                 0
  DEL PEAK 24(11Q25) WILD-TYPE                               1
                              vv
clus                           LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 24(11Q25) MUTATED                                               2
  DEL PEAK 24(11Q25) WILD-TYPE                                             3
                              vv
clus                           MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 24(11Q25) MUTATED                              2
  DEL PEAK 24(11Q25) WILD-TYPE                            5
D53V9, multiclass
                                                    clus
vv                                                   DEL PEAK 24(11Q25) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                  4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                          24
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         67
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                  0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                               2
  LUNG CLEAR CELL ADENOCARCINOMA                                              1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                          0
  LUNG MUCINOUS ADENOCARCINOMA                                                0
  LUNG PAPILLARY ADENOCARCINOMA                                               5
  LUNG SIGNET RING ADENOCARCINOMA                                             0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                               2
  MUCINOUS (COLLOID) CARCINOMA                                                2
                                                    clus
vv                                                   DEL PEAK 24(11Q25) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                   11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            70
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          236
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    5
  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"
D53V10, binary
                              cls
clus                             0   1
  DEL PEAK 24(11Q25) MUTATED     3 104
  DEL PEAK 24(11Q25) WILD-TYPE  18 351
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 24(11Q25) MUTATED      3  104
  DEL PEAK 24(11Q25) WILD-TYPE   18  351
     clus
vv    DEL PEAK 24(11Q25) MUTATED DEL PEAK 24(11Q25) WILD-TYPE
  NO                           3                           18
  YES                        104                          351
[1] 2 2
[1] FALSE
D53V11, continuous
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 24(11Q25) MUTATED    79   2   0   7
  DEL PEAK 24(11Q25) WILD-TYPE 248  10   4  14
D53V12, multiclass
    clus
vv   DEL PEAK 24(11Q25) MUTATED DEL PEAK 24(11Q25) WILD-TYPE
  R0                         79                          248
  R1                          2                           10
  R2                          0                            4
  RX                          7                           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 24(11Q25) MUTATED                                  0     2
  DEL PEAK 24(11Q25) WILD-TYPE                                1     4
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 24(11Q25) MUTATED                          10    78
  DEL PEAK 24(11Q25) WILD-TYPE                        25   289
D53V13, multiclass
                                  clus
vv                                 DEL PEAK 24(11Q25) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     2
  BLACK OR AFRICAN AMERICAN                                10
  WHITE                                                    78
                                  clus
vv                                 DEL PEAK 24(11Q25) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  25
  WHITE                                                     289
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V14, binary
                              cls
clus                             0   1
  DEL PEAK 24(11Q25) MUTATED     1  75
  DEL PEAK 24(11Q25) WILD-TYPE   6 270
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 24(11Q25) MUTATED      1   75
  DEL PEAK 24(11Q25) WILD-TYPE    6  270
                        clus
vv                       DEL PEAK 24(11Q25) MUTATED
  HISPANIC OR LATINO                              1
  NOT HISPANIC OR LATINO                         75
                        clus
vv                       DEL PEAK 24(11Q25) WILD-TYPE
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          270
[1] 2 2
[1] FALSE

Clustering(54) Variable = DEL PEAK 25(12P13.2) MUTATION ANALYSIS
D54V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 25(12P13.2) MUTATED    95  13
  DEL PEAK 25(12P13.2) WILD-TYPE 234  74
  DEL PEAK 25(12P13.2) MUTATED DEL PEAK 25(12P13.2) WILD-TYPE 
                           108                            308 
  DEL PEAK 25(12P13.2) MUTATED DEL PEAK 25(12P13.2) WILD-TYPE 
                            13                             74 
$`DEL PEAK 25(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 
         462           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-86-7955 TCGA-86-8073 TCGA-86-8074 TCGA-86-8279 
        1972          824          508           13           24          482 
TCGA-86-8358 TCGA-86-8672 TCGA-91-6828 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
          19           15          323           79          417          372 
TCGA-91-6847 TCGA-91-6849 TCGA-95-7567 TCGA-95-7947 TCGA-95-7948 TCGA-95-8494 
         842           35          568          477          476           84 
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-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N5 TCGA-MP-A4TC TCGA-MP-A4TH 
         287          111          102           84         1944          142 

$`DEL PEAK 25(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-49-AARQ TCGA-50-5045 
         157         1700          445          890         6443         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-50-5933 TCGA-50-5941 TCGA-50-5944 TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 
        2370          567          764         1015          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-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6971 
        1375            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-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
         121            6           95           40          705           39 
TCGA-55-7726 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 TCGA-55-7994 
          39           54           19           16           21           31 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8094 
           5           33          100            6          600            4 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
          47           15           33           46           66          674 
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-55-8512 TCGA-55-8513 TCGA-55-8615 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48Y 
           3          146           15           66          106           42 
TCGA-55-A490 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-62-8395 
          48            1           28            5           47         1216 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46U TCGA-62-A471 
        1289         1970         2696         1445         2067         1246 
TCGA-62-A472 TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-5774 
         910          628         1189         1686         1126         1959 
TCGA-64-5775 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 
          62          864         1559          866          573          427 
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-69-7978 TCGA-69-7980 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-73-4658 
          70          382           77          129          214         1600 
TCGA-73-4659 TCGA-73-4666 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-A9RS 
         711          800          131           40          164          305 
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-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
        1093         1963         1202         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-78-7167 TCGA-78-7220 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
        1937         1965         1949         1944          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-86-6851 TCGA-86-7701 TCGA-86-7711 
        1964         1965         1972         1959           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-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8281 
        1963          479          489          476           16         1955 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 
          26           35           45           34           18          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-91-6848 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
          60          310          224          492          505          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-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7944 TCGA-95-8039 TCGA-95-A4VK 
          34            2         1973          377          830          121 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 TCGA-97-7941 
         553          605         1932         1332          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-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
         115          197          271          459           44          170 
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-L9-A443 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MN-A4N4 
         116            6          266          312          827         1175 
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-A4TE TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TK 
        1980         1951         1970         1970         1955         1971 
TCGA-MP-A5C7 TCGA-S2-AA1A 
        1490          121 

  DEL PEAK 25(12P13.2) MUTATED DEL PEAK 25(12P13.2) WILD-TYPE 
                             3                              1 
  DEL PEAK 25(12P13.2) MUTATED DEL PEAK 25(12P13.2) WILD-TYPE 
                          2199                           6443 
  DEL PEAK 25(12P13.2) MUTATED DEL PEAK 25(12P13.2) WILD-TYPE 
                         424.5                          529.0 
[1] "3.0 - 2199.0 (424.5)" "1.0 - 6443.0 (529.0)"
[1] "hr=" "1.4"
D54V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 25(12P13.2) MUTATED         0       33       44         8        15
  DEL PEAK 25(12P13.2) WILD-TYPE       5       83       88        41        55
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 25(12P13.2) MUTATED           19          1        6
  DEL PEAK 25(12P13.2) WILD-TYPE         49         10       18
D54V3, multiclass
            clus
vv           DEL PEAK 25(12P13.2) MUTATED DEL PEAK 25(12P13.2) WILD-TYPE
  STAGE I                               0                              5
  STAGE IA                             33                             83
  STAGE IB                             44                             88
  STAGE IIA                             8                             41
  STAGE IIB                            15                             55
  STAGE IIIA                           19                             49
  STAGE IIIB                            1                             10
  STAGE IV                              6                             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(12P13.2) MUTATED    41  72   9   4
  DEL PEAK 25(12P13.2) WILD-TYPE 106 195  33  14
D54V4, multiclass
    clus
vv   DEL PEAK 25(12P13.2) MUTATED DEL PEAK 25(12P13.2) WILD-TYPE
  T1                           41                            106
  T2                           72                            195
  T3                            9                             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 25(12P13.2) MUTATED    85  22    18
  DEL PEAK 25(12P13.2) WILD-TYPE 216  69    56
D54V5, multiclass
       clus
vv      DEL PEAK 25(12P13.2) MUTATED DEL PEAK 25(12P13.2) WILD-TYPE
  N0                              85                            216
  N1                              22                             69
  N2+N3                           18                             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
  DEL PEAK 25(12P13.2) MUTATED    83   5   0   0  37
  DEL PEAK 25(12P13.2) WILD-TYPE 243  13   1   4  86
D54V6, multiclass
     clus
vv    DEL PEAK 25(12P13.2) MUTATED DEL PEAK 25(12P13.2) WILD-TYPE
  M0                            83                            243
  M1                             5                             13
  M1A                            0                              1
  M1B                            0                              4
  MX                            37                             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"
D54V7, binary
                                cls
clus                               0   1
  DEL PEAK 25(12P13.2) MUTATED    81  45
  DEL PEAK 25(12P13.2) WILD-TYPE 174 176
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(12P13.2) MUTATED     81   45
  DEL PEAK 25(12P13.2) WILD-TYPE  174  176
        clus
vv       DEL PEAK 25(12P13.2) MUTATED DEL PEAK 25(12P13.2) WILD-TYPE
  FEMALE                           81                            174
  MALE                             45                            176
[1] 2 2
[1] FALSE
D54V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 25(12P13.2) MUTATED                            2
  DEL PEAK 25(12P13.2) WILD-TYPE                         13
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 25(12P13.2) MUTATED                                  28
  DEL PEAK 25(12P13.2) WILD-TYPE                                66
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 25(12P13.2) MUTATED                                                   80
  DEL PEAK 25(12P13.2) WILD-TYPE                                                223
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 25(12P13.2) MUTATED                                            0
  DEL PEAK 25(12P13.2) WILD-TYPE                                          5
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 25(12P13.2) MUTATED                                               7
  DEL PEAK 25(12P13.2) WILD-TYPE                                            12
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 25(12P13.2) MUTATED                                1
  DEL PEAK 25(12P13.2) WILD-TYPE                              1
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 25(12P13.2) MUTATED                                    1
  DEL PEAK 25(12P13.2) WILD-TYPE                                  3
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 25(12P13.2) MUTATED                              0
  DEL PEAK 25(12P13.2) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 25(12P13.2) MUTATED                               4
  DEL PEAK 25(12P13.2) WILD-TYPE                            15
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 25(12P13.2) MUTATED                                 0
  DEL PEAK 25(12P13.2) WILD-TYPE                               1
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 25(12P13.2) MUTATED                                               1
  DEL PEAK 25(12P13.2) WILD-TYPE                                             4
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 25(12P13.2) MUTATED                              2
  DEL PEAK 25(12P13.2) WILD-TYPE                            5
D54V9, multiclass
                                                    clus
vv                                                   DEL PEAK 25(12P13.2) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            28
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           80
  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 25(12P13.2) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              66
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            223
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      5
  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                                   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"
D54V10, binary
                                cls
clus                               0   1
  DEL PEAK 25(12P13.2) MUTATED     4 122
  DEL PEAK 25(12P13.2) WILD-TYPE  17 333
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(12P13.2) MUTATED      4  122
  DEL PEAK 25(12P13.2) WILD-TYPE   17  333
     clus
vv    DEL PEAK 25(12P13.2) MUTATED DEL PEAK 25(12P13.2) WILD-TYPE
  NO                             4                             17
  YES                          122                            333
[1] 2 2
[1] FALSE
D54V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 25(12P13.2) MUTATED    80   4   2   5
  DEL PEAK 25(12P13.2) WILD-TYPE 247   8   2  16
D54V12, multiclass
    clus
vv   DEL PEAK 25(12P13.2) MUTATED DEL PEAK 25(12P13.2) WILD-TYPE
  R0                           80                            247
  R1                            4                              8
  R2                            2                              2
  RX                            5                             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 25(12P13.2) MUTATED                                  1     1
  DEL PEAK 25(12P13.2) WILD-TYPE                                0     5
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 25(12P13.2) MUTATED                          13    98
  DEL PEAK 25(12P13.2) WILD-TYPE                        22   269
D54V13, multiclass
                                  clus
vv                                 DEL PEAK 25(12P13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                  13
  WHITE                                                      98
                                  clus
vv                                 DEL PEAK 25(12P13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         5
  BLACK OR AFRICAN AMERICAN                                    22
  WHITE                                                       269
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V14, binary
                                cls
clus                               0   1
  DEL PEAK 25(12P13.2) MUTATED     2 100
  DEL PEAK 25(12P13.2) WILD-TYPE   5 245
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(12P13.2) MUTATED      2  100
  DEL PEAK 25(12P13.2) WILD-TYPE    5  245
                        clus
vv                       DEL PEAK 25(12P13.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          100
                        clus
vv                       DEL PEAK 25(12P13.2) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            245
[1] 2 2
[1] FALSE

Clustering(55) Variable = DEL PEAK 26(12Q12) MUTATION ANALYSIS
D55V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 26(12Q12) MUTATED    66  11
  DEL PEAK 26(12Q12) WILD-TYPE 263  76
  DEL PEAK 26(12Q12) MUTATED DEL PEAK 26(12Q12) WILD-TYPE 
                          77                          339 
  DEL PEAK 26(12Q12) MUTATED DEL PEAK 26(12Q12) WILD-TYPE 
                          11                           76 
$`DEL PEAK 26(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-95-8039 TCGA-97-7546 TCGA-97-7547 TCGA-97-7554 TCGA-97-8177 TCGA-99-7458 
         830          964         1965          775          147          392 
TCGA-99-8025 TCGA-J2-A4AD TCGA-L9-A8F4 TCGA-MP-A4TC TCGA-MP-A4TK 
         427          287          102         1944         1971 

$`DEL PEAK 26(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-49-AARQ TCGA-50-5045 TCGA-50-5055 
         369          890          354         6443         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-50-5935 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-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 
         255         1986         1971          424          280         1178 
TCGA-55-1595 TCGA-55-1596 TCGA-55-6543 TCGA-55-6642 TCGA-55-6969 TCGA-55-6971 
        1479         1375            2          993         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-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
          18          121            6            4           95           40 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 
         705           39           39           24           54           19 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
         197           21           31            5           33          462 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 
           6          600            4           47           15           33 
TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 
          46          674          216           44           23           11 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8615 
           8           15            9            3          146           15 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48Y TCGA-55-A490 TCGA-55-A492 TCGA-55-A493 
          66          106           42           48            1           28 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
           5           47          162         1216         1289         1970 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 TCGA-64-1677 
        2696         1445         2199         1246          910          628 
TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
        1189         1686         1126         1968         1959           62 
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-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 
         427          385          174          141          202          186 
TCGA-69-7764 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
         414          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-73-4676 TCGA-73-7499 TCGA-73-A9RS 
         912          800          467          164          519          305 
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-78-7150 TCGA-78-7152 TCGA-78-7154 TCGA-78-7155 
        1944         1093         1963         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-78-7220 TCGA-78-7536 TCGA-78-7537 
        1950         1934         1937         1965         1949         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-78-8660 TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 
        1981         1954         1964         1965         1972          824 
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-86-8054 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-86-8281 TCGA-86-8358 TCGA-86-8585 TCGA-86-8669 TCGA-86-8671 
         476         1955           19           35           34           18 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 
         455          405           10           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-91-6848 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
         372          224          492          505          174           36 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7562 
          44          218          297          127          186         1973 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
         568          377          477           84          121          553 
TCGA-95-A4VP TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 
         605         1932         1332          181           22          107 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
         182         1965           87           15          148          115 
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-L9-A50W TCGA-L9-A743 TCGA-L9-A7SV TCGA-MN-A4N1 TCGA-MN-A4N4 
           6          266          312          111          827         1175 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 
          84         1946         1967         1951         1954         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-A5C7 TCGA-S2-AA1A 
        1955         1490          121 

  DEL PEAK 26(12Q12) MUTATED DEL PEAK 26(12Q12) WILD-TYPE 
                           2                            1 
  DEL PEAK 26(12Q12) MUTATED DEL PEAK 26(12Q12) WILD-TYPE 
                        2146                         6443 
  DEL PEAK 26(12Q12) MUTATED DEL PEAK 26(12Q12) WILD-TYPE 
                         337                          519 
[1] "2.0 - 2146.0 (337.0)" "1.0 - 6443.0 (519.0)"
[1] "hr=" "1.3"
D55V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 26(12Q12) MUTATED         0       18       28         9        11
  DEL PEAK 26(12Q12) WILD-TYPE       5       98      104        40        59
                              vv
clus                           STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 26(12Q12) MUTATED           20          1        4
  DEL PEAK 26(12Q12) WILD-TYPE         48         10       20
D55V3, multiclass
            clus
vv           DEL PEAK 26(12Q12) MUTATED DEL PEAK 26(12Q12) WILD-TYPE
  STAGE I                             0                            5
  STAGE IA                           18                           98
  STAGE IB                           28                          104
  STAGE IIA                           9                           40
  STAGE IIB                          11                           59
  STAGE IIIA                         20                           48
  STAGE IIIB                          1                           10
  STAGE IV                            4                           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 26(12Q12) MUTATED    25  52  11   2
  DEL PEAK 26(12Q12) WILD-TYPE 122 215  31  16
D55V4, multiclass
    clus
vv   DEL PEAK 26(12Q12) MUTATED DEL PEAK 26(12Q12) WILD-TYPE
  T1                         25                          122
  T2                         52                          215
  T3                         11                           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 26(12Q12) MUTATED    54  18    18
  DEL PEAK 26(12Q12) WILD-TYPE 247  73    56
D55V5, multiclass
       clus
vv      DEL PEAK 26(12Q12) MUTATED DEL PEAK 26(12Q12) WILD-TYPE
  N0                            54                          247
  N1                            18                           73
  N2+N3                         18                           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
  DEL PEAK 26(12Q12) MUTATED    53   3   0   0  34
  DEL PEAK 26(12Q12) WILD-TYPE 273  15   1   4  89
D55V6, multiclass
     clus
vv    DEL PEAK 26(12Q12) MUTATED DEL PEAK 26(12Q12) WILD-TYPE
  M0                          53                          273
  M1                           3                           15
  M1A                          0                            1
  M1B                          0                            4
  MX                          34                           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"
D55V7, binary
                              cls
clus                             0   1
  DEL PEAK 26(12Q12) MUTATED    55  36
  DEL PEAK 26(12Q12) WILD-TYPE 200 185
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 26(12Q12) MUTATED     55   36
  DEL PEAK 26(12Q12) WILD-TYPE  200  185
        clus
vv       DEL PEAK 26(12Q12) MUTATED DEL PEAK 26(12Q12) WILD-TYPE
  FEMALE                         55                          200
  MALE                           36                          185
[1] 2 2
[1] FALSE
D55V8, continuous
                              vv
clus                           LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 26(12Q12) MUTATED                            3
  DEL PEAK 26(12Q12) WILD-TYPE                         12
                              vv
clus                           LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 26(12Q12) MUTATED                                  17
  DEL PEAK 26(12Q12) WILD-TYPE                                77
                              vv
clus                           LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 26(12Q12) MUTATED                                                   59
  DEL PEAK 26(12Q12) WILD-TYPE                                                244
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 26(12Q12) MUTATED                                            1
  DEL PEAK 26(12Q12) WILD-TYPE                                          4
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 26(12Q12) MUTATED                                               5
  DEL PEAK 26(12Q12) WILD-TYPE                                            14
                              vv
clus                           LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 26(12Q12) MUTATED                                0
  DEL PEAK 26(12Q12) WILD-TYPE                              2
                              vv
clus                           LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 26(12Q12) MUTATED                                    0
  DEL PEAK 26(12Q12) WILD-TYPE                                  4
                              vv
clus                           LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 26(12Q12) MUTATED                              0
  DEL PEAK 26(12Q12) WILD-TYPE                            2
                              vv
clus                           LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 26(12Q12) MUTATED                               5
  DEL PEAK 26(12Q12) WILD-TYPE                            14
                              vv
clus                           LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 26(12Q12) MUTATED                                 0
  DEL PEAK 26(12Q12) WILD-TYPE                               1
                              vv
clus                           LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 26(12Q12) MUTATED                                               0
  DEL PEAK 26(12Q12) WILD-TYPE                                             5
                              vv
clus                           MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 26(12Q12) MUTATED                              1
  DEL PEAK 26(12Q12) WILD-TYPE                            6
D55V9, multiclass
                                                    clus
vv                                                   DEL PEAK 26(12Q12) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                  3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                          17
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         59
  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 26(12Q12) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                   12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            77
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          244
  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                                                14
  LUNG SIGNET RING ADENOCARCINOMA                                               1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 5
  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"
D55V10, binary
                              cls
clus                             0   1
  DEL PEAK 26(12Q12) MUTATED     1  90
  DEL PEAK 26(12Q12) WILD-TYPE  20 365
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 26(12Q12) MUTATED      1   90
  DEL PEAK 26(12Q12) WILD-TYPE   20  365
     clus
vv    DEL PEAK 26(12Q12) MUTATED DEL PEAK 26(12Q12) WILD-TYPE
  NO                           1                           20
  YES                         90                          365
[1] 2 2
[1] FALSE
D55V11, continuous
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 26(12Q12) MUTATED    60   1   1   6
  DEL PEAK 26(12Q12) WILD-TYPE 267  11   3  15
D55V12, multiclass
    clus
vv   DEL PEAK 26(12Q12) MUTATED DEL PEAK 26(12Q12) WILD-TYPE
  R0                         60                          267
  R1                          1                           11
  R2                          1                            3
  RX                          6                           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 26(12Q12) MUTATED                                  0     1
  DEL PEAK 26(12Q12) WILD-TYPE                                1     5
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 26(12Q12) MUTATED                           8    77
  DEL PEAK 26(12Q12) WILD-TYPE                        27   290
D55V13, multiclass
                                  clus
vv                                 DEL PEAK 26(12Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     1
  BLACK OR AFRICAN AMERICAN                                 8
  WHITE                                                    77
                                  clus
vv                                 DEL PEAK 26(12Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  27
  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"
D55V14, binary
                              cls
clus                             0   1
  DEL PEAK 26(12Q12) MUTATED     2  77
  DEL PEAK 26(12Q12) WILD-TYPE   5 268
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 26(12Q12) MUTATED      2   77
  DEL PEAK 26(12Q12) WILD-TYPE    5  268
                        clus
vv                       DEL PEAK 26(12Q12) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                         77
                        clus
vv                       DEL PEAK 26(12Q12) WILD-TYPE
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          268
[1] 2 2
[1] FALSE

Clustering(56) Variable = DEL PEAK 27(12Q24.33) MUTATION ANALYSIS
D56V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 27(12Q24.33) MUTATED    78  22
  DEL PEAK 27(12Q24.33) WILD-TYPE 251  65
  DEL PEAK 27(12Q24.33) MUTATED DEL PEAK 27(12Q24.33) WILD-TYPE 
                            100                             316 
  DEL PEAK 27(12Q24.33) MUTATED DEL PEAK 27(12Q24.33) WILD-TYPE 
                             22                              65 
$`DEL PEAK 27(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-49-AARQ TCGA-50-5049 TCGA-50-5068 TCGA-50-5932 
         890          522         6443         2146         1499         1091 
TCGA-50-5946 TCGA-50-6597 TCGA-50-8460 TCGA-55-1592 TCGA-55-6980 TCGA-55-6986 
         686         1015          105          701           67         2151 
TCGA-55-7283 TCGA-55-7727 TCGA-55-7911 TCGA-55-7914 TCGA-55-8087 TCGA-55-8506 
          35           34           21            3          462           11 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8514 TCGA-55-8614 
          15          228            9            3          202          536 
TCGA-55-8616 TCGA-55-8619 TCGA-55-A48X TCGA-55-A48Z TCGA-55-A4DF TCGA-55-A4DG 
          48           49           33           29           47          162 
TCGA-62-A46U TCGA-64-5778 TCGA-67-3772 TCGA-67-3774 TCGA-67-6217 TCGA-69-7763 
        2067         1305          573          385          422          690 
TCGA-69-7765 TCGA-69-7974 TCGA-69-7979 TCGA-69-8253 TCGA-71-6725 TCGA-73-4658 
         165          184           89          100           61         1600 
TCGA-73-4670 TCGA-73-4677 TCGA-75-7025 TCGA-78-7150 TCGA-78-7153 TCGA-78-7154 
         131           38         1967         1963          760         1948 
TCGA-78-7155 TCGA-78-7167 TCGA-78-7535 TCGA-78-8640 TCGA-86-8075 TCGA-86-8278 
        1957         1937         1972         1949          479          476 
TCGA-86-8279 TCGA-86-8280 TCGA-86-A4D0 TCGA-91-6847 TCGA-91-6849 TCGA-91-7771 
         482           16           30          842           35          492 
TCGA-93-7348 TCGA-95-7039 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
         127           34         1973          477          476          830 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7554 TCGA-97-7937 TCGA-97-8174 TCGA-97-8552 
         964         1965          775          181         1965          115 
TCGA-99-7458 TCGA-99-8025 TCGA-J2-A4AD TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N5 
         392          427          287          102          827           84 
TCGA-MP-A4T4 TCGA-MP-A4T9 TCGA-MP-A4TC TCGA-MP-A4TK 
        1954         1980         1944         1971 

$`DEL PEAK 27(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          705 
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 
         600           26            4           47           15           33 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
          46           66          674          216           44           23 
TCGA-55-8505 TCGA-55-8507 TCGA-55-8513 TCGA-55-8615 TCGA-55-8620 TCGA-55-8621 
          29            8          146           15           66          106 
TCGA-55-A48Y TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
          42           48         1952            1           28            5 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46V 
        1216         1289         1970         2696         1445         2199 
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-64-5779 TCGA-64-5781 
        1126         1968         1959           62          864         1559 
TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
         866           31          610          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-73-4659 TCGA-73-4662 TCGA-73-4666 
          77          129          214          711          912          800 
TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS 
         467           40          164          621          519          305 
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-78-7156 TCGA-78-7158 TCGA-78-7159 
        1944         1093         1202         1961         1963         1221 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7220 
         678          215         1940         1950         1934         1965 
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-80-5608 
        1971         1981         1954         1964         1965         1972 
TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
         824         1959           11          630          422         1968 
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-86-8073 TCGA-86-8074 TCGA-86-8076 TCGA-86-8281 TCGA-86-8358 TCGA-86-8359 
          13           24          489         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-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-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
         505          174           36           44          218          297 
TCGA-93-8067 TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 TCGA-95-8494 TCGA-95-A4VK 
         186            2          568          377           84          121 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7552 TCGA-97-7553 TCGA-97-7941 TCGA-97-8171 
         553          605         1932         1332           22          107 
TCGA-97-8172 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-A4M2 
         182           87          147           15          148          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-L9-A50W TCGA-L9-A743 TCGA-L9-A7SV TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW 
         266          312          111         1175         1946         1967 
TCGA-MP-A4T2 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TE TCGA-MP-A4TF 
        1951         1954         1957         1951         1970         1970 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A5C7 TCGA-S2-AA1A 
         142         1955         1490          121 

  DEL PEAK 27(12Q24.33) MUTATED DEL PEAK 27(12Q24.33) WILD-TYPE 
                              3                               1 
  DEL PEAK 27(12Q24.33) MUTATED DEL PEAK 27(12Q24.33) WILD-TYPE 
                           6443                            2696 
  DEL PEAK 27(12Q24.33) MUTATED DEL PEAK 27(12Q24.33) WILD-TYPE 
                          478.0                           462.5 
[1] "3.0 - 6443.0 (478.0)" "1.0 - 2696.0 (462.5)"
[1] "hr=" "1.2"
D56V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 27(12Q24.33) MUTATED         2       20       39        13        20
  DEL PEAK 27(12Q24.33) WILD-TYPE       3       96       93        36        50
                                 vv
clus                              STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 27(12Q24.33) MUTATED           18          1        7
  DEL PEAK 27(12Q24.33) WILD-TYPE         50         10       17
D56V3, multiclass
            clus
vv           DEL PEAK 27(12Q24.33) MUTATED DEL PEAK 27(12Q24.33) WILD-TYPE
  STAGE I                                2                               3
  STAGE IA                              20                              96
  STAGE IB                              39                              93
  STAGE IIA                             13                              36
  STAGE IIB                             20                              50
  STAGE IIIA                            18                              50
  STAGE IIIB                             1                              10
  STAGE IV                               7                              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 27(12Q24.33) MUTATED    29  79   9   3
  DEL PEAK 27(12Q24.33) WILD-TYPE 118 188  33  15
D56V4, multiclass
    clus
vv   DEL PEAK 27(12Q24.33) MUTATED DEL PEAK 27(12Q24.33) WILD-TYPE
  T1                            29                             118
  T2                            79                             188
  T3                             9                              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
  DEL PEAK 27(12Q24.33) MUTATED    73  28    18
  DEL PEAK 27(12Q24.33) WILD-TYPE 228  63    56
D56V5, multiclass
       clus
vv      DEL PEAK 27(12Q24.33) MUTATED DEL PEAK 27(12Q24.33) WILD-TYPE
  N0                               73                             228
  N1                               28                              63
  N2+N3                            18                              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
  DEL PEAK 27(12Q24.33) MUTATED    68   5   0   1  45
  DEL PEAK 27(12Q24.33) WILD-TYPE 258  13   1   3  78
D56V6, multiclass
     clus
vv    DEL PEAK 27(12Q24.33) MUTATED DEL PEAK 27(12Q24.33) WILD-TYPE
  M0                             68                             258
  M1                              5                              13
  M1A                             0                               1
  M1B                             1                               3
  MX                             45                              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"
D56V7, binary
                                 cls
clus                                0   1
  DEL PEAK 27(12Q24.33) MUTATED    73  47
  DEL PEAK 27(12Q24.33) WILD-TYPE 182 174
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 27(12Q24.33) MUTATED     73   47
  DEL PEAK 27(12Q24.33) WILD-TYPE  182  174
        clus
vv       DEL PEAK 27(12Q24.33) MUTATED DEL PEAK 27(12Q24.33) WILD-TYPE
  FEMALE                            73                             182
  MALE                              47                             174
[1] 2 2
[1] FALSE
D56V8, continuous
                                 vv
clus                              LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 27(12Q24.33) MUTATED                            3
  DEL PEAK 27(12Q24.33) WILD-TYPE                         12
                                 vv
clus                              LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 27(12Q24.33) MUTATED                                  20
  DEL PEAK 27(12Q24.33) WILD-TYPE                                74
                                 vv
clus                              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 27(12Q24.33) MUTATED                                                   77
  DEL PEAK 27(12Q24.33) WILD-TYPE                                                226
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 27(12Q24.33) MUTATED                                            0
  DEL PEAK 27(12Q24.33) WILD-TYPE                                          5
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 27(12Q24.33) MUTATED                                               9
  DEL PEAK 27(12Q24.33) WILD-TYPE                                            10
                                 vv
clus                              LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 27(12Q24.33) MUTATED                                0
  DEL PEAK 27(12Q24.33) WILD-TYPE                              2
                                 vv
clus                              LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 27(12Q24.33) MUTATED                                    1
  DEL PEAK 27(12Q24.33) WILD-TYPE                                  3
                                 vv
clus                              LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 27(12Q24.33) MUTATED                              0
  DEL PEAK 27(12Q24.33) WILD-TYPE                            2
                                 vv
clus                              LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 27(12Q24.33) MUTATED                               7
  DEL PEAK 27(12Q24.33) WILD-TYPE                            12
                                 vv
clus                              LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 27(12Q24.33) MUTATED                                 0
  DEL PEAK 27(12Q24.33) WILD-TYPE                               1
                                 vv
clus                              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 27(12Q24.33) MUTATED                                               1
  DEL PEAK 27(12Q24.33) WILD-TYPE                                             4
                                 vv
clus                              MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 27(12Q24.33) MUTATED                              2
  DEL PEAK 27(12Q24.33) WILD-TYPE                            5
D56V9, multiclass
                                                    clus
vv                                                   DEL PEAK 27(12Q24.33) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                     3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             20
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            77
  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 27(12Q24.33) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                               74
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             226
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                       5
  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                                    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"
D56V10, binary
                                 cls
clus                                0   1
  DEL PEAK 27(12Q24.33) MUTATED     2 118
  DEL PEAK 27(12Q24.33) WILD-TYPE  19 337
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 27(12Q24.33) MUTATED      2  118
  DEL PEAK 27(12Q24.33) WILD-TYPE   19  337
     clus
vv    DEL PEAK 27(12Q24.33) MUTATED DEL PEAK 27(12Q24.33) WILD-TYPE
  NO                              2                              19
  YES                           118                             337
[1] 2 2
[1] FALSE
D56V11, continuous
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 27(12Q24.33) MUTATED    77   2   1   7
  DEL PEAK 27(12Q24.33) WILD-TYPE 250  10   3  14
D56V12, multiclass
    clus
vv   DEL PEAK 27(12Q24.33) MUTATED DEL PEAK 27(12Q24.33) WILD-TYPE
  R0                            77                             250
  R1                             2                              10
  R2                             1                               3
  RX                             7                              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 27(12Q24.33) MUTATED                                  0     1
  DEL PEAK 27(12Q24.33) WILD-TYPE                                1     5
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 27(12Q24.33) MUTATED                          14    96
  DEL PEAK 27(12Q24.33) WILD-TYPE                        21   271
D56V13, multiclass
                                  clus
vv                                 DEL PEAK 27(12Q24.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                   14
  WHITE                                                       96
                                  clus
vv                                 DEL PEAK 27(12Q24.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          5
  BLACK OR AFRICAN AMERICAN                                     21
  WHITE                                                        271
[1] 4 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 27(12Q24.33) MUTATED     1  93
  DEL PEAK 27(12Q24.33) WILD-TYPE   6 252
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 27(12Q24.33) MUTATED      1   93
  DEL PEAK 27(12Q24.33) WILD-TYPE    6  252
                        clus
vv                       DEL PEAK 27(12Q24.33) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            93
                        clus
vv                       DEL PEAK 27(12Q24.33) WILD-TYPE
  HISPANIC OR LATINO                                   6
  NOT HISPANIC OR LATINO                             252
[1] 2 2
[1] FALSE

Clustering(57) Variable = DEL PEAK 28(13Q12.11) MUTATION ANALYSIS
D57V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 28(13Q12.11) MUTATED   187  49
  DEL PEAK 28(13Q12.11) WILD-TYPE 142  38
  DEL PEAK 28(13Q12.11) MUTATED DEL PEAK 28(13Q12.11) WILD-TYPE 
                            236                             180 
  DEL PEAK 28(13Q12.11) MUTATED DEL PEAK 28(13Q12.11) WILD-TYPE 
                             49                              38 
$`DEL PEAK 28(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-38-4629 TCGA-38-4632 TCGA-38-6178 
         264         1952         1492          864         1357          448 
TCGA-44-2656 TCGA-44-2662 TCGA-44-2665 TCGA-44-3919 TCGA-44-5643 TCGA-44-5644 
        1429         1280         1301          190         1013          863 
TCGA-44-6147 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 TCGA-44-7662 
         845         1942         1864         1978          592          218 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
         557         1970          882          385           99          260 
TCGA-44-A479 TCGA-44-A47B TCGA-44-A47F TCGA-44-A4SU TCGA-49-4501 TCGA-49-4506 
         486          287          337           76         1421          999 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-6743 TCGA-49-6761 TCGA-50-5045 
         268          896          157          369          354         2174 
TCGA-50-5051 TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 
         455          944         1499          282          267         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-53-7813 TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 
         105          424          701         1178         1479         1375 
TCGA-55-5899 TCGA-55-6642 TCGA-55-6712 TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 
          87          993           24           25         1475           67 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7570 TCGA-55-7573 TCGA-55-7576 
        1233         2151         1170            6            4           40 
TCGA-55-7724 TCGA-55-7727 TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 TCGA-55-7994 
         705           34           54           19           21           31 
TCGA-55-7995 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
           5          100            6          600           26            4 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8507 
          46           66           44           23           11            8 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
          15          228            9          536           15           48 
TCGA-55-8620 TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A493 TCGA-55-A4DG 
          66           29           48         1952           28          162 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 
        1216         1289         2696         2067         2199         1246 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
         910         1728          628         1686         1968         1959 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-6217 
        1305          864         1559          866           31          422 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 TCGA-69-7978 TCGA-69-7980 
         202          186          414          165           70          382 
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-73-4675 TCGA-73-7499 TCGA-75-6214 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
          40          519         1970         1973         1988         1950 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7160 TCGA-78-7161 TCGA-78-7167 TCGA-78-7535 
        1948         1957          678          215         1937         1972 
TCGA-78-7537 TCGA-78-7539 TCGA-78-8640 TCGA-78-8660 TCGA-83-5908 TCGA-86-6851 
        1944          327         1949         1954          824         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-86-8073 TCGA-86-8075 TCGA-86-8279 TCGA-86-8280 
         745           10           13          479          482           16 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 
          19           26           45           34           18          455 
TCGA-86-A456 TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 
          10           30          323         1940          310           79 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-7771 TCGA-91-8499 
         417          372          842          224          492           36 
TCGA-93-8067 TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
         186           34         1973          568          377          477 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
         476          830           84          553          605          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-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MP-A4SV TCGA-MP-A4T2 
         116          312          111          102         1946         1951 
TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TF 
        1954         1957         1980         1944         1970         1970 
TCGA-MP-A4TI TCGA-MP-A4TK 
        1955         1971 

$`DEL PEAK 28(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-38-4630 TCGA-38-4631 TCGA-38-7271 TCGA-38-A44F 
        1962         1147         1073          354         1971          133 
TCGA-44-2655 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2666 TCGA-44-2668 
        1324          400         1367          741           97          246 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-4112 TCGA-44-5645 TCGA-44-6144 
        1130         1163         1036          722          383          723 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
         328          302          704          658          705         1938 
TCGA-44-7659 TCGA-44-7661 TCGA-44-7671 TCGA-44-7672 TCGA-44-A47A TCGA-44-A47G 
         444          366          535          719          466          351 
TCGA-44-A4SS TCGA-49-4486 TCGA-49-4494 TCGA-49-4505 TCGA-49-4514 TCGA-49-6742 
         415         1932         1081          428         1700          445 
TCGA-49-6744 TCGA-49-6745 TCGA-49-AARQ TCGA-50-5049 TCGA-50-5055 TCGA-50-5072 
         890          522         6443         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-55-8208 
          33          462           47           15           33          674 
TCGA-55-8299 TCGA-55-8505 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8619 
         216           29            3          146          202           49 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A492 TCGA-55-A494 TCGA-55-A4DF 
         106           33           42            1            5           47 
TCGA-62-8398 TCGA-62-8402 TCGA-64-1678 TCGA-64-1680 TCGA-64-5775 TCGA-67-3771 
        1970         1445         1189         1126           62          610 
TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-69-7763 
         573          427          385          174          141          690 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-73-4666 
         230          184           89          100           77          800 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-A9RS 
         467          131          164           38          621          305 
TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
        1967         1956         1965         1944         1093         1963 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7162 
        1202          760         1961         1963         1221         1940 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7220 TCGA-78-7536 TCGA-78-7540 TCGA-78-7542 
        1950         1934         1965         1949          881         1952 
TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 
         994         1971         1981         1964         1965         1972 
TCGA-86-7714 TCGA-86-8056 TCGA-86-8074 TCGA-86-8076 TCGA-86-8278 TCGA-86-8281 
        1968         1963           24          489          476         1955 
TCGA-86-8585 TCGA-86-8672 TCGA-86-8674 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6830 
          35           15          405           14           39           60 
TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
          35          505          174           44          218          297 
TCGA-93-7348 TCGA-95-7043 TCGA-95-A4VK TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
         127            2          121         1965         1932         1332 
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-L4-A4E6 TCGA-L9-A444 TCGA-L9-A50W TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
         435            6          266          827         1175           84 
TCGA-MP-A4SW TCGA-MP-A4T7 TCGA-MP-A4TA TCGA-MP-A4TH TCGA-MP-A5C7 TCGA-S2-AA1A 
        1967         1954         1951          142         1490          121 

  DEL PEAK 28(13Q12.11) MUTATED DEL PEAK 28(13Q12.11) WILD-TYPE 
                              4                               1 
  DEL PEAK 28(13Q12.11) MUTATED DEL PEAK 28(13Q12.11) WILD-TYPE 
                           2696                            6443 
  DEL PEAK 28(13Q12.11) MUTATED DEL PEAK 28(13Q12.11) WILD-TYPE 
                          484.0                           459.5 
[1] "4.0 - 2696.0 (484.0)" "1.0 - 6443.0 (459.5)"
[1] "hr=" "1.1"
D57V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 28(13Q12.11) MUTATED         4       59       78        27        43
  DEL PEAK 28(13Q12.11) WILD-TYPE       1       57       54        22        27
                                 vv
clus                              STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 28(13Q12.11) MUTATED           39          7       14
  DEL PEAK 28(13Q12.11) WILD-TYPE         29          4       10
D57V3, multiclass
            clus
vv           DEL PEAK 28(13Q12.11) MUTATED DEL PEAK 28(13Q12.11) WILD-TYPE
  STAGE I                                4                               1
  STAGE IA                              59                              57
  STAGE IB                              78                              54
  STAGE IIA                             27                              22
  STAGE IIB                             43                              27
  STAGE IIIA                            39                              29
  STAGE IIIB                             7                               4
  STAGE IV                              14                              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 28(13Q12.11) MUTATED    75 161  24  10
  DEL PEAK 28(13Q12.11) WILD-TYPE  72 106  18   8
D57V4, multiclass
    clus
vv   DEL PEAK 28(13Q12.11) MUTATED DEL PEAK 28(13Q12.11) WILD-TYPE
  T1                            75                              72
  T2                           161                             106
  T3                            24                              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 28(13Q12.11) MUTATED   172  52    43
  DEL PEAK 28(13Q12.11) WILD-TYPE 129  39    31
D57V5, multiclass
       clus
vv      DEL PEAK 28(13Q12.11) MUTATED DEL PEAK 28(13Q12.11) WILD-TYPE
  N0                              172                             129
  N1                               52                              39
  N2+N3                            43                              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
  DEL PEAK 28(13Q12.11) MUTATED   183  11   0   2  73
  DEL PEAK 28(13Q12.11) WILD-TYPE 143   7   1   2  50
D57V6, multiclass
     clus
vv    DEL PEAK 28(13Q12.11) MUTATED DEL PEAK 28(13Q12.11) WILD-TYPE
  M0                            183                             143
  M1                             11                               7
  M1A                             0                               1
  M1B                             2                               2
  MX                             73                              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"
D57V7, binary
                                 cls
clus                                0   1
  DEL PEAK 28(13Q12.11) MUTATED   130 141
  DEL PEAK 28(13Q12.11) WILD-TYPE 125  80
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(13Q12.11) MUTATED    130  141
  DEL PEAK 28(13Q12.11) WILD-TYPE  125   80
        clus
vv       DEL PEAK 28(13Q12.11) MUTATED DEL PEAK 28(13Q12.11) WILD-TYPE
  FEMALE                           130                             125
  MALE                             141                              80
[1] 2 2
[1] FALSE
D57V8, continuous
                                 vv
clus                              LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 28(13Q12.11) MUTATED                            9
  DEL PEAK 28(13Q12.11) WILD-TYPE                          6
                                 vv
clus                              LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 28(13Q12.11) MUTATED                                  53
  DEL PEAK 28(13Q12.11) WILD-TYPE                                41
                                 vv
clus                              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 28(13Q12.11) MUTATED                                                  176
  DEL PEAK 28(13Q12.11) WILD-TYPE                                                127
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 28(13Q12.11) MUTATED                                            1
  DEL PEAK 28(13Q12.11) WILD-TYPE                                          4
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 28(13Q12.11) MUTATED                                              13
  DEL PEAK 28(13Q12.11) WILD-TYPE                                             6
                                 vv
clus                              LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 28(13Q12.11) MUTATED                                2
  DEL PEAK 28(13Q12.11) WILD-TYPE                              0
                                 vv
clus                              LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 28(13Q12.11) MUTATED                                    1
  DEL PEAK 28(13Q12.11) WILD-TYPE                                  3
                                 vv
clus                              LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 28(13Q12.11) MUTATED                              0
  DEL PEAK 28(13Q12.11) WILD-TYPE                            2
                                 vv
clus                              LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 28(13Q12.11) MUTATED                              10
  DEL PEAK 28(13Q12.11) WILD-TYPE                             9
                                 vv
clus                              LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 28(13Q12.11) MUTATED                                 1
  DEL PEAK 28(13Q12.11) WILD-TYPE                               0
                                 vv
clus                              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 28(13Q12.11) MUTATED                                               3
  DEL PEAK 28(13Q12.11) WILD-TYPE                                             2
                                 vv
clus                              MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 28(13Q12.11) MUTATED                              2
  DEL PEAK 28(13Q12.11) WILD-TYPE                            5
D57V9, multiclass
                                                    clus
vv                                                   DEL PEAK 28(13Q12.11) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                     9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             53
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           176
  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                                  3
  MUCINOUS (COLLOID) CARCINOMA                                                   2
                                                    clus
vv                                                   DEL PEAK 28(13Q12.11) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                       6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                               41
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             127
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                    6
  LUNG CLEAR CELL ADENOCARCINOMA                                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                               3
  LUNG MUCINOUS ADENOCARCINOMA                                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                                    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"
D57V10, binary
                                 cls
clus                                0   1
  DEL PEAK 28(13Q12.11) MUTATED     8 263
  DEL PEAK 28(13Q12.11) WILD-TYPE  13 192
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(13Q12.11) MUTATED      8  263
  DEL PEAK 28(13Q12.11) WILD-TYPE   13  192
     clus
vv    DEL PEAK 28(13Q12.11) MUTATED DEL PEAK 28(13Q12.11) WILD-TYPE
  NO                              8                              13
  YES                           263                             192
[1] 2 2
[1] FALSE
D57V11, continuous
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 28(13Q12.11) MUTATED   186   7   2  13
  DEL PEAK 28(13Q12.11) WILD-TYPE 141   5   2   8
D57V12, multiclass
    clus
vv   DEL PEAK 28(13Q12.11) MUTATED DEL PEAK 28(13Q12.11) WILD-TYPE
  R0                           186                             141
  R1                             7                               5
  R2                             2                               2
  RX                            13                               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 28(13Q12.11) MUTATED                                  0     5
  DEL PEAK 28(13Q12.11) WILD-TYPE                                1     1
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 28(13Q12.11) MUTATED                          20   207
  DEL PEAK 28(13Q12.11) WILD-TYPE                        15   160
D57V13, multiclass
                                  clus
vv                                 DEL PEAK 28(13Q12.11) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                   20
  WHITE                                                      207
                                  clus
vv                                 DEL PEAK 28(13Q12.11) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          1
  BLACK OR AFRICAN AMERICAN                                     15
  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"
D57V14, binary
                                 cls
clus                                0   1
  DEL PEAK 28(13Q12.11) MUTATED     3 200
  DEL PEAK 28(13Q12.11) WILD-TYPE   4 145
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(13Q12.11) MUTATED      3  200
  DEL PEAK 28(13Q12.11) WILD-TYPE    4  145
                        clus
vv                       DEL PEAK 28(13Q12.11) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           200
                        clus
vv                       DEL PEAK 28(13Q12.11) WILD-TYPE
  HISPANIC OR LATINO                                   4
  NOT HISPANIC OR LATINO                             145
[1] 2 2
[1] FALSE

Clustering(58) Variable = DEL PEAK 29(13Q12.13) MUTATION ANALYSIS
D58V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 29(13Q12.13) MUTATED   185  48
  DEL PEAK 29(13Q12.13) WILD-TYPE 144  39
  DEL PEAK 29(13Q12.13) MUTATED DEL PEAK 29(13Q12.13) WILD-TYPE 
                            233                             183 
  DEL PEAK 29(13Q12.13) MUTATED DEL PEAK 29(13Q12.13) WILD-TYPE 
                             48                              39 
$`DEL PEAK 29(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          705           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          600 
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-95-7562 TCGA-95-7567 
         492           36          186           34         1973          568 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VN 
         377          477          476          830           84          553 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7554 TCGA-97-8174 TCGA-97-8177 TCGA-97-8547 
         605          964          775         1965          147          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-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-L9-A743 TCGA-L9-A7SV 
         238          578          116            6          312          111 
TCGA-L9-A8F4 TCGA-MP-A4SV TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4T9 
         102         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 29(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-49-AARQ 
         428         1700          445          890          522         6443 
TCGA-50-5049 TCGA-50-5055 TCGA-50-5072 TCGA-50-5930 TCGA-50-5932 TCGA-50-5942 
        2146          785          246          282         1091          883 
TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-6543 TCGA-55-6969 TCGA-55-6983 
        1986         1971          280            2         1239         1826 
TCGA-55-7281 TCGA-55-7284 TCGA-55-7574 TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 
          18          121           95           39           39           24 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
          16          197            3            5           33          462 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8208 TCGA-55-8299 TCGA-55-8302 
          47           15           33          674          216           23 
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-73-A9RS TCGA-75-7025 
         131          164           38          621          305         1967 
TCGA-75-7027 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
        1956         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          505 
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-A50W 
         107          182           87           15          435          266 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T7 TCGA-MP-A4TA 
         827         1175           84         1967         1954         1951 
TCGA-MP-A4TH TCGA-MP-A5C7 TCGA-S2-AA1A 
         142         1490          121 

  DEL PEAK 29(13Q12.13) MUTATED DEL PEAK 29(13Q12.13) WILD-TYPE 
                              4                               1 
  DEL PEAK 29(13Q12.13) MUTATED DEL PEAK 29(13Q12.13) WILD-TYPE 
                           2696                            6443 
  DEL PEAK 29(13Q12.13) MUTATED DEL PEAK 29(13Q12.13) WILD-TYPE 
                            482                             462 
[1] "4.0 - 2696.0 (482.0)" "1.0 - 6443.0 (462.0)"
[1] "hr=" "1.2"
D58V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 29(13Q12.13) MUTATED         4       59       77        27        42
  DEL PEAK 29(13Q12.13) WILD-TYPE       1       57       55        22        28
                                 vv
clus                              STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 29(13Q12.13) MUTATED           39          7       14
  DEL PEAK 29(13Q12.13) WILD-TYPE         29          4       10
D58V3, multiclass
            clus
vv           DEL PEAK 29(13Q12.13) MUTATED DEL PEAK 29(13Q12.13) WILD-TYPE
  STAGE I                                4                               1
  STAGE IA                              59                              57
  STAGE IB                              77                              55
  STAGE IIA                             27                              22
  STAGE IIB                             42                              28
  STAGE IIIA                            39                              29
  STAGE IIIB                             7                               4
  STAGE IV                              14                              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 29(13Q12.13) MUTATED    75 158  25  10
  DEL PEAK 29(13Q12.13) WILD-TYPE  72 109  17   8
D58V4, multiclass
    clus
vv   DEL PEAK 29(13Q12.13) MUTATED DEL PEAK 29(13Q12.13) WILD-TYPE
  T1                            75                              72
  T2                           158                             109
  T3                            25                              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 29(13Q12.13) MUTATED   171  51    43
  DEL PEAK 29(13Q12.13) WILD-TYPE 130  40    31
D58V5, multiclass
       clus
vv      DEL PEAK 29(13Q12.13) MUTATED DEL PEAK 29(13Q12.13) WILD-TYPE
  N0                              171                             130
  N1                               51                              40
  N2+N3                            43                              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
  DEL PEAK 29(13Q12.13) MUTATED   181  11   0   2  73
  DEL PEAK 29(13Q12.13) WILD-TYPE 145   7   1   2  50
D58V6, multiclass
     clus
vv    DEL PEAK 29(13Q12.13) MUTATED DEL PEAK 29(13Q12.13) WILD-TYPE
  M0                            181                             145
  M1                             11                               7
  M1A                             0                               1
  M1B                             2                               2
  MX                             73                              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"
D58V7, binary
                                 cls
clus                                0   1
  DEL PEAK 29(13Q12.13) MUTATED   132 137
  DEL PEAK 29(13Q12.13) WILD-TYPE 123  84
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 29(13Q12.13) MUTATED    132  137
  DEL PEAK 29(13Q12.13) WILD-TYPE  123   84
        clus
vv       DEL PEAK 29(13Q12.13) MUTATED DEL PEAK 29(13Q12.13) WILD-TYPE
  FEMALE                           132                             123
  MALE                             137                              84
[1] 2 2
[1] FALSE
D58V8, continuous
                                 vv
clus                              LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 29(13Q12.13) MUTATED                            9
  DEL PEAK 29(13Q12.13) WILD-TYPE                          6
                                 vv
clus                              LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 29(13Q12.13) MUTATED                                  51
  DEL PEAK 29(13Q12.13) WILD-TYPE                                43
                                 vv
clus                              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 29(13Q12.13) MUTATED                                                  175
  DEL PEAK 29(13Q12.13) WILD-TYPE                                                128
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 29(13Q12.13) MUTATED                                            1
  DEL PEAK 29(13Q12.13) WILD-TYPE                                          4
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 29(13Q12.13) MUTATED                                              14
  DEL PEAK 29(13Q12.13) WILD-TYPE                                             5
                                 vv
clus                              LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 29(13Q12.13) MUTATED                                2
  DEL PEAK 29(13Q12.13) WILD-TYPE                              0
                                 vv
clus                              LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 29(13Q12.13) MUTATED                                    1
  DEL PEAK 29(13Q12.13) WILD-TYPE                                  3
                                 vv
clus                              LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 29(13Q12.13) MUTATED                              0
  DEL PEAK 29(13Q12.13) WILD-TYPE                            2
                                 vv
clus                              LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 29(13Q12.13) MUTATED                              10
  DEL PEAK 29(13Q12.13) WILD-TYPE                             9
                                 vv
clus                              LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 29(13Q12.13) MUTATED                                 1
  DEL PEAK 29(13Q12.13) WILD-TYPE                               0
                                 vv
clus                              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 29(13Q12.13) MUTATED                                               3
  DEL PEAK 29(13Q12.13) WILD-TYPE                                             2
                                 vv
clus                              MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 29(13Q12.13) MUTATED                              2
  DEL PEAK 29(13Q12.13) WILD-TYPE                            5
D58V9, multiclass
                                                    clus
vv                                                   DEL PEAK 29(13Q12.13) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                     9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             51
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           175
  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                                  3
  MUCINOUS (COLLOID) CARCINOMA                                                   2
                                                    clus
vv                                                   DEL PEAK 29(13Q12.13) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                       6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                               43
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             128
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                    5
  LUNG CLEAR CELL ADENOCARCINOMA                                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                               3
  LUNG MUCINOUS ADENOCARCINOMA                                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                                    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"
D58V10, binary
                                 cls
clus                                0   1
  DEL PEAK 29(13Q12.13) MUTATED     7 262
  DEL PEAK 29(13Q12.13) WILD-TYPE  14 193
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 29(13Q12.13) MUTATED      7  262
  DEL PEAK 29(13Q12.13) WILD-TYPE   14  193
     clus
vv    DEL PEAK 29(13Q12.13) MUTATED DEL PEAK 29(13Q12.13) WILD-TYPE
  NO                              7                              14
  YES                           262                             193
[1] 2 2
[1] FALSE
D58V11, continuous
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 29(13Q12.13) MUTATED   185   7   2  13
  DEL PEAK 29(13Q12.13) WILD-TYPE 142   5   2   8
D58V12, multiclass
    clus
vv   DEL PEAK 29(13Q12.13) MUTATED DEL PEAK 29(13Q12.13) WILD-TYPE
  R0                           185                             142
  R1                             7                               5
  R2                             2                               2
  RX                            13                               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 29(13Q12.13) MUTATED                                  0     5
  DEL PEAK 29(13Q12.13) WILD-TYPE                                1     1
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 29(13Q12.13) MUTATED                          20   204
  DEL PEAK 29(13Q12.13) WILD-TYPE                        15   163
D58V13, multiclass
                                  clus
vv                                 DEL PEAK 29(13Q12.13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                   20
  WHITE                                                      204
                                  clus
vv                                 DEL PEAK 29(13Q12.13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          1
  BLACK OR AFRICAN AMERICAN                                     15
  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"
D58V14, binary
                                 cls
clus                                0   1
  DEL PEAK 29(13Q12.13) MUTATED     3 198
  DEL PEAK 29(13Q12.13) WILD-TYPE   4 147
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 29(13Q12.13) MUTATED      3  198
  DEL PEAK 29(13Q12.13) WILD-TYPE    4  147
                        clus
vv                       DEL PEAK 29(13Q12.13) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           198
                        clus
vv                       DEL PEAK 29(13Q12.13) WILD-TYPE
  HISPANIC OR LATINO                                   4
  NOT HISPANIC OR LATINO                             147
[1] 2 2
[1] FALSE

Clustering(59) Variable = DEL PEAK 30(13Q14.2) MUTATION ANALYSIS
D59V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 30(13Q14.2) MUTATED   179  46
  DEL PEAK 30(13Q14.2) WILD-TYPE 150  41
  DEL PEAK 30(13Q14.2) MUTATED DEL PEAK 30(13Q14.2) WILD-TYPE 
                           225                            191 
  DEL PEAK 30(13Q14.2) MUTATED DEL PEAK 30(13Q14.2) WILD-TYPE 
                            46                             41 
$`DEL PEAK 30(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          705           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          600            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-95-7562 TCGA-95-7567 
         372           36          186           34         1973          568 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VN 
         377          477          476          830           84          553 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7554 TCGA-97-8174 TCGA-97-8177 TCGA-97-8547 
         605          964          775         1965          147          148 
TCGA-97-8552 TCGA-97-A4M2 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
         115          197          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-A4E5 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 
         578          116            6          312          111          102 
TCGA-MP-A4SV TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TC 
        1946         1951         1954         1957         1980         1944 
TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TK 
        1970         1955         1971 

$`DEL PEAK 30(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-49-AARQ TCGA-50-5049 TCGA-50-5055 TCGA-50-5072 TCGA-50-5932 
         522         6443         2146          785          246         1091 
TCGA-50-5942 TCGA-53-7624 TCGA-53-7626 TCGA-55-1594 TCGA-55-6543 TCGA-55-6969 
         883         1986         1971         1178            2         1239 
TCGA-55-6983 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7574 TCGA-55-7725 
        1826           18           35          121           95           39 
TCGA-55-7726 TCGA-55-7728 TCGA-55-7907 TCGA-55-7910 TCGA-55-7914 TCGA-55-8085 
          39           24           16          197            3           33 
TCGA-55-8087 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 
         462           26           47           15           33           46 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8505 TCGA-55-8512 TCGA-55-8513 TCGA-55-8616 
         674          216           29            3          146           48 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A492 
          49           66          106           33           42            1 
TCGA-55-A4DF TCGA-62-8398 TCGA-62-8402 TCGA-64-1680 TCGA-64-5775 TCGA-64-5815 
          47         1970         1445         1126           62          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-73-A9RS TCGA-75-6214 
         131          164           38          621          305         1970 
TCGA-75-7025 TCGA-75-7027 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        1967         1956         1944         1093         1963         1202 
TCGA-78-7153 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7162 TCGA-78-7163 
         760         1961         1963         1221         1940         1950 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7537 TCGA-78-7540 
        1934         1937         1965         1972         1944          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-86-8073 TCGA-86-8074 TCGA-86-8076 
        1972         1968         1963           13           24          489 
TCGA-86-8278 TCGA-86-8281 TCGA-86-8672 TCGA-86-8674 TCGA-86-A4P7 TCGA-86-A4P8 
         476         1955           15          405           14           39 
TCGA-91-6830 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
          60          842          224           35          492          505 
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-97-A4M7 TCGA-L4-A4E6 
         107          182           87           15          271          435 
TCGA-L9-A50W TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T7 
         266          827         1175           84         1967         1954 
TCGA-MP-A4TA TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A5C7 TCGA-S2-AA1A 
        1951         1970          142         1490          121 

  DEL PEAK 30(13Q14.2) MUTATED DEL PEAK 30(13Q14.2) WILD-TYPE 
                             4                              1 
  DEL PEAK 30(13Q14.2) MUTATED DEL PEAK 30(13Q14.2) WILD-TYPE 
                          2696                           6443 
  DEL PEAK 30(13Q14.2) MUTATED DEL PEAK 30(13Q14.2) WILD-TYPE 
                           467                            489 
[1] "4.0 - 2696.0 (467.0)" "1.0 - 6443.0 (489.0)"
[1] "hr=" "1"  
D59V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 30(13Q14.2) MUTATED         3       57       73        29        40
  DEL PEAK 30(13Q14.2) WILD-TYPE       2       59       59        20        30
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 30(13Q14.2) MUTATED           38          6       13
  DEL PEAK 30(13Q14.2) WILD-TYPE         30          5       11
D59V3, multiclass
            clus
vv           DEL PEAK 30(13Q14.2) MUTATED DEL PEAK 30(13Q14.2) WILD-TYPE
  STAGE I                               3                              2
  STAGE IA                             57                             59
  STAGE IB                             73                             59
  STAGE IIA                            29                             20
  STAGE IIB                            40                             30
  STAGE IIIA                           38                             30
  STAGE IIIB                            6                              5
  STAGE IV                             13                             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 30(13Q14.2) MUTATED    73 155  21   9
  DEL PEAK 30(13Q14.2) WILD-TYPE  74 112  21   9
D59V4, multiclass
    clus
vv   DEL PEAK 30(13Q14.2) MUTATED DEL PEAK 30(13Q14.2) WILD-TYPE
  T1                           73                             74
  T2                          155                            112
  T3                           21                             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 30(13Q14.2) MUTATED   161  53    41
  DEL PEAK 30(13Q14.2) WILD-TYPE 140  38    33
D59V5, multiclass
       clus
vv      DEL PEAK 30(13Q14.2) MUTATED DEL PEAK 30(13Q14.2) WILD-TYPE
  N0                             161                            140
  N1                              53                             38
  N2+N3                           41                             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 30(13Q14.2) MUTATED   174  11   0   1  71
  DEL PEAK 30(13Q14.2) WILD-TYPE 152   7   1   3  52
D59V6, multiclass
     clus
vv    DEL PEAK 30(13Q14.2) MUTATED DEL PEAK 30(13Q14.2) WILD-TYPE
  M0                           174                            152
  M1                            11                              7
  M1A                            0                              1
  M1B                            1                              3
  MX                            71                             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"
D59V7, binary
                                cls
clus                               0   1
  DEL PEAK 30(13Q14.2) MUTATED   135 124
  DEL PEAK 30(13Q14.2) WILD-TYPE 120  97
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(13Q14.2) MUTATED    135  124
  DEL PEAK 30(13Q14.2) WILD-TYPE  120   97
        clus
vv       DEL PEAK 30(13Q14.2) MUTATED DEL PEAK 30(13Q14.2) WILD-TYPE
  FEMALE                          135                            120
  MALE                            124                             97
[1] 2 2
[1] FALSE
D59V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 30(13Q14.2) MUTATED                           11
  DEL PEAK 30(13Q14.2) WILD-TYPE                          4
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 30(13Q14.2) MUTATED                                  49
  DEL PEAK 30(13Q14.2) WILD-TYPE                                45
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 30(13Q14.2) MUTATED                                                  168
  DEL PEAK 30(13Q14.2) WILD-TYPE                                                135
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 30(13Q14.2) MUTATED                                            1
  DEL PEAK 30(13Q14.2) WILD-TYPE                                          4
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 30(13Q14.2) MUTATED                                              11
  DEL PEAK 30(13Q14.2) WILD-TYPE                                             8
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 30(13Q14.2) MUTATED                                2
  DEL PEAK 30(13Q14.2) WILD-TYPE                              0
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 30(13Q14.2) MUTATED                                    2
  DEL PEAK 30(13Q14.2) WILD-TYPE                                  2
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 30(13Q14.2) MUTATED                              0
  DEL PEAK 30(13Q14.2) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 30(13Q14.2) MUTATED                               9
  DEL PEAK 30(13Q14.2) WILD-TYPE                            10
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 30(13Q14.2) MUTATED                                 1
  DEL PEAK 30(13Q14.2) WILD-TYPE                               0
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 30(13Q14.2) MUTATED                                               3
  DEL PEAK 30(13Q14.2) WILD-TYPE                                             2
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 30(13Q14.2) MUTATED                              2
  DEL PEAK 30(13Q14.2) WILD-TYPE                            5
D59V9, multiclass
                                                    clus
vv                                                   DEL PEAK 30(13Q14.2) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            49
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          168
  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                                 3
  MUCINOUS (COLLOID) CARCINOMA                                                  2
                                                    clus
vv                                                   DEL PEAK 30(13Q14.2) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              45
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            135
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                   8
  LUNG CLEAR CELL ADENOCARCINOMA                                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              2
  LUNG MUCINOUS ADENOCARCINOMA                                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                                  10
  LUNG SIGNET RING ADENOCARCINOMA                                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                   2
  MUCINOUS (COLLOID) CARCINOMA                                                    5
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V10, binary
                                cls
clus                               0   1
  DEL PEAK 30(13Q14.2) MUTATED    10 249
  DEL PEAK 30(13Q14.2) WILD-TYPE  11 206
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(13Q14.2) MUTATED     10  249
  DEL PEAK 30(13Q14.2) WILD-TYPE   11  206
     clus
vv    DEL PEAK 30(13Q14.2) MUTATED DEL PEAK 30(13Q14.2) WILD-TYPE
  NO                            10                             11
  YES                          249                            206
[1] 2 2
[1] FALSE
D59V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 30(13Q14.2) MUTATED   181   7   2  12
  DEL PEAK 30(13Q14.2) WILD-TYPE 146   5   2   9
D59V12, multiclass
    clus
vv   DEL PEAK 30(13Q14.2) MUTATED DEL PEAK 30(13Q14.2) WILD-TYPE
  R0                          181                            146
  R1                            7                              5
  R2                            2                              2
  RX                           12                              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 30(13Q14.2) MUTATED                                  1     5
  DEL PEAK 30(13Q14.2) WILD-TYPE                                0     1
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 30(13Q14.2) MUTATED                          20   199
  DEL PEAK 30(13Q14.2) WILD-TYPE                        15   168
D59V13, multiclass
                                  clus
vv                                 DEL PEAK 30(13Q14.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  20
  WHITE                                                     199
                                  clus
vv                                 DEL PEAK 30(13Q14.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         1
  BLACK OR AFRICAN AMERICAN                                    15
  WHITE                                                       168
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V14, binary
                                cls
clus                               0   1
  DEL PEAK 30(13Q14.2) MUTATED     4 192
  DEL PEAK 30(13Q14.2) WILD-TYPE   3 153
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(13Q14.2) MUTATED      4  192
  DEL PEAK 30(13Q14.2) WILD-TYPE    3  153
                        clus
vv                       DEL PEAK 30(13Q14.2) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          192
                        clus
vv                       DEL PEAK 30(13Q14.2) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            153
[1] 2 2
[1] FALSE

Clustering(60) Variable = DEL PEAK 31(13Q34) MUTATION ANALYSIS
D60V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 31(13Q34) MUTATED   152  41
  DEL PEAK 31(13Q34) WILD-TYPE 177  46
  DEL PEAK 31(13Q34) MUTATED DEL PEAK 31(13Q34) WILD-TYPE 
                         193                          223 
  DEL PEAK 31(13Q34) MUTATED DEL PEAK 31(13Q34) WILD-TYPE 
                          41                           46 
$`DEL PEAK 31(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          705 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 TCGA-55-8090 TCGA-55-8091 TCGA-55-8207 
          54           19           21            6          600           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-95-7562 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
         186           34         1973          476          830           84 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7554 TCGA-97-8171 TCGA-97-8174 TCGA-97-8547 
         553          605          775          107         1965          148 
TCGA-97-8552 TCGA-97-A4M2 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
         115          197          392          427          459           44 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L4-A4E5 
         170          154          114          287          238          578 
TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MP-A4SV 
         116            6          312          111          102         1946 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T9 TCGA-MP-A4TC TCGA-MP-A4TF TCGA-MP-A4TI 
        1951         1954         1980         1944         1970         1955 
TCGA-MP-A4TK 
        1971 

$`DEL PEAK 31(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-49-AARQ TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 
         522         6443         2174         2146          785          944 
TCGA-50-5072 TCGA-50-5932 TCGA-50-5942 TCGA-53-7624 TCGA-53-7626 TCGA-55-1594 
         246         1091          883         1986         1971         1178 
TCGA-55-6543 TCGA-55-6969 TCGA-55-6983 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
           2         1239         1826           18           35          121 
TCGA-55-7574 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7907 
          95           39           39           34           24           16 
TCGA-55-7910 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
         197            3           31            5           33          462 
TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 
         100           26            4           47           15           33 
TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 
          46          674          216           29            8           15 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
           9            3          146           49           66          106 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A492 TCGA-55-A494 
          33           42           29           48            1            5 
TCGA-55-A4DF TCGA-62-8398 TCGA-62-8402 TCGA-62-A46U TCGA-64-1680 TCGA-64-5774 
          47         1970         1445         2067         1126         1959 
TCGA-64-5778 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 
        1305          866          610          573          427          385 
TCGA-67-6215 TCGA-67-6216 TCGA-69-7763 TCGA-69-7973 TCGA-69-7974 TCGA-69-7980 
         174          141          690          230          184          382 
TCGA-69-8253 TCGA-69-8254 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
         100           77          131          164           38          621 
TCGA-73-A9RS TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 TCGA-78-7147 
         305         1970         1967         1956         1965         1950 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7155 
        1944         1093         1963         1202          760         1957 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
        1961         1963         1221         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-78-7542 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 TCGA-80-5607 TCGA-80-5608 
        1952          994         1971         1981         1965         1972 
TCGA-86-6851 TCGA-86-7714 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
        1959         1968         1963           13           24          479 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8358 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 
         489          476           19           18          455          405 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6830 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
          14           39           60          842          224           35 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
         492          505          174           44          218          297 
TCGA-93-7348 TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-A4VK 
         127            2          568          377          477          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-97-8172 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-A4M7 TCGA-J2-A4AE 
         182           87          147           15          271          282 
TCGA-L4-A4E6 TCGA-L9-A50W TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SW 
         435          266          827         1175           84         1967 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A5C7 
        1954         1957         1951         1970          142         1490 
TCGA-S2-AA1A 
         121 

  DEL PEAK 31(13Q34) MUTATED DEL PEAK 31(13Q34) WILD-TYPE 
                           4                            1 
  DEL PEAK 31(13Q34) MUTATED DEL PEAK 31(13Q34) WILD-TYPE 
                        2696                         6443 
  DEL PEAK 31(13Q34) MUTATED DEL PEAK 31(13Q34) WILD-TYPE 
                         467                          477 
[1] "4.0 - 2696.0 (467.0)" "1.0 - 6443.0 (477.0)"
[1] "hr=" "1.2"
D60V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 31(13Q34) MUTATED         3       49       61        23        35
  DEL PEAK 31(13Q34) WILD-TYPE       2       67       71        26        35
                              vv
clus                           STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 31(13Q34) MUTATED           34          4       12
  DEL PEAK 31(13Q34) WILD-TYPE         34          7       12
D60V3, multiclass
            clus
vv           DEL PEAK 31(13Q34) MUTATED DEL PEAK 31(13Q34) WILD-TYPE
  STAGE I                             3                            2
  STAGE IA                           49                           67
  STAGE IB                           61                           71
  STAGE IIA                          23                           26
  STAGE IIB                          35                           35
  STAGE IIIA                         34                           34
  STAGE IIIB                          4                            7
  STAGE IV                           12                           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 31(13Q34) MUTATED    60 130  21   9
  DEL PEAK 31(13Q34) WILD-TYPE  87 137  21   9
D60V4, multiclass
    clus
vv   DEL PEAK 31(13Q34) MUTATED DEL PEAK 31(13Q34) WILD-TYPE
  T1                         60                           87
  T2                        130                          137
  T3                         21                           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 31(13Q34) MUTATED   138  43    35
  DEL PEAK 31(13Q34) WILD-TYPE 163  48    39
D60V5, multiclass
       clus
vv      DEL PEAK 31(13Q34) MUTATED DEL PEAK 31(13Q34) WILD-TYPE
  N0                           138                          163
  N1                            43                           48
  N2+N3                         35                           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 31(13Q34) MUTATED   147  10   1   0  61
  DEL PEAK 31(13Q34) WILD-TYPE 179   8   0   4  62
D60V6, multiclass
     clus
vv    DEL PEAK 31(13Q34) MUTATED DEL PEAK 31(13Q34) WILD-TYPE
  M0                         147                          179
  M1                          10                            8
  M1A                          1                            0
  M1B                          0                            4
  MX                          61                           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"
D60V7, binary
                              cls
clus                             0   1
  DEL PEAK 31(13Q34) MUTATED   115 106
  DEL PEAK 31(13Q34) WILD-TYPE 140 115
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 31(13Q34) MUTATED    115  106
  DEL PEAK 31(13Q34) WILD-TYPE  140  115
        clus
vv       DEL PEAK 31(13Q34) MUTATED DEL PEAK 31(13Q34) WILD-TYPE
  FEMALE                        115                          140
  MALE                          106                          115
[1] 2 2
[1] FALSE
D60V8, continuous
                              vv
clus                           LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 31(13Q34) MUTATED                           10
  DEL PEAK 31(13Q34) WILD-TYPE                          5
                              vv
clus                           LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 31(13Q34) MUTATED                                  38
  DEL PEAK 31(13Q34) WILD-TYPE                                56
                              vv
clus                           LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 31(13Q34) MUTATED                                                  147
  DEL PEAK 31(13Q34) WILD-TYPE                                                156
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 31(13Q34) MUTATED                                            1
  DEL PEAK 31(13Q34) WILD-TYPE                                          4
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 31(13Q34) MUTATED                                               8
  DEL PEAK 31(13Q34) WILD-TYPE                                            11
                              vv
clus                           LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 31(13Q34) MUTATED                                1
  DEL PEAK 31(13Q34) WILD-TYPE                              1
                              vv
clus                           LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 31(13Q34) MUTATED                                    2
  DEL PEAK 31(13Q34) WILD-TYPE                                  2
                              vv
clus                           LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 31(13Q34) MUTATED                              0
  DEL PEAK 31(13Q34) WILD-TYPE                            2
                              vv
clus                           LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 31(13Q34) MUTATED                               9
  DEL PEAK 31(13Q34) WILD-TYPE                            10
                              vv
clus                           LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 31(13Q34) MUTATED                                 0
  DEL PEAK 31(13Q34) WILD-TYPE                               1
                              vv
clus                           LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 31(13Q34) MUTATED                                               4
  DEL PEAK 31(13Q34) WILD-TYPE                                             1
                              vv
clus                           MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 31(13Q34) MUTATED                              1
  DEL PEAK 31(13Q34) WILD-TYPE                            6
D60V9, multiclass
                                                    clus
vv                                                   DEL PEAK 31(13Q34) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                 10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                          38
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                        147
  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                               4
  MUCINOUS (COLLOID) CARCINOMA                                                1
                                                    clus
vv                                                   DEL PEAK 31(13Q34) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                    5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            56
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          156
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                11
  LUNG CLEAR CELL ADENOCARCINOMA                                                1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            2
  LUNG MUCINOUS ADENOCARCINOMA                                                  2
  LUNG PAPILLARY ADENOCARCINOMA                                                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"
D60V10, binary
                              cls
clus                             0   1
  DEL PEAK 31(13Q34) MUTATED     8 213
  DEL PEAK 31(13Q34) WILD-TYPE  13 242
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 31(13Q34) MUTATED      8  213
  DEL PEAK 31(13Q34) WILD-TYPE   13  242
     clus
vv    DEL PEAK 31(13Q34) MUTATED DEL PEAK 31(13Q34) WILD-TYPE
  NO                           8                           13
  YES                        213                          242
[1] 2 2
[1] FALSE
D60V11, continuous
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 31(13Q34) MUTATED   147   7   2  12
  DEL PEAK 31(13Q34) WILD-TYPE 180   5   2   9
D60V12, multiclass
    clus
vv   DEL PEAK 31(13Q34) MUTATED DEL PEAK 31(13Q34) WILD-TYPE
  R0                        147                          180
  R1                          7                            5
  R2                          2                            2
  RX                         12                            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 31(13Q34) MUTATED                                  1     6
  DEL PEAK 31(13Q34) WILD-TYPE                                0     0
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 31(13Q34) MUTATED                          18   166
  DEL PEAK 31(13Q34) WILD-TYPE                        17   201
D60V13, multiclass
                                  clus
vv                                 DEL PEAK 31(13Q34) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          1
  ASIAN                                                     6
  BLACK OR AFRICAN AMERICAN                                18
  WHITE                                                   166
                                  clus
vv                                 DEL PEAK 31(13Q34) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                  17
  WHITE                                                     201
[1] 4 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 31(13Q34) MUTATED     3 164
  DEL PEAK 31(13Q34) WILD-TYPE   4 181
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 31(13Q34) MUTATED      3  164
  DEL PEAK 31(13Q34) WILD-TYPE    4  181
                        clus
vv                       DEL PEAK 31(13Q34) MUTATED
  HISPANIC OR LATINO                              3
  NOT HISPANIC OR LATINO                        164
                        clus
vv                       DEL PEAK 31(13Q34) WILD-TYPE
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          181
[1] 2 2
[1] FALSE

Clustering(61) Variable = DEL PEAK 32(14Q32.33) MUTATION ANALYSIS
D61V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 32(14Q32.33) MUTATED    99  29
  DEL PEAK 32(14Q32.33) WILD-TYPE 230  58
  DEL PEAK 32(14Q32.33) MUTATED DEL PEAK 32(14Q32.33) WILD-TYPE 
                            128                             288 
  DEL PEAK 32(14Q32.33) MUTATED DEL PEAK 32(14Q32.33) WILD-TYPE 
                             29                              58 
$`DEL PEAK 32(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-73-A9RS TCGA-75-6214 TCGA-75-7027 TCGA-78-7146 TCGA-78-7147 
          40          305         1970         1956         1988         1950 
TCGA-78-7155 TCGA-78-7220 TCGA-78-7535 TCGA-78-8640 TCGA-78-8660 TCGA-86-7711 
        1957         1965         1972         1949         1954          630 
TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8056 
         422          591         1963          508          745         1963 
TCGA-86-8279 TCGA-86-8359 TCGA-86-8668 TCGA-86-8669 TCGA-86-8672 TCGA-86-A4D0 
         482           26           45           34           15           30 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6848 TCGA-91-7771 TCGA-91-8497 TCGA-93-7347 
        1940           60          224          492          174          297 
TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-7948 TCGA-95-A4VN TCGA-95-A4VP 
          34          568          377          476          553          605 
TCGA-97-7546 TCGA-97-7547 TCGA-97-8174 TCGA-97-8177 TCGA-99-8025 TCGA-99-8028 
         964         1965         1965          147          427          459 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L9-A443 
          44          170          287          238          578          116 
TCGA-L9-A743 TCGA-L9-A7SV TCGA-MN-A4N1 TCGA-MP-A4SW TCGA-MP-A4T7 TCGA-MP-A4T8 
         312          111          827         1967         1954         1957 
TCGA-MP-A4TC TCGA-MP-A4TK 
        1944         1971 

$`DEL PEAK 32(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-49-AARQ 
         428          999          157          522          354         6443 
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-50-5930 TCGA-50-5932 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
         282         1091          567          883          764          686 
TCGA-50-7109 TCGA-50-8460 TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 
         255          105         1986          424          280         1178 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 
          87            2          993         1239           25         1475 
TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7284 
          67         1826         1233         2151         1170          121 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
           6            4           95           40          705           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          462          100 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8096 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
           6          600           47           33           46           66 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8507 
         674          216           44           23           11            8 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-8615 
         228            9            3          146          536           15 
TCGA-55-8616 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
          48           66          106           33           42           29 
TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 
          48           28            5           47          162         1216 
TCGA-62-8397 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46V TCGA-62-A472 TCGA-64-1676 
        1289         2696         1445         2199          910         1728 
TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
         628         1189         1686         1968         1959           62 
TCGA-64-5815 TCGA-67-3770 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
         866           31          573          427          174          141 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 
         690          414          230           70           89          100 
TCGA-69-8254 TCGA-69-8255 TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4666 
          77          129           61         1600          711          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-75-7025 TCGA-75-7031 TCGA-78-7145 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
        1967         1965         1973         1944         1093         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-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
         678          215         1940         1950         1934         1937 
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-78-8662 TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 
        1971         1981         1964         1965         1972          824 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7714 TCGA-86-8055 TCGA-86-8073 TCGA-86-8074 
        1959           11         1968           10           13           24 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8281 TCGA-86-8358 
         479          489          476           16         1955           19 
TCGA-86-8585 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 
          35           18          455          405           10           14 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
          39          323          310           79          417          372 
TCGA-91-6847 TCGA-91-6849 TCGA-91-8496 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
         842           35          505           36           44          218 
TCGA-93-7348 TCGA-93-8067 TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-8039 
         127          186            2         1973          477          830 
TCGA-95-8494 TCGA-95-A4VK TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
          84          121         1932         1332          775          181 
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-J2-8192 TCGA-J2-8194 
         115          197          271          392          154          114 
TCGA-J2-A4AE TCGA-L4-A4E6 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A8F4 TCGA-MN-A4N4 
         282          435            6          266          102         1175 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T9 TCGA-MP-A4TA 
          84         1946         1951         1954         1980         1951 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A5C7 TCGA-S2-AA1A 
        1970         1970          142         1955         1490          121 

  DEL PEAK 32(14Q32.33) MUTATED DEL PEAK 32(14Q32.33) WILD-TYPE 
                              1                               2 
  DEL PEAK 32(14Q32.33) MUTATED DEL PEAK 32(14Q32.33) WILD-TYPE 
                           2370                            6443 
  DEL PEAK 32(14Q32.33) MUTATED DEL PEAK 32(14Q32.33) WILD-TYPE 
                          562.5                           455.0 
[1] "1.0 - 2370.0 (562.5)" "2.0 - 6443.0 (455.0)"
[1] "hr=" "1"  
D61V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 32(14Q32.33) MUTATED         2       27       32        19        29
  DEL PEAK 32(14Q32.33) WILD-TYPE       3       89      100        30        41
                                 vv
clus                              STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 32(14Q32.33) MUTATED           24          3        6
  DEL PEAK 32(14Q32.33) WILD-TYPE         44          8       18
D61V3, multiclass
            clus
vv           DEL PEAK 32(14Q32.33) MUTATED DEL PEAK 32(14Q32.33) WILD-TYPE
  STAGE I                                2                               3
  STAGE IA                              27                              89
  STAGE IB                              32                             100
  STAGE IIA                             19                              30
  STAGE IIB                             29                              41
  STAGE IIIA                            24                              44
  STAGE IIIB                             3                               8
  STAGE IV                               6                              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 32(14Q32.33) MUTATED    39  79  18   5
  DEL PEAK 32(14Q32.33) WILD-TYPE 108 188  24  13
D61V4, multiclass
    clus
vv   DEL PEAK 32(14Q32.33) MUTATED DEL PEAK 32(14Q32.33) WILD-TYPE
  T1                            39                             108
  T2                            79                             188
  T3                            18                              24
  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 32(14Q32.33) MUTATED    79  38    24
  DEL PEAK 32(14Q32.33) WILD-TYPE 222  53    50
D61V5, multiclass
       clus
vv      DEL PEAK 32(14Q32.33) MUTATED DEL PEAK 32(14Q32.33) WILD-TYPE
  N0                               79                             222
  N1                               38                              53
  N2+N3                            24                              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 32(14Q32.33) MUTATED   102   4   0   1  34
  DEL PEAK 32(14Q32.33) WILD-TYPE 224  14   1   3  89
D61V6, multiclass
     clus
vv    DEL PEAK 32(14Q32.33) MUTATED DEL PEAK 32(14Q32.33) WILD-TYPE
  M0                            102                             224
  M1                              4                              14
  M1A                             0                               1
  M1B                             1                               3
  MX                             34                              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"
D61V7, binary
                                 cls
clus                                0   1
  DEL PEAK 32(14Q32.33) MUTATED    73  69
  DEL PEAK 32(14Q32.33) WILD-TYPE 182 152
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(14Q32.33) MUTATED     73   69
  DEL PEAK 32(14Q32.33) WILD-TYPE  182  152
        clus
vv       DEL PEAK 32(14Q32.33) MUTATED DEL PEAK 32(14Q32.33) WILD-TYPE
  FEMALE                            73                             182
  MALE                              69                             152
[1] 2 2
[1] FALSE
D61V8, continuous
                                 vv
clus                              LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 32(14Q32.33) MUTATED                            6
  DEL PEAK 32(14Q32.33) WILD-TYPE                          9
                                 vv
clus                              LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 32(14Q32.33) MUTATED                                  26
  DEL PEAK 32(14Q32.33) WILD-TYPE                                68
                                 vv
clus                              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 32(14Q32.33) MUTATED                                                   93
  DEL PEAK 32(14Q32.33) WILD-TYPE                                                210
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 32(14Q32.33) MUTATED                                            1
  DEL PEAK 32(14Q32.33) WILD-TYPE                                          4
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 32(14Q32.33) MUTATED                                               4
  DEL PEAK 32(14Q32.33) WILD-TYPE                                            15
                                 vv
clus                              LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 32(14Q32.33) MUTATED                                2
  DEL PEAK 32(14Q32.33) WILD-TYPE                              0
                                 vv
clus                              LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 32(14Q32.33) MUTATED                                    0
  DEL PEAK 32(14Q32.33) WILD-TYPE                                  4
                                 vv
clus                              LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 32(14Q32.33) MUTATED                              1
  DEL PEAK 32(14Q32.33) WILD-TYPE                            1
                                 vv
clus                              LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 32(14Q32.33) MUTATED                               4
  DEL PEAK 32(14Q32.33) WILD-TYPE                            15
                                 vv
clus                              LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 32(14Q32.33) MUTATED                                 0
  DEL PEAK 32(14Q32.33) WILD-TYPE                               1
                                 vv
clus                              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 32(14Q32.33) MUTATED                                               1
  DEL PEAK 32(14Q32.33) WILD-TYPE                                             4
                                 vv
clus                              MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 32(14Q32.33) MUTATED                              4
  DEL PEAK 32(14Q32.33) WILD-TYPE                            3
D61V9, multiclass
                                                    clus
vv                                                   DEL PEAK 32(14Q32.33) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                     6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             26
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            93
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  4
  LUNG CLEAR CELL ADENOCARCINOMA                                                 2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             0
  LUNG MUCINOUS ADENOCARCINOMA                                                   1
  LUNG PAPILLARY ADENOCARCINOMA                                                  4
  LUNG SIGNET RING ADENOCARCINOMA                                                0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                  1
  MUCINOUS (COLLOID) CARCINOMA                                                   4
                                                    clus
vv                                                   DEL PEAK 32(14Q32.33) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                       9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                               68
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             210
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                       4
  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"
D61V10, binary
                                 cls
clus                                0   1
  DEL PEAK 32(14Q32.33) MUTATED     8 134
  DEL PEAK 32(14Q32.33) WILD-TYPE  13 321
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(14Q32.33) MUTATED      8  134
  DEL PEAK 32(14Q32.33) WILD-TYPE   13  321
     clus
vv    DEL PEAK 32(14Q32.33) MUTATED DEL PEAK 32(14Q32.33) WILD-TYPE
  NO                              8                              13
  YES                           134                             321
[1] 2 2
[1] FALSE
D61V11, continuous
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 32(14Q32.33) MUTATED    97   0   0   6
  DEL PEAK 32(14Q32.33) WILD-TYPE 230  12   4  15
D61V12, multiclass
    clus
vv   DEL PEAK 32(14Q32.33) MUTATED DEL PEAK 32(14Q32.33) WILD-TYPE
  R0                            97                             230
  R1                             0                              12
  R2                             0                               4
  RX                             6                              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 32(14Q32.33) MUTATED                                  0     2
  DEL PEAK 32(14Q32.33) WILD-TYPE                                1     4
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 32(14Q32.33) MUTATED                          19   101
  DEL PEAK 32(14Q32.33) WILD-TYPE                        16   266
D61V13, multiclass
                                  clus
vv                                 DEL PEAK 32(14Q32.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   19
  WHITE                                                      101
                                  clus
vv                                 DEL PEAK 32(14Q32.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          4
  BLACK OR AFRICAN AMERICAN                                     16
  WHITE                                                        266
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V14, binary
                                 cls
clus                                0   1
  DEL PEAK 32(14Q32.33) MUTATED     3 106
  DEL PEAK 32(14Q32.33) WILD-TYPE   4 239
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(14Q32.33) MUTATED      3  106
  DEL PEAK 32(14Q32.33) WILD-TYPE    4  239
                        clus
vv                       DEL PEAK 32(14Q32.33) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           106
                        clus
vv                       DEL PEAK 32(14Q32.33) WILD-TYPE
  HISPANIC OR LATINO                                   4
  NOT HISPANIC OR LATINO                             239
[1] 2 2
[1] FALSE

Clustering(62) Variable = DEL PEAK 33(15Q11.2) MUTATION ANALYSIS
D62V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 33(15Q11.2) MUTATED   173  39
  DEL PEAK 33(15Q11.2) WILD-TYPE 156  48
  DEL PEAK 33(15Q11.2) MUTATED DEL PEAK 33(15Q11.2) WILD-TYPE 
                           212                            204 
  DEL PEAK 33(15Q11.2) MUTATED DEL PEAK 33(15Q11.2) WILD-TYPE 
                            39                             48 
$`DEL PEAK 33(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-49-AARQ 
         157         1700          890          522          354         6443 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5066 TCGA-50-5933 TCGA-50-5935 
        2174         2146          455          944         2370          653 
TCGA-50-5941 TCGA-50-5946 TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 TCGA-53-7626 
         567          686         1015          255          105         1971 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6642 TCGA-55-6712 
         280          701         1479           87          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-55-7281 TCGA-55-7283 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7815 
          18           35           95           40           34           54 
TCGA-55-7903 TCGA-55-7910 TCGA-55-7914 TCGA-55-8089 TCGA-55-8091 TCGA-55-8094 
          19          197            3          100          600            4 
TCGA-55-8205 TCGA-55-8207 TCGA-55-8301 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
          33           66           44           11            8           15 
TCGA-55-8510 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48X 
         228          536           15           48           66           33 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A493 TCGA-55-A4DF TCGA-55-A4DG 
          29           48         1952           28           47          162 
TCGA-62-8397 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 
        1289          910         1728          628         1189         1686 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 TCGA-67-3770 TCGA-67-3771 
        1968         1959         1305          864           31          610 
TCGA-67-3772 TCGA-67-6217 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
         573          422          165          230          184           70 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-A59K TCGA-73-4659 TCGA-73-4662 
          89          382          100          214          711          912 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4675 TCGA-73-7499 TCGA-73-A9RS TCGA-75-6214 
         800          467           40          519          305         1970 
TCGA-75-7025 TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7153 
        1967         1965         1973         1988         1950          760 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7167 TCGA-78-7535 TCGA-78-7539 TCGA-78-7542 
        1963         1221         1937         1972          327         1952 
TCGA-78-8640 TCGA-80-5608 TCGA-86-6851 TCGA-86-7701 TCGA-86-7953 TCGA-86-7954 
        1949         1972         1959           11          591         1963 
TCGA-86-7955 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 TCGA-86-8358 
         508           13           24          479          482           19 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8669 TCGA-86-8671 TCGA-86-A456 TCGA-86-A4D0 
          26           35           34           18           10           30 
TCGA-91-6828 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-7771 TCGA-91-8499 
         323           79          372          842          492           36 
TCGA-91-A4BC TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7562 
          44          297          127          186           34         1973 
TCGA-95-7567 TCGA-95-8494 TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7554 
         568           84          553          605          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-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW 
         111          102          827         1175         1946         1967 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TF 
        1951         1954         1957         1944         1970         1970 
TCGA-MP-A4TI TCGA-MP-A4TK 
        1955         1971 

$`DEL PEAK 33(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          705           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          462 
TCGA-55-8090 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 
           6           26           47           15           46          674 
TCGA-55-8299 TCGA-55-8302 TCGA-55-8505 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
         216           23           29            9            3          146 
TCGA-55-8514 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48Y TCGA-55-A492 TCGA-55-A494 
         202           49          106           42            1            5 
TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46U TCGA-62-A46V 
        1216         1970         2696         1445         2067         2199 
TCGA-62-A471 TCGA-64-1680 TCGA-64-5775 TCGA-64-5781 TCGA-64-5815 TCGA-67-3773 
        1246         1126           62         1559          866          427 
TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
         385          174          141          202          186          690 
TCGA-69-7764 TCGA-69-8254 TCGA-69-8255 TCGA-71-6725 TCGA-73-4658 TCGA-73-4670 
         414           77          129           61         1600          131 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-75-7027 TCGA-78-7148 TCGA-78-7149 
         164           38          621         1956         1944         1093 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7160 
        1963         1202         1948         1957         1961          678 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7220 TCGA-78-7536 
         215         1940         1950         1934         1965         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-83-5908 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
        1964         1965          824          630          422         1968 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 
         745           10         1963          489          476           16 
TCGA-86-8281 TCGA-86-8668 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4P7 
        1955           45           15          455          405           14 
TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6836 TCGA-91-6848 
          39         1940           60          310          417          224 
TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD TCGA-95-7043 TCGA-95-7944 
          35          505          174          218            2          377 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-A4VK TCGA-97-7547 TCGA-97-7552 
         477          476          830          121         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-99-8025 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8194 
         115          197          427           44          170          114 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A743 TCGA-MN-A4N5 
         287          282          435          266          312           84 
TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TH TCGA-MP-A5C7 TCGA-S2-AA1A 
        1954         1980         1951          142         1490          121 

  DEL PEAK 33(15Q11.2) MUTATED DEL PEAK 33(15Q11.2) WILD-TYPE 
                             3                              1 
  DEL PEAK 33(15Q11.2) MUTATED DEL PEAK 33(15Q11.2) WILD-TYPE 
                          6443                           2696 
  DEL PEAK 33(15Q11.2) MUTATED DEL PEAK 33(15Q11.2) WILD-TYPE 
                         529.0                          444.5 
[1] "3.0 - 6443.0 (529.0)" "1.0 - 2696.0 (444.5)"
[1] "hr=" "1.3"
D62V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 33(15Q11.2) MUTATED         4       55       69        33        33
  DEL PEAK 33(15Q11.2) WILD-TYPE       1       61       63        16        37
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 33(15Q11.2) MUTATED           33          6       13
  DEL PEAK 33(15Q11.2) WILD-TYPE         35          5       11
D62V3, multiclass
            clus
vv           DEL PEAK 33(15Q11.2) MUTATED DEL PEAK 33(15Q11.2) WILD-TYPE
  STAGE I                               4                              1
  STAGE IA                             55                             61
  STAGE IB                             69                             63
  STAGE IIA                            33                             16
  STAGE IIB                            33                             37
  STAGE IIIA                           33                             35
  STAGE IIIB                            6                              5
  STAGE IV                             13                             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 33(15Q11.2) MUTATED    77 142  19   8
  DEL PEAK 33(15Q11.2) WILD-TYPE  70 125  23  10
D62V4, multiclass
    clus
vv   DEL PEAK 33(15Q11.2) MUTATED DEL PEAK 33(15Q11.2) WILD-TYPE
  T1                           77                             70
  T2                          142                            125
  T3                           19                             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 33(15Q11.2) MUTATED   151  51    39
  DEL PEAK 33(15Q11.2) WILD-TYPE 150  40    35
D62V5, multiclass
       clus
vv      DEL PEAK 33(15Q11.2) MUTATED DEL PEAK 33(15Q11.2) WILD-TYPE
  N0                             151                            150
  N1                              51                             40
  N2+N3                           39                             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 33(15Q11.2) MUTATED   173   9   0   3  60
  DEL PEAK 33(15Q11.2) WILD-TYPE 153   9   1   1  63
D62V6, multiclass
     clus
vv    DEL PEAK 33(15Q11.2) MUTATED DEL PEAK 33(15Q11.2) WILD-TYPE
  M0                           173                            153
  M1                             9                              9
  M1A                            0                              1
  M1B                            3                              1
  MX                            60                             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"
D62V7, binary
                                cls
clus                               0   1
  DEL PEAK 33(15Q11.2) MUTATED   135 111
  DEL PEAK 33(15Q11.2) WILD-TYPE 120 110
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(15Q11.2) MUTATED    135  111
  DEL PEAK 33(15Q11.2) WILD-TYPE  120  110
        clus
vv       DEL PEAK 33(15Q11.2) MUTATED DEL PEAK 33(15Q11.2) WILD-TYPE
  FEMALE                          135                            120
  MALE                            111                            110
[1] 2 2
[1] FALSE
D62V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 33(15Q11.2) MUTATED                            7
  DEL PEAK 33(15Q11.2) WILD-TYPE                          8
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 33(15Q11.2) MUTATED                                  42
  DEL PEAK 33(15Q11.2) WILD-TYPE                                52
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 33(15Q11.2) MUTATED                                                  169
  DEL PEAK 33(15Q11.2) WILD-TYPE                                                134
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 33(15Q11.2) MUTATED                                            0
  DEL PEAK 33(15Q11.2) WILD-TYPE                                          5
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 33(15Q11.2) MUTATED                                               7
  DEL PEAK 33(15Q11.2) WILD-TYPE                                            12
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 33(15Q11.2) MUTATED                                1
  DEL PEAK 33(15Q11.2) WILD-TYPE                              1
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 33(15Q11.2) MUTATED                                    3
  DEL PEAK 33(15Q11.2) WILD-TYPE                                  1
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 33(15Q11.2) MUTATED                              0
  DEL PEAK 33(15Q11.2) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 33(15Q11.2) MUTATED                              11
  DEL PEAK 33(15Q11.2) WILD-TYPE                             8
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 33(15Q11.2) MUTATED                                 1
  DEL PEAK 33(15Q11.2) WILD-TYPE                               0
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 33(15Q11.2) MUTATED                                               3
  DEL PEAK 33(15Q11.2) WILD-TYPE                                             2
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 33(15Q11.2) MUTATED                              2
  DEL PEAK 33(15Q11.2) WILD-TYPE                            5
D62V9, multiclass
                                                    clus
vv                                                   DEL PEAK 33(15Q11.2) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            42
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          169
  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                                 3
  MUCINOUS (COLLOID) CARCINOMA                                                  2
                                                    clus
vv                                                   DEL PEAK 33(15Q11.2) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              52
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            134
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      5
  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"
D62V10, binary
                                cls
clus                               0   1
  DEL PEAK 33(15Q11.2) MUTATED    10 236
  DEL PEAK 33(15Q11.2) WILD-TYPE  11 219
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(15Q11.2) MUTATED     10  236
  DEL PEAK 33(15Q11.2) WILD-TYPE   11  219
     clus
vv    DEL PEAK 33(15Q11.2) MUTATED DEL PEAK 33(15Q11.2) WILD-TYPE
  NO                            10                             11
  YES                          236                            219
[1] 2 2
[1] FALSE
D62V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 33(15Q11.2) MUTATED   169   8   2  12
  DEL PEAK 33(15Q11.2) WILD-TYPE 158   4   2   9
D62V12, multiclass
    clus
vv   DEL PEAK 33(15Q11.2) MUTATED DEL PEAK 33(15Q11.2) WILD-TYPE
  R0                          169                            158
  R1                            8                              4
  R2                            2                              2
  RX                           12                              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 33(15Q11.2) MUTATED                                  1     3
  DEL PEAK 33(15Q11.2) WILD-TYPE                                0     3
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 33(15Q11.2) MUTATED                          21   186
  DEL PEAK 33(15Q11.2) WILD-TYPE                        14   181
D62V13, multiclass
                                  clus
vv                                 DEL PEAK 33(15Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  21
  WHITE                                                     186
                                  clus
vv                                 DEL PEAK 33(15Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         3
  BLACK OR AFRICAN AMERICAN                                    14
  WHITE                                                       181
[1] 4 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 33(15Q11.2) MUTATED     3 176
  DEL PEAK 33(15Q11.2) WILD-TYPE   4 169
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(15Q11.2) MUTATED      3  176
  DEL PEAK 33(15Q11.2) WILD-TYPE    4  169
                        clus
vv                       DEL PEAK 33(15Q11.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          176
                        clus
vv                       DEL PEAK 33(15Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            169
[1] 2 2
[1] FALSE

Clustering(63) Variable = DEL PEAK 34(16Q23.1) MUTATION ANALYSIS
D63V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 34(16Q23.1) MUTATED   112  27
  DEL PEAK 34(16Q23.1) WILD-TYPE 217  60
  DEL PEAK 34(16Q23.1) MUTATED DEL PEAK 34(16Q23.1) WILD-TYPE 
                           139                            277 
  DEL PEAK 34(16Q23.1) MUTATED DEL PEAK 34(16Q23.1) WILD-TYPE 
                            27                             60 
$`DEL PEAK 34(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 
         705           39           34           19          600           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-95-7562 TCGA-95-7567 TCGA-95-8494 TCGA-95-A4VN TCGA-97-7546 
         186         1973          568           84          553          964 
TCGA-97-7554 TCGA-97-7937 TCGA-97-8171 TCGA-97-8175 TCGA-J2-A4AG TCGA-L4-A4E5 
         775          181          107           87          238          578 
TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A7SV TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4TC 
         116            6          111          827           84         1944 
TCGA-MP-A4TF 
        1970 

$`DEL PEAK 34(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-49-AARQ TCGA-50-5045 TCGA-50-5051 
         999          157         1700         6443         2174          455 
TCGA-50-5055 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5935 
         785          246          282          267         1091          653 
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-53-7626 TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 
        1971          701         1178         1375           87            2 
TCGA-55-6642 TCGA-55-6969 TCGA-55-6972 TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 
         993         1239         1475           67         1826         1233 
TCGA-55-6987 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        1170           35          121            6            4           95 
TCGA-55-7725 TCGA-55-7728 TCGA-55-7815 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
          39           24           54           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          462          100 
TCGA-55-8090 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 
           6           26            4           47           15           46 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8508 TCGA-55-8510 
         674          216           44           23           15          228 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-8615 TCGA-55-8619 
           9            3          146          536           15           49 
TCGA-55-8621 TCGA-55-A48Y TCGA-55-A492 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
         106           42            1            5           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-64-1678 TCGA-64-1680 TCGA-64-1681 TCGA-64-5775 TCGA-64-5781 TCGA-64-5815 
        1189         1126         1968           62         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-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 
         141          422          202          186          414          165 
TCGA-69-7973 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-73-4659 TCGA-73-4666 
         230          382          100           77          711          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-73-A9RS TCGA-75-7025 TCGA-75-7027 TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 
         305         1967         1956         1973         1950         1944 
TCGA-78-7149 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 
        1093          760         1948         1961         1963          678 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7537 TCGA-78-7539 
         215         1940         1950         1934         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-86-7701 TCGA-86-7714 
        1954         1964         1965         1972           11         1968 
TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 TCGA-86-8076 TCGA-86-8279 
         508           10         1963           24          489          482 
TCGA-86-8280 TCGA-86-8281 TCGA-86-8358 TCGA-86-8585 TCGA-86-8669 TCGA-86-8671 
          16         1955           19           35           34           18 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 
         455          405           10           30           14           39 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 
         323         1940           60          310           79          372 
TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD 
         224           35          505          174           44          218 
TCGA-93-7347 TCGA-95-7039 TCGA-95-7043 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
         297           34            2          377          477          476 
TCGA-95-8039 TCGA-95-A4VK TCGA-95-A4VP TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
         830          121          605         1965         1932         1332 
TCGA-97-7941 TCGA-97-8172 TCGA-97-8174 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
          22          182         1965          147           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-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
          44          170          154          114          287          282 
TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A743 TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4SV 
         435          266          312          102         1175         1946 
TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
        1967         1951         1954         1954         1957         1980 
TCGA-MP-A4TA TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
        1951         1970          142         1955         1971         1490 
TCGA-S2-AA1A 
         121 

  DEL PEAK 34(16Q23.1) MUTATED DEL PEAK 34(16Q23.1) WILD-TYPE 
                             6                              1 
  DEL PEAK 34(16Q23.1) MUTATED DEL PEAK 34(16Q23.1) WILD-TYPE 
                          2370                           6443 
  DEL PEAK 34(16Q23.1) MUTATED DEL PEAK 34(16Q23.1) WILD-TYPE 
                           610                            435 
[1] "6.0 - 2370.0 (610.0)" "1.0 - 6443.0 (435.0)"
[1] "hr=" "1.4"
D63V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 34(16Q23.1) MUTATED         1       29       48        17        26
  DEL PEAK 34(16Q23.1) WILD-TYPE       4       87       84        32        44
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 34(16Q23.1) MUTATED           24          6        8
  DEL PEAK 34(16Q23.1) WILD-TYPE         44          5       16
D63V3, multiclass
            clus
vv           DEL PEAK 34(16Q23.1) MUTATED DEL PEAK 34(16Q23.1) WILD-TYPE
  STAGE I                               1                              4
  STAGE IA                             29                             87
  STAGE IB                             48                             84
  STAGE IIA                            17                             32
  STAGE IIB                            26                             44
  STAGE IIIA                           24                             44
  STAGE IIIB                            6                              5
  STAGE IV                              8                             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 34(16Q23.1) MUTATED    43  96  15   5
  DEL PEAK 34(16Q23.1) WILD-TYPE 104 171  27  13
D63V4, multiclass
    clus
vv   DEL PEAK 34(16Q23.1) MUTATED DEL PEAK 34(16Q23.1) WILD-TYPE
  T1                           43                            104
  T2                           96                            171
  T3                           15                             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 34(16Q23.1) MUTATED    96  31    29
  DEL PEAK 34(16Q23.1) WILD-TYPE 205  60    45
D63V5, multiclass
       clus
vv      DEL PEAK 34(16Q23.1) MUTATED DEL PEAK 34(16Q23.1) WILD-TYPE
  N0                              96                            205
  N1                              31                             60
  N2+N3                           29                             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 34(16Q23.1) MUTATED   110   6   1   1  40
  DEL PEAK 34(16Q23.1) WILD-TYPE 216  12   0   3  83
D63V6, multiclass
     clus
vv    DEL PEAK 34(16Q23.1) MUTATED DEL PEAK 34(16Q23.1) WILD-TYPE
  M0                           110                            216
  M1                             6                             12
  M1A                            1                              0
  M1B                            1                              3
  MX                            40                             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"
D63V7, binary
                                cls
clus                               0   1
  DEL PEAK 34(16Q23.1) MUTATED    83  76
  DEL PEAK 34(16Q23.1) WILD-TYPE 172 145
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(16Q23.1) MUTATED     83   76
  DEL PEAK 34(16Q23.1) WILD-TYPE  172  145
        clus
vv       DEL PEAK 34(16Q23.1) MUTATED DEL PEAK 34(16Q23.1) WILD-TYPE
  FEMALE                           83                            172
  MALE                             76                            145
[1] 2 2
[1] FALSE
D63V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 34(16Q23.1) MUTATED                            7
  DEL PEAK 34(16Q23.1) WILD-TYPE                          8
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 34(16Q23.1) MUTATED                                  32
  DEL PEAK 34(16Q23.1) WILD-TYPE                                62
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 34(16Q23.1) MUTATED                                                  100
  DEL PEAK 34(16Q23.1) WILD-TYPE                                                203
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 34(16Q23.1) MUTATED                                            1
  DEL PEAK 34(16Q23.1) WILD-TYPE                                          4
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 34(16Q23.1) MUTATED                                               6
  DEL PEAK 34(16Q23.1) WILD-TYPE                                            13
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 34(16Q23.1) MUTATED                                2
  DEL PEAK 34(16Q23.1) WILD-TYPE                              0
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 34(16Q23.1) MUTATED                                    1
  DEL PEAK 34(16Q23.1) WILD-TYPE                                  3
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 34(16Q23.1) MUTATED                              0
  DEL PEAK 34(16Q23.1) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 34(16Q23.1) MUTATED                               5
  DEL PEAK 34(16Q23.1) WILD-TYPE                            14
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 34(16Q23.1) MUTATED                                 0
  DEL PEAK 34(16Q23.1) WILD-TYPE                               1
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 34(16Q23.1) MUTATED                                               3
  DEL PEAK 34(16Q23.1) WILD-TYPE                                             2
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 34(16Q23.1) MUTATED                              2
  DEL PEAK 34(16Q23.1) WILD-TYPE                            5
D63V9, multiclass
                                                    clus
vv                                                   DEL PEAK 34(16Q23.1) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            32
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          100
  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                                 3
  MUCINOUS (COLLOID) CARCINOMA                                                  2
                                                    clus
vv                                                   DEL PEAK 34(16Q23.1) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              62
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            203
  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                                                  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"
D63V10, binary
                                cls
clus                               0   1
  DEL PEAK 34(16Q23.1) MUTATED     9 150
  DEL PEAK 34(16Q23.1) WILD-TYPE  12 305
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(16Q23.1) MUTATED      9  150
  DEL PEAK 34(16Q23.1) WILD-TYPE   12  305
     clus
vv    DEL PEAK 34(16Q23.1) MUTATED DEL PEAK 34(16Q23.1) WILD-TYPE
  NO                             9                             12
  YES                          150                            305
[1] 2 2
[1] FALSE
D63V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 34(16Q23.1) MUTATED   108   2   1   8
  DEL PEAK 34(16Q23.1) WILD-TYPE 219  10   3  13
D63V12, multiclass
    clus
vv   DEL PEAK 34(16Q23.1) MUTATED DEL PEAK 34(16Q23.1) WILD-TYPE
  R0                          108                            219
  R1                            2                             10
  R2                            1                              3
  RX                            8                             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 34(16Q23.1) MUTATED                                  0     4
  DEL PEAK 34(16Q23.1) WILD-TYPE                                1     2
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 34(16Q23.1) MUTATED                          10   125
  DEL PEAK 34(16Q23.1) WILD-TYPE                        25   242
D63V13, multiclass
                                  clus
vv                                 DEL PEAK 34(16Q23.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  10
  WHITE                                                     125
                                  clus
vv                                 DEL PEAK 34(16Q23.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         2
  BLACK OR AFRICAN AMERICAN                                    25
  WHITE                                                       242
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V14, binary
                                cls
clus                               0   1
  DEL PEAK 34(16Q23.1) MUTATED     5 114
  DEL PEAK 34(16Q23.1) WILD-TYPE   2 231
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(16Q23.1) MUTATED      5  114
  DEL PEAK 34(16Q23.1) WILD-TYPE    2  231
                        clus
vv                       DEL PEAK 34(16Q23.1) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          114
                        clus
vv                       DEL PEAK 34(16Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            231
[1] 2 2
[1] FALSE

Clustering(64) Variable = DEL PEAK 35(17P13.3) MUTATION ANALYSIS
D64V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 35(17P13.3) MUTATED   181  42
  DEL PEAK 35(17P13.3) WILD-TYPE 148  45
  DEL PEAK 35(17P13.3) MUTATED DEL PEAK 35(17P13.3) WILD-TYPE 
                           223                            193 
  DEL PEAK 35(17P13.3) MUTATED DEL PEAK 35(17P13.3) WILD-TYPE 
                            42                             45 
$`DEL PEAK 35(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-49-AARQ TCGA-50-5049 TCGA-50-5051 TCGA-50-5068 
         522          354         6443         2146          455         1499 
TCGA-50-5931 TCGA-50-5941 TCGA-50-5944 TCGA-50-6597 TCGA-50-7109 TCGA-53-7624 
         267          567          764         1015          255         1986 
TCGA-53-7626 TCGA-53-7813 TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 
        1971          424          701         1178         1479         1375 
TCGA-55-6712 TCGA-55-6972 TCGA-55-6980 TCGA-55-6985 TCGA-55-7281 TCGA-55-7573 
          24         1475           67         1233           18            4 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7726 TCGA-55-7727 TCGA-55-7815 TCGA-55-7903 
          95           40           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-55-8089 TCGA-55-8091 TCGA-55-8094 TCGA-55-8097 TCGA-55-8205 TCGA-55-8207 
         100          600            4           15           33           66 
TCGA-55-8302 TCGA-55-8506 TCGA-55-8510 TCGA-55-8511 TCGA-55-8514 TCGA-55-8614 
          23           11          228            9          202          536 
TCGA-55-8620 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 TCGA-62-8397 
          66           33           42           29         1952         1289 
TCGA-62-A46U TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 
        2067          910         1728         1189         1686         1968 
TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 
        1959         1305          864          866           31          610 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
         573          427          174          422          202          186 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-8255 
         414          165          184           70           89          129 
TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4668 TCGA-73-4670 
         214           61         1600          711          467          131 
TCGA-73-7499 TCGA-73-A9RS TCGA-75-6214 TCGA-75-7025 TCGA-75-7031 TCGA-78-7145 
         519          305         1970         1967         1965         1973 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7150 TCGA-78-7154 TCGA-78-7159 TCGA-78-7535 
        1988         1950         1963         1948         1221         1972 
TCGA-78-7536 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8655 
        1949          327          881         1952         1949         1981 
TCGA-80-5608 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 
        1972         1959           11          630          422          591 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
        1963          508          745           10         1963           13 
TCGA-86-8075 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8668 
         479          476          482           16           19           45 
TCGA-86-8669 TCGA-91-6828 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
          34          323          310           79          417          372 
TCGA-91-6847 TCGA-91-7771 TCGA-91-A4BC TCGA-93-7347 TCGA-93-8067 TCGA-95-7039 
         842          492           44          297          186           34 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        1973          568          377          477          476          830 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7554 TCGA-97-7937 
          84          121          553          605          775          181 
TCGA-97-8175 TCGA-97-8547 TCGA-99-7458 TCGA-99-8025 TCGA-99-8033 TCGA-J2-8192 
          87          148          392          427          170          154 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L9-A443 TCGA-L9-A50W TCGA-L9-A743 
         287          282          578          116          266          312 
TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
         111          102          827         1175           84         1946 
TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
        1967         1954         1957         1970         1970          142 
TCGA-MP-A4TI 
        1955 

$`DEL PEAK 35(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          705           39 
TCGA-55-7728 TCGA-55-7907 TCGA-55-8087 TCGA-55-8090 TCGA-55-8092 TCGA-55-8096 
          24           16          462            6           26           47 
TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8507 
          46          674          216           44           29            8 
TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
          15            3          146           15           48           49 
TCGA-55-8621 TCGA-55-A490 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
         106           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-64-1680 TCGA-64-5775 TCGA-64-5781 TCGA-67-3774 
        1246          628         1126           62         1559          385 
TCGA-67-6216 TCGA-69-7763 TCGA-69-7973 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
         141          690          230          382          100           77 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
         912          800           40          164           38          621 
TCGA-75-7027 TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7155 
        1956         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-78-7633 TCGA-78-8648 
        1934         1937         1965         1944          994         1971 
TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 TCGA-83-5908 TCGA-86-7714 TCGA-86-8074 
        1954         1964         1965          824         1968           24 
TCGA-86-8076 TCGA-86-8281 TCGA-86-8359 TCGA-86-8585 TCGA-86-8671 TCGA-86-8672 
         489         1955           26           35           18           15 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 
         455          405           10           30           14           39 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 
        1940           60          224           35          505          174 
TCGA-91-8499 TCGA-91-A4BD TCGA-93-7348 TCGA-95-7043 TCGA-97-7546 TCGA-97-7547 
          36          218          127            2          964         1965 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        1932         1332           22          107          182         1965 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-8028 
         147           15          115          197          271          459 
TCGA-99-8032 TCGA-J2-8194 TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A444 TCGA-MP-A4T2 
          44          114          238          435            6         1951 
TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TK TCGA-MP-A5C7 
        1954         1980         1951         1944         1971         1490 
TCGA-S2-AA1A 
         121 

  DEL PEAK 35(17P13.3) MUTATED DEL PEAK 35(17P13.3) WILD-TYPE 
                             3                              1 
  DEL PEAK 35(17P13.3) MUTATED DEL PEAK 35(17P13.3) WILD-TYPE 
                          6443                           2696 
  DEL PEAK 35(17P13.3) MUTATED DEL PEAK 35(17P13.3) WILD-TYPE 
                           482                            455 
[1] "3.0 - 6443.0 (482.0)" "1.0 - 2696.0 (455.0)"
[1] "hr=" "1.3"
D64V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 35(17P13.3) MUTATED         3       50       75        33        40
  DEL PEAK 35(17P13.3) WILD-TYPE       2       66       57        16        30
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 35(17P13.3) MUTATED           37          7       14
  DEL PEAK 35(17P13.3) WILD-TYPE         31          4       10
D64V3, multiclass
            clus
vv           DEL PEAK 35(17P13.3) MUTATED DEL PEAK 35(17P13.3) WILD-TYPE
  STAGE I                               3                              2
  STAGE IA                             50                             66
  STAGE IB                             75                             57
  STAGE IIA                            33                             16
  STAGE IIB                            40                             30
  STAGE IIIA                           37                             31
  STAGE IIIB                            7                              4
  STAGE IV                             14                             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 35(17P13.3) MUTATED    69 160  19  10
  DEL PEAK 35(17P13.3) WILD-TYPE  78 107  23   8
D64V4, multiclass
    clus
vv   DEL PEAK 35(17P13.3) MUTATED DEL PEAK 35(17P13.3) WILD-TYPE
  T1                           69                             78
  T2                          160                            107
  T3                           19                             23
  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 35(17P13.3) MUTATED   160  54    40
  DEL PEAK 35(17P13.3) WILD-TYPE 141  37    34
D64V5, multiclass
       clus
vv      DEL PEAK 35(17P13.3) MUTATED DEL PEAK 35(17P13.3) WILD-TYPE
  N0                             160                            141
  N1                              54                             37
  N2+N3                           40                             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
  DEL PEAK 35(17P13.3) MUTATED   185  11   0   2  60
  DEL PEAK 35(17P13.3) WILD-TYPE 141   7   1   2  63
D64V6, multiclass
     clus
vv    DEL PEAK 35(17P13.3) MUTATED DEL PEAK 35(17P13.3) WILD-TYPE
  M0                           185                            141
  M1                            11                              7
  M1A                            0                              1
  M1B                            2                              2
  MX                            60                             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"
D64V7, binary
                                cls
clus                               0   1
  DEL PEAK 35(17P13.3) MUTATED   143 116
  DEL PEAK 35(17P13.3) WILD-TYPE 112 105
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(17P13.3) MUTATED    143  116
  DEL PEAK 35(17P13.3) WILD-TYPE  112  105
        clus
vv       DEL PEAK 35(17P13.3) MUTATED DEL PEAK 35(17P13.3) WILD-TYPE
  FEMALE                          143                            112
  MALE                            116                            105
[1] 2 2
[1] FALSE
D64V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 35(17P13.3) MUTATED                            9
  DEL PEAK 35(17P13.3) WILD-TYPE                          6
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 35(17P13.3) MUTATED                                  45
  DEL PEAK 35(17P13.3) WILD-TYPE                                49
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 35(17P13.3) MUTATED                                                  177
  DEL PEAK 35(17P13.3) WILD-TYPE                                                126
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 35(17P13.3) MUTATED                                            2
  DEL PEAK 35(17P13.3) WILD-TYPE                                          3
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 35(17P13.3) MUTATED                                               9
  DEL PEAK 35(17P13.3) WILD-TYPE                                            10
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 35(17P13.3) MUTATED                                2
  DEL PEAK 35(17P13.3) WILD-TYPE                              0
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 35(17P13.3) MUTATED                                    4
  DEL PEAK 35(17P13.3) WILD-TYPE                                  0
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 35(17P13.3) MUTATED                              0
  DEL PEAK 35(17P13.3) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 35(17P13.3) MUTATED                               5
  DEL PEAK 35(17P13.3) WILD-TYPE                            14
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 35(17P13.3) MUTATED                                 1
  DEL PEAK 35(17P13.3) WILD-TYPE                               0
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 35(17P13.3) MUTATED                                               4
  DEL PEAK 35(17P13.3) WILD-TYPE                                             1
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 35(17P13.3) MUTATED                              1
  DEL PEAK 35(17P13.3) WILD-TYPE                            6
D64V9, multiclass
                                                    clus
vv                                                   DEL PEAK 35(17P13.3) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            45
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          177
  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                                 4
  MUCINOUS (COLLOID) CARCINOMA                                                  1
                                                    clus
vv                                                   DEL PEAK 35(17P13.3) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              49
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            126
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  10
  LUNG CLEAR CELL ADENOCARCINOMA                                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              0
  LUNG MUCINOUS ADENOCARCINOMA                                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                                  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"
D64V10, binary
                                cls
clus                               0   1
  DEL PEAK 35(17P13.3) MUTATED     8 251
  DEL PEAK 35(17P13.3) WILD-TYPE  13 204
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(17P13.3) MUTATED      8  251
  DEL PEAK 35(17P13.3) WILD-TYPE   13  204
     clus
vv    DEL PEAK 35(17P13.3) MUTATED DEL PEAK 35(17P13.3) WILD-TYPE
  NO                             8                             13
  YES                          251                            204
[1] 2 2
[1] FALSE
D64V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 35(17P13.3) MUTATED   184   4   1  14
  DEL PEAK 35(17P13.3) WILD-TYPE 143   8   3   7
D64V12, multiclass
    clus
vv   DEL PEAK 35(17P13.3) MUTATED DEL PEAK 35(17P13.3) WILD-TYPE
  R0                          184                            143
  R1                            4                              8
  R2                            1                              3
  RX                           14                              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 35(17P13.3) MUTATED                                  1     4
  DEL PEAK 35(17P13.3) WILD-TYPE                                0     2
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 35(17P13.3) MUTATED                          21   193
  DEL PEAK 35(17P13.3) WILD-TYPE                        14   174
D64V13, multiclass
                                  clus
vv                                 DEL PEAK 35(17P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  21
  WHITE                                                     193
                                  clus
vv                                 DEL PEAK 35(17P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         2
  BLACK OR AFRICAN AMERICAN                                    14
  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"
D64V14, binary
                                cls
clus                               0   1
  DEL PEAK 35(17P13.3) MUTATED     5 181
  DEL PEAK 35(17P13.3) WILD-TYPE   2 164
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(17P13.3) MUTATED      5  181
  DEL PEAK 35(17P13.3) WILD-TYPE    2  164
                        clus
vv                       DEL PEAK 35(17P13.3) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          181
                        clus
vv                       DEL PEAK 35(17P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            164
[1] 2 2
[1] FALSE

Clustering(65) Variable = DEL PEAK 36(18Q21.32) MUTATION ANALYSIS
D65V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 36(18Q21.32) MUTATED   159  45
  DEL PEAK 36(18Q21.32) WILD-TYPE 170  42
  DEL PEAK 36(18Q21.32) MUTATED DEL PEAK 36(18Q21.32) WILD-TYPE 
                            204                             212 
  DEL PEAK 36(18Q21.32) MUTATED DEL PEAK 36(18Q21.32) WILD-TYPE 
                             45                              42 
$`DEL PEAK 36(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          462          100            6 
TCGA-55-8091 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8207 TCGA-55-8301 
         600            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-73-A9RS TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 
         519          305         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-83-5908 TCGA-86-6851 
        1972         1949          327         1954          824         1959 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7954 TCGA-86-8055 
          11          630          422         1968         1963           10 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
          13           24          479          476          482           16 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8672 TCGA-91-6829 TCGA-91-6830 
          19           26           35           15         1940           60 
TCGA-91-6831 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-7771 
         310          417          372          842          224          492 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7348 TCGA-95-7043 TCGA-95-7567 TCGA-95-7947 
          44          218          127            2          568          477 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VN TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
         830           84          553          964         1965         1932 
TCGA-97-7937 TCGA-97-7941 TCGA-97-8174 TCGA-97-8177 TCGA-97-8547 TCGA-97-8552 
         181           22         1965          147          148          115 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L9-A50W 
         170          154          114          287          282          266 
TCGA-L9-A743 TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SW 
         312          102          827         1175           84         1967 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TK 
        1951         1954         1954         1970         1955         1971 

$`DEL PEAK 36(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-49-AARQ 
        1081          896         1700          890          522         6443 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
        2174         2146          785          282          267         1091 
TCGA-50-5935 TCGA-50-5942 TCGA-50-5944 TCGA-50-7109 TCGA-50-8460 TCGA-53-7813 
         653          883          764          255          105          424 
TCGA-55-1592 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6969 TCGA-55-6983 
         701           87            2          993         1239         1826 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7284 TCGA-55-7570 TCGA-55-7724 TCGA-55-7815 
        2151         1170          121            6          705           54 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 TCGA-55-7914 TCGA-55-8085 TCGA-55-8092 
          19           16           21            3           33           26 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8302 TCGA-55-8506 
          33           46          674          216           23           11 
TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
          15            3          146          202          536           15 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A494 
          49           66          106           33           42            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-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-1680 TCGA-64-5774 TCGA-64-5779 
        1728          628         1189         1126         1959          864 
TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
         427          385          174          186          690          414 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7980 TCGA-69-8253 TCGA-69-8255 TCGA-71-6725 
         230          184          382          100          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-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-78-7162 TCGA-78-7163 TCGA-78-7166 
        1963         1221          678         1940         1950         1934 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        1937         1965         1944          881         1952          994 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 
        1949         1971         1981         1964         1965         1972 
TCGA-86-7953 TCGA-86-7955 TCGA-86-8054 TCGA-86-8056 TCGA-86-8076 TCGA-86-8281 
         591          508          745         1963          489         1955 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
          45           34           18          455          405           10 
TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6835 TCGA-91-6849 
          30           14           39          323           79           35 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-93-7347 TCGA-93-8067 TCGA-95-7039 
         505          174           36          297          186           34 
TCGA-95-7562 TCGA-95-7944 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VP TCGA-97-7553 
        1973          377          476          121          605         1332 
TCGA-97-7554 TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 TCGA-97-8179 TCGA-97-A4M2 
         775          107          182           87           15          197 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-J2-A4AG 
         271          392          427          459           44          238 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A7SV TCGA-MP-A4SV 
         578          435          116            6          111         1946 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TH 
        1957         1980         1951         1944         1970          142 
TCGA-MP-A5C7 TCGA-S2-AA1A 
        1490          121 

  DEL PEAK 36(18Q21.32) MUTATED DEL PEAK 36(18Q21.32) WILD-TYPE 
                              1                               2 
  DEL PEAK 36(18Q21.32) MUTATED DEL PEAK 36(18Q21.32) WILD-TYPE 
                           2370                            6443 
  DEL PEAK 36(18Q21.32) MUTATED DEL PEAK 36(18Q21.32) WILD-TYPE 
                          436.5                           528.5 
[1] "1.0 - 2370.0 (436.5)" "2.0 - 6443.0 (528.5)"
[1] "hr=" "1.2"
D65V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 36(18Q21.32) MUTATED         1       43       67        30        42
  DEL PEAK 36(18Q21.32) WILD-TYPE       4       73       65        19        28
                                 vv
clus                              STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 36(18Q21.32) MUTATED           31          6       14
  DEL PEAK 36(18Q21.32) WILD-TYPE         37          5       10
D65V3, multiclass
            clus
vv           DEL PEAK 36(18Q21.32) MUTATED DEL PEAK 36(18Q21.32) WILD-TYPE
  STAGE I                                1                               4
  STAGE IA                              43                              73
  STAGE IB                              67                              65
  STAGE IIA                             30                              19
  STAGE IIB                             42                              28
  STAGE IIIA                            31                              37
  STAGE IIIB                             6                               5
  STAGE IV                              14                              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 36(18Q21.32) MUTATED    63 139  22   9
  DEL PEAK 36(18Q21.32) WILD-TYPE  84 128  20   9
D65V4, multiclass
    clus
vv   DEL PEAK 36(18Q21.32) MUTATED DEL PEAK 36(18Q21.32) WILD-TYPE
  T1                            63                              84
  T2                           139                             128
  T3                            22                              20
  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 36(18Q21.32) MUTATED   141  56    33
  DEL PEAK 36(18Q21.32) WILD-TYPE 160  35    41
D65V5, multiclass
       clus
vv      DEL PEAK 36(18Q21.32) MUTATED DEL PEAK 36(18Q21.32) WILD-TYPE
  N0                              141                             160
  N1                               56                              35
  N2+N3                            33                              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 36(18Q21.32) MUTATED   150  12   0   1  70
  DEL PEAK 36(18Q21.32) WILD-TYPE 176   6   1   3  53
D65V6, multiclass
     clus
vv    DEL PEAK 36(18Q21.32) MUTATED DEL PEAK 36(18Q21.32) WILD-TYPE
  M0                            150                             176
  M1                             12                               6
  M1A                             0                               1
  M1B                             1                               3
  MX                             70                              53
[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 36(18Q21.32) MUTATED   131 104
  DEL PEAK 36(18Q21.32) WILD-TYPE 124 117
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 36(18Q21.32) MUTATED    131  104
  DEL PEAK 36(18Q21.32) WILD-TYPE  124  117
        clus
vv       DEL PEAK 36(18Q21.32) MUTATED DEL PEAK 36(18Q21.32) WILD-TYPE
  FEMALE                           131                             124
  MALE                             104                             117
[1] 2 2
[1] FALSE
D65V8, continuous
                                 vv
clus                              LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 36(18Q21.32) MUTATED                            8
  DEL PEAK 36(18Q21.32) WILD-TYPE                          7
                                 vv
clus                              LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 36(18Q21.32) MUTATED                                  46
  DEL PEAK 36(18Q21.32) WILD-TYPE                                48
                                 vv
clus                              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 36(18Q21.32) MUTATED                                                  153
  DEL PEAK 36(18Q21.32) WILD-TYPE                                                150
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 36(18Q21.32) MUTATED                                            1
  DEL PEAK 36(18Q21.32) WILD-TYPE                                          4
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 36(18Q21.32) MUTATED                                              10
  DEL PEAK 36(18Q21.32) WILD-TYPE                                             9
                                 vv
clus                              LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 36(18Q21.32) MUTATED                                2
  DEL PEAK 36(18Q21.32) WILD-TYPE                              0
                                 vv
clus                              LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 36(18Q21.32) MUTATED                                    3
  DEL PEAK 36(18Q21.32) WILD-TYPE                                  1
                                 vv
clus                              LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 36(18Q21.32) MUTATED                              1
  DEL PEAK 36(18Q21.32) WILD-TYPE                            1
                                 vv
clus                              LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 36(18Q21.32) MUTATED                               4
  DEL PEAK 36(18Q21.32) WILD-TYPE                            15
                                 vv
clus                              LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 36(18Q21.32) MUTATED                                 1
  DEL PEAK 36(18Q21.32) WILD-TYPE                               0
                                 vv
clus                              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 36(18Q21.32) MUTATED                                               3
  DEL PEAK 36(18Q21.32) WILD-TYPE                                             2
                                 vv
clus                              MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 36(18Q21.32) MUTATED                              3
  DEL PEAK 36(18Q21.32) WILD-TYPE                            4
D65V9, multiclass
                                                    clus
vv                                                   DEL PEAK 36(18Q21.32) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                     8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             46
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           153
  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                                  3
  MUCINOUS (COLLOID) CARCINOMA                                                   3
                                                    clus
vv                                                   DEL PEAK 36(18Q21.32) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                       7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                               48
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             150
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                    9
  LUNG CLEAR CELL ADENOCARCINOMA                                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                               1
  LUNG MUCINOUS ADENOCARCINOMA                                                     1
  LUNG PAPILLARY ADENOCARCINOMA                                                   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"
D65V10, binary
                                 cls
clus                                0   1
  DEL PEAK 36(18Q21.32) MUTATED     7 228
  DEL PEAK 36(18Q21.32) WILD-TYPE  14 227
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 36(18Q21.32) MUTATED      7  228
  DEL PEAK 36(18Q21.32) WILD-TYPE   14  227
     clus
vv    DEL PEAK 36(18Q21.32) MUTATED DEL PEAK 36(18Q21.32) WILD-TYPE
  NO                              7                              14
  YES                           228                             227
[1] 2 2
[1] FALSE
D65V11, continuous
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 36(18Q21.32) MUTATED   161   8   3   6
  DEL PEAK 36(18Q21.32) WILD-TYPE 166   4   1  15
D65V12, multiclass
    clus
vv   DEL PEAK 36(18Q21.32) MUTATED DEL PEAK 36(18Q21.32) WILD-TYPE
  R0                           161                             166
  R1                             8                               4
  R2                             3                               1
  RX                             6                              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 36(18Q21.32) MUTATED                                  0     2
  DEL PEAK 36(18Q21.32) WILD-TYPE                                1     4
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 36(18Q21.32) MUTATED                          15   181
  DEL PEAK 36(18Q21.32) WILD-TYPE                        20   186
D65V13, multiclass
                                  clus
vv                                 DEL PEAK 36(18Q21.32) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   15
  WHITE                                                      181
                                  clus
vv                                 DEL PEAK 36(18Q21.32) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          4
  BLACK OR AFRICAN AMERICAN                                     20
  WHITE                                                        186
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V14, binary
                                 cls
clus                                0   1
  DEL PEAK 36(18Q21.32) MUTATED     5 168
  DEL PEAK 36(18Q21.32) WILD-TYPE   2 177
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 36(18Q21.32) MUTATED      5  168
  DEL PEAK 36(18Q21.32) WILD-TYPE    2  177
                        clus
vv                       DEL PEAK 36(18Q21.32) MUTATED
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           168
                        clus
vv                       DEL PEAK 36(18Q21.32) WILD-TYPE
  HISPANIC OR LATINO                                   2
  NOT HISPANIC OR LATINO                             177
[1] 2 2
[1] FALSE

Clustering(66) Variable = DEL PEAK 37(18Q23) MUTATION ANALYSIS
D66V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 37(18Q23) MUTATED   160  45
  DEL PEAK 37(18Q23) WILD-TYPE 169  42
  DEL PEAK 37(18Q23) MUTATED DEL PEAK 37(18Q23) WILD-TYPE 
                         205                          211 
  DEL PEAK 37(18Q23) MUTATED DEL PEAK 37(18Q23) WILD-TYPE 
                          45                           42 
$`DEL PEAK 37(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          462          100            6 
TCGA-55-8091 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8207 TCGA-55-8301 
         600            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-73-A9RS TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 
         621          519          305         1970         1967         1956 
TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7150 TCGA-78-7155 
        1965         1973         1988         1950         1963         1957 
TCGA-78-7161 TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 TCGA-78-8660 TCGA-78-8662 
         215         1972         1949          327         1954         1964 
TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 TCGA-86-7954 
         824         1959           11          630         1968         1963 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8278 
         745           10           13           24          479          476 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8672 
         482           16           19           26           35           15 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6836 TCGA-91-6840 TCGA-91-6848 TCGA-91-7771 
        1940           60          417          372          224          492 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7348 TCGA-95-7039 TCGA-95-7567 
          36           44          218          127           34          568 
TCGA-95-7947 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VN TCGA-97-7546 TCGA-97-7552 
         477          830           84          553          964         1932 
TCGA-97-7937 TCGA-97-7941 TCGA-97-8174 TCGA-97-8177 TCGA-97-8547 TCGA-99-8025 
         181           22         1965          147          148          427 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L9-A50W 
         170          154          114          287          282          266 
TCGA-L9-A743 TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SW 
         312          102          827         1175           84         1967 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        1951         1954         1954         1970          142         1955 
TCGA-MP-A4TK 
        1971 

$`DEL PEAK 37(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-49-AARQ 
        1081          896         1700          890          522         6443 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
        2174         2146          785          282          267         1091 
TCGA-50-5935 TCGA-50-5942 TCGA-50-5944 TCGA-50-7109 TCGA-50-8460 TCGA-53-7813 
         653          883          764          255          105          424 
TCGA-55-1592 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6969 TCGA-55-6983 
         701           87            2          993         1239         1826 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7284 TCGA-55-7570 TCGA-55-7724 TCGA-55-7815 
        2151         1170          121            6          705           54 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 TCGA-55-7914 TCGA-55-8085 TCGA-55-8092 
          19           16           21            3           33           26 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8302 TCGA-55-8506 
          33           46          674          216           23           11 
TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
          15            3          146          202          536           15 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A494 
          49           66          106           33           42            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-64-1677 TCGA-64-1678 TCGA-64-1680 TCGA-64-5774 TCGA-64-5779 TCGA-67-3773 
         628         1189         1126         1959          864          427 
TCGA-67-3774 TCGA-67-6215 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 
         385          174          186          690          414          230 
TCGA-69-7974 TCGA-69-7980 TCGA-69-8253 TCGA-69-8255 TCGA-71-6725 TCGA-73-4658 
         184          382          100          129           61         1600 
TCGA-73-4659 TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-78-7148 
         711          467           40          164           38         1944 
TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 
        1093         1202          760         1948         1961         1963 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
        1221          678         1940         1950         1934         1937 
TCGA-78-7220 TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
        1965         1944          881         1952          994         1949 
TCGA-78-8648 TCGA-78-8655 TCGA-80-5607 TCGA-80-5608 TCGA-86-7713 TCGA-86-7953 
        1971         1981         1965         1972          422          591 
TCGA-86-7955 TCGA-86-8056 TCGA-86-8076 TCGA-86-8281 TCGA-86-8668 TCGA-86-8669 
         508         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-91-6831 TCGA-91-6835 TCGA-91-6847 TCGA-91-6849 
          39          323          310           79          842           35 
TCGA-91-8496 TCGA-91-8497 TCGA-93-7347 TCGA-93-8067 TCGA-95-7043 TCGA-95-7562 
         505          174          297          186            2         1973 
TCGA-95-7944 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VP TCGA-97-7547 TCGA-97-7553 
         377          476          121          605         1965         1332 
TCGA-97-7554 TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 TCGA-97-8179 TCGA-97-8552 
         775          107          182           87           15          115 
TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 TCGA-J2-A4AG 
         197          271          392          459           44          238 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A7SV TCGA-MP-A4SV 
         578          435          116            6          111         1946 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A5C7 
        1957         1980         1951         1944         1970         1490 
TCGA-S2-AA1A 
         121 

  DEL PEAK 37(18Q23) MUTATED DEL PEAK 37(18Q23) WILD-TYPE 
                           1                            2 
  DEL PEAK 37(18Q23) MUTATED DEL PEAK 37(18Q23) WILD-TYPE 
                        2370                         6443 
  DEL PEAK 37(18Q23) MUTATED DEL PEAK 37(18Q23) WILD-TYPE 
                         445                          522 
[1] "1.0 - 2370.0 (445.0)" "2.0 - 6443.0 (522.0)"
[1] "hr=" "1.2"
D66V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 37(18Q23) MUTATED         0       43       64        29        44
  DEL PEAK 37(18Q23) WILD-TYPE       5       73       68        20        26
                              vv
clus                           STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 37(18Q23) MUTATED           32          5       13
  DEL PEAK 37(18Q23) WILD-TYPE         36          6       11
D66V3, multiclass
            clus
vv           DEL PEAK 37(18Q23) MUTATED DEL PEAK 37(18Q23) WILD-TYPE
  STAGE I                             0                            5
  STAGE IA                           43                           73
  STAGE IB                           64                           68
  STAGE IIA                          29                           20
  STAGE IIB                          44                           26
  STAGE IIIA                         32                           36
  STAGE IIIB                          5                            6
  STAGE IV                           13                           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(18Q23) MUTATED    62 136  24   8
  DEL PEAK 37(18Q23) WILD-TYPE  85 131  18  10
D66V4, multiclass
    clus
vv   DEL PEAK 37(18Q23) MUTATED DEL PEAK 37(18Q23) WILD-TYPE
  T1                         62                           85
  T2                        136                          131
  T3                         24                           18
  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(18Q23) MUTATED   136  56    34
  DEL PEAK 37(18Q23) WILD-TYPE 165  35    40
D66V5, multiclass
       clus
vv      DEL PEAK 37(18Q23) MUTATED DEL PEAK 37(18Q23) WILD-TYPE
  N0                           136                          165
  N1                            56                           35
  N2+N3                         34                           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 37(18Q23) MUTATED   150  11   0   1  66
  DEL PEAK 37(18Q23) WILD-TYPE 176   7   1   3  57
D66V6, multiclass
     clus
vv    DEL PEAK 37(18Q23) MUTATED DEL PEAK 37(18Q23) WILD-TYPE
  M0                         150                          176
  M1                          11                            7
  M1A                          0                            1
  M1B                          1                            3
  MX                          66                           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"
D66V7, binary
                              cls
clus                             0   1
  DEL PEAK 37(18Q23) MUTATED   130 101
  DEL PEAK 37(18Q23) WILD-TYPE 125 120
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 37(18Q23) MUTATED    130  101
  DEL PEAK 37(18Q23) WILD-TYPE  125  120
        clus
vv       DEL PEAK 37(18Q23) MUTATED DEL PEAK 37(18Q23) WILD-TYPE
  FEMALE                        130                          125
  MALE                          101                          120
[1] 2 2
[1] FALSE
D66V8, continuous
                              vv
clus                           LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 37(18Q23) MUTATED                            9
  DEL PEAK 37(18Q23) WILD-TYPE                          6
                              vv
clus                           LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 37(18Q23) MUTATED                                  45
  DEL PEAK 37(18Q23) WILD-TYPE                                49
                              vv
clus                           LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 37(18Q23) MUTATED                                                  153
  DEL PEAK 37(18Q23) WILD-TYPE                                                150
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 37(18Q23) MUTATED                                            1
  DEL PEAK 37(18Q23) WILD-TYPE                                          4
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 37(18Q23) MUTATED                                               8
  DEL PEAK 37(18Q23) WILD-TYPE                                            11
                              vv
clus                           LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 37(18Q23) MUTATED                                2
  DEL PEAK 37(18Q23) WILD-TYPE                              0
                              vv
clus                           LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 37(18Q23) MUTATED                                    3
  DEL PEAK 37(18Q23) WILD-TYPE                                  1
                              vv
clus                           LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 37(18Q23) MUTATED                              1
  DEL PEAK 37(18Q23) WILD-TYPE                            1
                              vv
clus                           LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 37(18Q23) MUTATED                               3
  DEL PEAK 37(18Q23) WILD-TYPE                            16
                              vv
clus                           LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 37(18Q23) MUTATED                                 1
  DEL PEAK 37(18Q23) WILD-TYPE                               0
                              vv
clus                           LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 37(18Q23) MUTATED                                               2
  DEL PEAK 37(18Q23) WILD-TYPE                                             3
                              vv
clus                           MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 37(18Q23) MUTATED                              3
  DEL PEAK 37(18Q23) WILD-TYPE                            4
D66V9, multiclass
                                                    clus
vv                                                   DEL PEAK 37(18Q23) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                  9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                          45
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                        153
  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                               2
  MUCINOUS (COLLOID) CARCINOMA                                                3
                                                    clus
vv                                                   DEL PEAK 37(18Q23) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                    6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            49
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          150
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                11
  LUNG CLEAR CELL ADENOCARCINOMA                                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            1
  LUNG MUCINOUS ADENOCARCINOMA                                                  1
  LUNG PAPILLARY ADENOCARCINOMA                                                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"
D66V10, binary
                              cls
clus                             0   1
  DEL PEAK 37(18Q23) MUTATED     7 224
  DEL PEAK 37(18Q23) WILD-TYPE  14 231
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 37(18Q23) MUTATED      7  224
  DEL PEAK 37(18Q23) WILD-TYPE   14  231
     clus
vv    DEL PEAK 37(18Q23) MUTATED DEL PEAK 37(18Q23) WILD-TYPE
  NO                           7                           14
  YES                        224                          231
[1] 2 2
[1] FALSE
D66V11, continuous
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 37(18Q23) MUTATED   160   8   3   6
  DEL PEAK 37(18Q23) WILD-TYPE 167   4   1  15
D66V12, multiclass
    clus
vv   DEL PEAK 37(18Q23) MUTATED DEL PEAK 37(18Q23) WILD-TYPE
  R0                        160                          167
  R1                          8                            4
  R2                          3                            1
  RX                          6                           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 37(18Q23) MUTATED                                  0     2
  DEL PEAK 37(18Q23) WILD-TYPE                                1     4
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 37(18Q23) MUTATED                          16   177
  DEL PEAK 37(18Q23) WILD-TYPE                        19   190
D66V13, multiclass
                                  clus
vv                                 DEL PEAK 37(18Q23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     2
  BLACK OR AFRICAN AMERICAN                                16
  WHITE                                                   177
                                  clus
vv                                 DEL PEAK 37(18Q23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  19
  WHITE                                                     190
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V14, binary
                              cls
clus                             0   1
  DEL PEAK 37(18Q23) MUTATED     5 166
  DEL PEAK 37(18Q23) WILD-TYPE   2 179
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 37(18Q23) MUTATED      5  166
  DEL PEAK 37(18Q23) WILD-TYPE    2  179
                        clus
vv                       DEL PEAK 37(18Q23) MUTATED
  HISPANIC OR LATINO                              5
  NOT HISPANIC OR LATINO                        166
                        clus
vv                       DEL PEAK 37(18Q23) WILD-TYPE
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          179
[1] 2 2
[1] FALSE

Clustering(67) Variable = DEL PEAK 38(19P13.3) MUTATION ANALYSIS
D67V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 38(19P13.3) MUTATED   168  56
  DEL PEAK 38(19P13.3) WILD-TYPE 161  31
  DEL PEAK 38(19P13.3) MUTATED DEL PEAK 38(19P13.3) WILD-TYPE 
                           224                            192 
  DEL PEAK 38(19P13.3) MUTATED DEL PEAK 38(19P13.3) WILD-TYPE 
                            56                             31 
$`DEL PEAK 38(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-49-AARQ TCGA-50-5049 TCGA-50-5051 TCGA-50-5066 TCGA-50-5068 
         522         6443         2146          455          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-50-5944 TCGA-50-6597 TCGA-50-7109 TCGA-53-7624 TCGA-53-7813 
         567          764         1015          255         1986          424 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6971 
         280          701         1178         1375           87           25 
TCGA-55-6972 TCGA-55-7570 TCGA-55-7576 TCGA-55-7727 TCGA-55-7907 TCGA-55-7910 
        1475            6           40           34           16          197 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8089 TCGA-55-8092 
           3           31            5           33          100           26 
TCGA-55-8094 TCGA-55-8302 TCGA-55-8505 TCGA-55-8508 TCGA-55-8512 TCGA-55-8614 
           4           23           29           15            3          536 
TCGA-55-8616 TCGA-55-A48X TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
          48           33           48         1952            1           28 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
           5           47          162         1216         1289         1970 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46U TCGA-62-A471 TCGA-64-1676 TCGA-64-1681 
        2696         1445         2067         1246         1728         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-67-3774 TCGA-67-6217 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 
         385          422          186          690          414          230 
TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
          70          382          100          129          214           61 
TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4677 
         711          800          467          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-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
        1973         1988         1950         1944         1093         1963 
TCGA-78-7153 TCGA-78-7156 TCGA-78-7160 TCGA-78-7162 TCGA-78-7166 TCGA-78-7167 
         760         1961          678         1940         1934         1937 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 TCGA-78-7633 TCGA-80-5608 
        1965         1972         1949          327          994         1972 
TCGA-83-5908 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 
         824           11          630          422          591         1963 
TCGA-86-7955 TCGA-86-8055 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 
         508           10           13           24          479          482 
TCGA-86-8280 TCGA-86-8281 TCGA-86-8358 TCGA-86-8669 TCGA-86-8672 TCGA-86-8674 
          16         1955           19           34           15          405 
TCGA-86-A456 TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
          10           30          323         1940           60          310 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8497 
         417          372          224           35          492          174 
TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7944 TCGA-95-7948 
         186           34            2         1973          377          476 
TCGA-95-A4VK TCGA-95-A4VN TCGA-97-7937 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
         121          553          181          107          182         1965 
TCGA-99-7458 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-A4AD TCGA-L4-A4E5 TCGA-L9-A443 
         392          170          154          287          578          116 
TCGA-L9-A50W TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4T4 
         266          111          102         1175         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 38(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          705           39           39 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 TCGA-55-8087 TCGA-55-8090 
          24           54           19           21          462            6 
TCGA-55-8091 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
         600           47           15           33           46           66 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 
         674          216           44           11            8          228 
TCGA-55-8511 TCGA-55-8513 TCGA-55-8514 TCGA-55-8615 TCGA-55-8619 TCGA-55-8620 
           9          146          202           15           49           66 
TCGA-55-8621 TCGA-55-A48Y TCGA-55-A48Z TCGA-62-A46V TCGA-62-A472 TCGA-64-1677 
         106           42           29         2199          910          628 
TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-5775 TCGA-64-5781 TCGA-64-5815 
        1189         1686         1126           62         1559          866 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7765 TCGA-69-7974 
         427          174          141          202          165          184 
TCGA-69-7979 TCGA-69-8254 TCGA-73-4658 TCGA-73-4662 TCGA-73-4676 TCGA-73-A9RS 
          89           77         1600          912          164          305 
TCGA-78-7152 TCGA-78-7154 TCGA-78-7155 TCGA-78-7158 TCGA-78-7159 TCGA-78-7161 
        1202         1948         1957         1963         1221          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-86-6851 TCGA-86-7714 
        1981         1954         1964         1965         1959         1968 
TCGA-86-8054 TCGA-86-8056 TCGA-86-8076 TCGA-86-8278 TCGA-86-8359 TCGA-86-8585 
         745         1963          489          476           26           35 
TCGA-86-8668 TCGA-86-8671 TCGA-86-8673 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6835 
          45           18          455           14           39           79 
TCGA-91-6847 TCGA-91-8496 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
         842          505           36           44          218          297 
TCGA-93-7348 TCGA-95-7567 TCGA-95-7947 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP 
         127          568          477          830           84          605 
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-97-8175 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-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-J2-8194 TCGA-J2-A4AE 
         271          427          459           44          114          282 
TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A444 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MN-A4N5 
         238          435            6          312          827           84 
TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T9 TCGA-MP-A4TC TCGA-MP-A4TE TCGA-S2-AA1A 
        1967         1951         1980         1944         1970          121 

  DEL PEAK 38(19P13.3) MUTATED DEL PEAK 38(19P13.3) WILD-TYPE 
                             1                              2 
  DEL PEAK 38(19P13.3) MUTATED DEL PEAK 38(19P13.3) WILD-TYPE 
                          6443                           2199 
  DEL PEAK 38(19P13.3) MUTATED DEL PEAK 38(19P13.3) WILD-TYPE 
                         513.5                          449.5 
[1] "1.0 - 6443.0 (513.5)" "2.0 - 2199.0 (449.5)"
[1] "hr=" "1.2"
D67V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 38(19P13.3) MUTATED         4       52       65        32        40
  DEL PEAK 38(19P13.3) WILD-TYPE       1       64       67        17        30
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 38(19P13.3) MUTATED           39          8       16
  DEL PEAK 38(19P13.3) WILD-TYPE         29          3        8
D67V3, multiclass
            clus
vv           DEL PEAK 38(19P13.3) MUTATED DEL PEAK 38(19P13.3) WILD-TYPE
  STAGE I                               4                              1
  STAGE IA                             52                             64
  STAGE IB                             65                             67
  STAGE IIA                            32                             17
  STAGE IIB                            40                             30
  STAGE IIIA                           39                             29
  STAGE IIIB                            8                              3
  STAGE IV                             16                              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 38(19P13.3) MUTATED    67 156  19  12
  DEL PEAK 38(19P13.3) WILD-TYPE  80 111  23   6
D67V4, multiclass
    clus
vv   DEL PEAK 38(19P13.3) MUTATED DEL PEAK 38(19P13.3) WILD-TYPE
  T1                           67                             80
  T2                          156                            111
  T3                           19                             23
  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 38(19P13.3) MUTATED   151  59    42
  DEL PEAK 38(19P13.3) WILD-TYPE 150  32    32
D67V5, multiclass
       clus
vv      DEL PEAK 38(19P13.3) MUTATED DEL PEAK 38(19P13.3) WILD-TYPE
  N0                             151                            150
  N1                              59                             32
  N2+N3                           42                             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 38(19P13.3) MUTATED   183  13   1   2  55
  DEL PEAK 38(19P13.3) WILD-TYPE 143   5   0   2  68
D67V6, multiclass
     clus
vv    DEL PEAK 38(19P13.3) MUTATED DEL PEAK 38(19P13.3) WILD-TYPE
  M0                           183                            143
  M1                            13                              5
  M1A                            1                              0
  M1B                            2                              2
  MX                            55                             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"
D67V7, binary
                                cls
clus                               0   1
  DEL PEAK 38(19P13.3) MUTATED   123 133
  DEL PEAK 38(19P13.3) WILD-TYPE 132  88
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(19P13.3) MUTATED    123  133
  DEL PEAK 38(19P13.3) WILD-TYPE  132   88
        clus
vv       DEL PEAK 38(19P13.3) MUTATED DEL PEAK 38(19P13.3) WILD-TYPE
  FEMALE                          123                            132
  MALE                            133                             88
[1] 2 2
[1] FALSE
D67V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 38(19P13.3) MUTATED                            6
  DEL PEAK 38(19P13.3) WILD-TYPE                          9
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 38(19P13.3) MUTATED                                  53
  DEL PEAK 38(19P13.3) WILD-TYPE                                41
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 38(19P13.3) MUTATED                                                  164
  DEL PEAK 38(19P13.3) WILD-TYPE                                                139
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 38(19P13.3) MUTATED                                            0
  DEL PEAK 38(19P13.3) WILD-TYPE                                          5
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 38(19P13.3) MUTATED                                               9
  DEL PEAK 38(19P13.3) WILD-TYPE                                            10
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 38(19P13.3) MUTATED                                1
  DEL PEAK 38(19P13.3) WILD-TYPE                              1
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 38(19P13.3) MUTATED                                    3
  DEL PEAK 38(19P13.3) WILD-TYPE                                  1
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 38(19P13.3) MUTATED                              1
  DEL PEAK 38(19P13.3) WILD-TYPE                            1
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 38(19P13.3) MUTATED                              12
  DEL PEAK 38(19P13.3) WILD-TYPE                             7
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 38(19P13.3) MUTATED                                 1
  DEL PEAK 38(19P13.3) WILD-TYPE                               0
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 38(19P13.3) MUTATED                                               3
  DEL PEAK 38(19P13.3) WILD-TYPE                                             2
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 38(19P13.3) MUTATED                              3
  DEL PEAK 38(19P13.3) WILD-TYPE                            4
D67V9, multiclass
                                                    clus
vv                                                   DEL PEAK 38(19P13.3) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            53
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          164
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 9
  LUNG CLEAR CELL ADENOCARCINOMA                                                1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            3
  LUNG MUCINOUS ADENOCARCINOMA                                                  1
  LUNG PAPILLARY ADENOCARCINOMA                                                12
  LUNG SIGNET RING ADENOCARCINOMA                                               1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 3
  MUCINOUS (COLLOID) CARCINOMA                                                  3
                                                    clus
vv                                                   DEL PEAK 38(19P13.3) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              41
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            139
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  10
  LUNG CLEAR CELL ADENOCARCINOMA                                                  1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              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"
D67V10, binary
                                cls
clus                               0   1
  DEL PEAK 38(19P13.3) MUTATED    13 243
  DEL PEAK 38(19P13.3) WILD-TYPE   8 212
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(19P13.3) MUTATED     13  243
  DEL PEAK 38(19P13.3) WILD-TYPE    8  212
     clus
vv    DEL PEAK 38(19P13.3) MUTATED DEL PEAK 38(19P13.3) WILD-TYPE
  NO                            13                              8
  YES                          243                            212
[1] 2 2
[1] FALSE
D67V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 38(19P13.3) MUTATED   174   4   2  13
  DEL PEAK 38(19P13.3) WILD-TYPE 153   8   2   8
D67V12, multiclass
    clus
vv   DEL PEAK 38(19P13.3) MUTATED DEL PEAK 38(19P13.3) WILD-TYPE
  R0                          174                            153
  R1                            4                              8
  R2                            2                              2
  RX                           13                              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 38(19P13.3) MUTATED                                  1     5
  DEL PEAK 38(19P13.3) WILD-TYPE                                0     1
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 38(19P13.3) MUTATED                          23   189
  DEL PEAK 38(19P13.3) WILD-TYPE                        12   178
D67V13, multiclass
                                  clus
vv                                 DEL PEAK 38(19P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  23
  WHITE                                                     189
                                  clus
vv                                 DEL PEAK 38(19P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         1
  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"
D67V14, binary
                                cls
clus                               0   1
  DEL PEAK 38(19P13.3) MUTATED     5 182
  DEL PEAK 38(19P13.3) WILD-TYPE   2 163
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(19P13.3) MUTATED      5  182
  DEL PEAK 38(19P13.3) WILD-TYPE    2  163
                        clus
vv                       DEL PEAK 38(19P13.3) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          182
                        clus
vv                       DEL PEAK 38(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            163
[1] 2 2
[1] FALSE

Clustering(68) Variable = DEL PEAK 39(19P13.2) MUTATION ANALYSIS
D68V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 39(19P13.2) MUTATED   166  50
  DEL PEAK 39(19P13.2) WILD-TYPE 163  37
  DEL PEAK 39(19P13.2) MUTATED DEL PEAK 39(19P13.2) WILD-TYPE 
                           216                            200 
  DEL PEAK 39(19P13.2) MUTATED DEL PEAK 39(19P13.2) WILD-TYPE 
                            50                             37 
$`DEL PEAK 39(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-95-A4VN 
          34            2          568          476          121          553 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-99-7458 TCGA-99-8025 TCGA-99-8033 
         107          182         1965          392          427          170 
TCGA-J2-8192 TCGA-J2-A4AD TCGA-L4-A4E5 TCGA-L9-A443 TCGA-L9-A7SV TCGA-L9-A8F4 
         154          287          578          116          111          102 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 
        1175           84         1946         1954         1954         1957 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
        1951         1944         1970          142         1955         1971 

$`DEL PEAK 39(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-49-AARQ TCGA-50-5045 TCGA-50-5055 TCGA-50-5068 TCGA-50-5935 TCGA-50-5942 
        6443         2174          785         1499          653          883 
TCGA-50-5946 TCGA-50-8460 TCGA-53-7626 TCGA-55-1595 TCGA-55-6543 TCGA-55-6642 
         686          105         1971         1479            2          993 
TCGA-55-6712 TCGA-55-6969 TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 
          24         1239           67         1826         1233         2151 
TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7573 TCGA-55-7574 
        1170           18           35          121            4           95 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 
         705           39           39           24           54           19 
TCGA-55-7911 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8096 TCGA-55-8097 
          21          462            6          600           47           15 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
          33           46           66          674          216           44 
TCGA-55-8506 TCGA-55-8510 TCGA-55-8511 TCGA-55-8513 TCGA-55-8514 TCGA-55-8619 
          11          228            9          146          202           49 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48Y TCGA-55-A48Z TCGA-62-A46V TCGA-62-A472 
          66          106           42           29         2199          910 
TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-5775 TCGA-64-5781 
         628         1189         1686         1126           62         1559 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
         866          610          427          174          141          422 
TCGA-69-7760 TCGA-69-7765 TCGA-69-7974 TCGA-69-7979 TCGA-69-8254 TCGA-73-4658 
         202          165          184           89           77         1600 
TCGA-73-4662 TCGA-73-4675 TCGA-73-4676 TCGA-73-A9RS TCGA-78-7152 TCGA-78-7154 
         912           40          164          305         1202         1948 
TCGA-78-7155 TCGA-78-7158 TCGA-78-7161 TCGA-78-7163 TCGA-78-7537 TCGA-78-7540 
        1957         1963          215         1950         1944          881 
TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
        1952         1949         1971         1981         1954         1964 
TCGA-80-5607 TCGA-83-5908 TCGA-86-6851 TCGA-86-7714 TCGA-86-8056 TCGA-86-8076 
        1965          824         1959         1968         1963          489 
TCGA-86-8278 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 
         476           19           26           35           45           18 
TCGA-86-8673 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 
         455           14           39           79          372          842 
TCGA-91-6848 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 
         224          505          174           36          218          297 
TCGA-93-7348 TCGA-93-8067 TCGA-95-7562 TCGA-95-7944 TCGA-95-7947 TCGA-95-8039 
         127          186         1973          377          477          830 
TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
          84          605          964         1965         1932         1332 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 
         775          181           22           87          147           15 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-8028 TCGA-99-8032 
         148          115          197          271          459           44 
TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A444 TCGA-L9-A50W 
         114          282          238          435            6          266 
TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T9 TCGA-MP-A4TE 
         312          827         1967         1951         1980         1970 
TCGA-MP-A5C7 TCGA-S2-AA1A 
        1490          121 

  DEL PEAK 39(19P13.2) MUTATED DEL PEAK 39(19P13.2) WILD-TYPE 
                             1                              2 
  DEL PEAK 39(19P13.2) MUTATED DEL PEAK 39(19P13.2) WILD-TYPE 
                          2696                           6443 
  DEL PEAK 39(19P13.2) MUTATED DEL PEAK 39(19P13.2) WILD-TYPE 
                         520.5                          449.5 
[1] "1.0 - 2696.0 (520.5)" "2.0 - 6443.0 (449.5)"
[1] "hr=" "1.1"
D68V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 39(19P13.2) MUTATED         3       49       62        30        41
  DEL PEAK 39(19P13.2) WILD-TYPE       2       67       70        19        29
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 39(19P13.2) MUTATED           40          7       16
  DEL PEAK 39(19P13.2) WILD-TYPE         28          4        8
D68V3, multiclass
            clus
vv           DEL PEAK 39(19P13.2) MUTATED DEL PEAK 39(19P13.2) WILD-TYPE
  STAGE I                               3                              2
  STAGE IA                             49                             67
  STAGE IB                             62                             70
  STAGE IIA                            30                             19
  STAGE IIB                            41                             29
  STAGE IIIA                           40                             28
  STAGE IIIB                            7                              4
  STAGE IV                             16                              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 39(19P13.2) MUTATED    66 149  20  11
  DEL PEAK 39(19P13.2) WILD-TYPE  81 118  22   7
D68V4, multiclass
    clus
vv   DEL PEAK 39(19P13.2) MUTATED DEL PEAK 39(19P13.2) WILD-TYPE
  T1                           66                             81
  T2                          149                            118
  T3                           20                             22
  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 39(19P13.2) MUTATED   144  56    43
  DEL PEAK 39(19P13.2) WILD-TYPE 157  35    31
D68V5, multiclass
       clus
vv      DEL PEAK 39(19P13.2) MUTATED DEL PEAK 39(19P13.2) WILD-TYPE
  N0                             144                            157
  N1                              56                             35
  N2+N3                           43                             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
  DEL PEAK 39(19P13.2) MUTATED   180  13   1   2  50
  DEL PEAK 39(19P13.2) WILD-TYPE 146   5   0   2  73
D68V6, multiclass
     clus
vv    DEL PEAK 39(19P13.2) MUTATED DEL PEAK 39(19P13.2) WILD-TYPE
  M0                           180                            146
  M1                            13                              5
  M1A                            1                              0
  M1B                            2                              2
  MX                            50                             73
[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 39(19P13.2) MUTATED   114 134
  DEL PEAK 39(19P13.2) WILD-TYPE 141  87
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(19P13.2) MUTATED    114  134
  DEL PEAK 39(19P13.2) WILD-TYPE  141   87
        clus
vv       DEL PEAK 39(19P13.2) MUTATED DEL PEAK 39(19P13.2) WILD-TYPE
  FEMALE                          114                            141
  MALE                            134                             87
[1] 2 2
[1] FALSE
D68V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 39(19P13.2) MUTATED                            7
  DEL PEAK 39(19P13.2) WILD-TYPE                          8
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 39(19P13.2) MUTATED                                  56
  DEL PEAK 39(19P13.2) WILD-TYPE                                38
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 39(19P13.2) MUTATED                                                  154
  DEL PEAK 39(19P13.2) WILD-TYPE                                                149
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 39(19P13.2) MUTATED                                            0
  DEL PEAK 39(19P13.2) WILD-TYPE                                          5
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 39(19P13.2) MUTATED                                               9
  DEL PEAK 39(19P13.2) WILD-TYPE                                            10
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 39(19P13.2) MUTATED                                1
  DEL PEAK 39(19P13.2) WILD-TYPE                              1
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 39(19P13.2) MUTATED                                    2
  DEL PEAK 39(19P13.2) WILD-TYPE                                  2
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 39(19P13.2) MUTATED                              1
  DEL PEAK 39(19P13.2) WILD-TYPE                            1
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 39(19P13.2) MUTATED                              11
  DEL PEAK 39(19P13.2) WILD-TYPE                             8
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 39(19P13.2) MUTATED                                 1
  DEL PEAK 39(19P13.2) WILD-TYPE                               0
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 39(19P13.2) MUTATED                                               3
  DEL PEAK 39(19P13.2) WILD-TYPE                                             2
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 39(19P13.2) MUTATED                              3
  DEL PEAK 39(19P13.2) WILD-TYPE                            4
D68V9, multiclass
                                                    clus
vv                                                   DEL PEAK 39(19P13.2) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            56
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          154
  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                                 3
  MUCINOUS (COLLOID) CARCINOMA                                                  3
                                                    clus
vv                                                   DEL PEAK 39(19P13.2) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              38
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            149
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      5
  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"
D68V10, binary
                                cls
clus                               0   1
  DEL PEAK 39(19P13.2) MUTATED    11 237
  DEL PEAK 39(19P13.2) WILD-TYPE  10 218
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(19P13.2) MUTATED     11  237
  DEL PEAK 39(19P13.2) WILD-TYPE   10  218
     clus
vv    DEL PEAK 39(19P13.2) MUTATED DEL PEAK 39(19P13.2) WILD-TYPE
  NO                            11                             10
  YES                          237                            218
[1] 2 2
[1] FALSE
D68V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 39(19P13.2) MUTATED   174   3   2  10
  DEL PEAK 39(19P13.2) WILD-TYPE 153   9   2  11
D68V12, multiclass
    clus
vv   DEL PEAK 39(19P13.2) MUTATED DEL PEAK 39(19P13.2) WILD-TYPE
  R0                          174                            153
  R1                            3                              9
  R2                            2                              2
  RX                           10                             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 39(19P13.2) MUTATED                                  1     4
  DEL PEAK 39(19P13.2) WILD-TYPE                                0     2
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 39(19P13.2) MUTATED                          18   187
  DEL PEAK 39(19P13.2) WILD-TYPE                        17   180
D68V13, multiclass
                                  clus
vv                                 DEL PEAK 39(19P13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  18
  WHITE                                                     187
                                  clus
vv                                 DEL PEAK 39(19P13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         2
  BLACK OR AFRICAN AMERICAN                                    17
  WHITE                                                       180
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V14, binary
                                cls
clus                               0   1
  DEL PEAK 39(19P13.2) MUTATED     5 173
  DEL PEAK 39(19P13.2) WILD-TYPE   2 172
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(19P13.2) MUTATED      5  173
  DEL PEAK 39(19P13.2) WILD-TYPE    2  172
                        clus
vv                       DEL PEAK 39(19P13.2) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          173
                        clus
vv                       DEL PEAK 39(19P13.2) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            172
[1] 2 2
[1] FALSE

Clustering(69) Variable = DEL PEAK 40(19Q13.33) MUTATION ANALYSIS
D69V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 40(19Q13.33) MUTATED   116  35
  DEL PEAK 40(19Q13.33) WILD-TYPE 213  52
  DEL PEAK 40(19Q13.33) MUTATED DEL PEAK 40(19Q13.33) WILD-TYPE 
                            151                             265 
  DEL PEAK 40(19Q13.33) MUTATED DEL PEAK 40(19Q13.33) WILD-TYPE 
                             35                              52 
$`DEL PEAK 40(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          600            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-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
          34          568          476           84          121          553 
TCGA-97-8171 TCGA-97-8174 TCGA-97-8547 TCGA-99-7458 TCGA-99-8033 TCGA-J2-8192 
         107         1965          148          392          170          154 
TCGA-J2-A4AD TCGA-L4-A4E5 TCGA-L9-A7SV TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV 
         287          578          111          827           84         1946 
TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TI TCGA-MP-A4TK 
        1967         1951         1957         1951         1955         1971 
TCGA-MP-A5C7 
        1490 

$`DEL PEAK 40(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-49-AARQ TCGA-50-5045 
         157          369          890          354         6443         2174 
TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 
        2146          785          944         1499          282          267 
TCGA-50-5933 TCGA-50-5942 TCGA-50-7109 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
        2370          883          255          105         1986         1971 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1595 TCGA-55-6543 TCGA-55-6642 
         424          280         1178         1479            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-55-7573 TCGA-55-7574 TCGA-55-7576 
        1170           18          121            4           95           40 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 
         705           39           39           24           54           19 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-8087 TCGA-55-8089 
          16          197           21            3          462          100 
TCGA-55-8090 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 
           6           26           47           15           33           46 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
          66          674          216           44           23           29 
TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 
          11           15          228            3          146          536 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
          49           66          106           42           29           48 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-62-8398 TCGA-62-8399 TCGA-62-A46U 
          28            5           47         1970         2696         2067 
TCGA-62-A472 TCGA-64-1677 TCGA-64-1680 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
         910          628         1126         1959           62         1305 
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-69-7761 TCGA-69-7763 TCGA-69-7765 
         174          141          422          186          690          165 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-73-4658 
         230          184          382          100           77         1600 
TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 TCGA-73-A9RS TCGA-75-7025 TCGA-75-7027 
         467           40          164          305         1967         1956 
TCGA-78-7145 TCGA-78-7147 TCGA-78-7150 TCGA-78-7152 TCGA-78-7154 TCGA-78-7155 
        1973         1950         1963         1202         1948         1957 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7163 TCGA-78-7166 TCGA-78-7537 
        1963         1221          678         1950         1934         1944 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
         327          881          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-86-8054 TCGA-86-8055 
         630          422         1968          591          745           10 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 
        1963           13          479          489          476           16 
TCGA-86-8281 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 
        1955           19           26           35           45           18 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6835 TCGA-91-6840 
         455          405           14           39           79          372 
TCGA-91-6847 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 
         842           35          505          174          218          297 
TCGA-93-7348 TCGA-93-8067 TCGA-95-7043 TCGA-95-7562 TCGA-95-7944 TCGA-95-7947 
         127          186            2         1973          377          477 
TCGA-95-8039 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
         830          605          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-L9-A50W TCGA-L9-A743 TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4T4 
           6          266          312          102         1175         1954 
TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
        1954         1980         1944         1970         1970          142 
TCGA-S2-AA1A 
         121 

  DEL PEAK 40(19Q13.33) MUTATED DEL PEAK 40(19Q13.33) WILD-TYPE 
                              1                               2 
  DEL PEAK 40(19Q13.33) MUTATED DEL PEAK 40(19Q13.33) WILD-TYPE 
                           2199                            6443 
  DEL PEAK 40(19Q13.33) MUTATED DEL PEAK 40(19Q13.33) WILD-TYPE 
                            567                             435 
[1] "1.0 - 2199.0 (567.0)" "2.0 - 6443.0 (435.0)"
[1] "hr=" "1.4"
D69V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 40(19Q13.33) MUTATED         1       39       45        17        30
  DEL PEAK 40(19Q13.33) WILD-TYPE       4       77       87        32        40
                                 vv
clus                              STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 40(19Q13.33) MUTATED           30          5       12
  DEL PEAK 40(19Q13.33) WILD-TYPE         38          6       12
D69V3, multiclass
            clus
vv           DEL PEAK 40(19Q13.33) MUTATED DEL PEAK 40(19Q13.33) WILD-TYPE
  STAGE I                                1                               4
  STAGE IA                              39                              77
  STAGE IB                              45                              87
  STAGE IIA                             17                              32
  STAGE IIB                             30                              40
  STAGE IIIA                            30                              38
  STAGE IIIB                             5                               6
  STAGE IV                              12                              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(19Q13.33) MUTATED    47 106  17   8
  DEL PEAK 40(19Q13.33) WILD-TYPE 100 161  25  10
D69V4, multiclass
    clus
vv   DEL PEAK 40(19Q13.33) MUTATED DEL PEAK 40(19Q13.33) WILD-TYPE
  T1                            47                             100
  T2                           106                             161
  T3                            17                              25
  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 40(19Q13.33) MUTATED   108  38    31
  DEL PEAK 40(19Q13.33) WILD-TYPE 193  53    43
D69V5, multiclass
       clus
vv      DEL PEAK 40(19Q13.33) MUTATED DEL PEAK 40(19Q13.33) WILD-TYPE
  N0                              108                             193
  N1                               38                              53
  N2+N3                            31                              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 40(19Q13.33) MUTATED   129  10   1   1  36
  DEL PEAK 40(19Q13.33) WILD-TYPE 197   8   0   3  87
D69V6, multiclass
     clus
vv    DEL PEAK 40(19Q13.33) MUTATED DEL PEAK 40(19Q13.33) WILD-TYPE
  M0                            129                             197
  M1                             10                               8
  M1A                             1                               0
  M1B                             1                               3
  MX                             36                              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"
D69V7, binary
                                 cls
clus                                0   1
  DEL PEAK 40(19Q13.33) MUTATED    90  89
  DEL PEAK 40(19Q13.33) WILD-TYPE 165 132
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 40(19Q13.33) MUTATED     90   89
  DEL PEAK 40(19Q13.33) WILD-TYPE  165  132
        clus
vv       DEL PEAK 40(19Q13.33) MUTATED DEL PEAK 40(19Q13.33) WILD-TYPE
  FEMALE                            90                             165
  MALE                              89                             132
[1] 2 2
[1] FALSE
D69V8, continuous
                                 vv
clus                              LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 40(19Q13.33) MUTATED                            4
  DEL PEAK 40(19Q13.33) WILD-TYPE                         11
                                 vv
clus                              LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 40(19Q13.33) MUTATED                                  42
  DEL PEAK 40(19Q13.33) WILD-TYPE                                52
                                 vv
clus                              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 40(19Q13.33) MUTATED                                                  113
  DEL PEAK 40(19Q13.33) WILD-TYPE                                                190
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 40(19Q13.33) MUTATED                                            0
  DEL PEAK 40(19Q13.33) WILD-TYPE                                          5
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 40(19Q13.33) MUTATED                                               5
  DEL PEAK 40(19Q13.33) WILD-TYPE                                            14
                                 vv
clus                              LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 40(19Q13.33) MUTATED                                0
  DEL PEAK 40(19Q13.33) WILD-TYPE                              2
                                 vv
clus                              LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 40(19Q13.33) MUTATED                                    2
  DEL PEAK 40(19Q13.33) WILD-TYPE                                  2
                                 vv
clus                              LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 40(19Q13.33) MUTATED                              0
  DEL PEAK 40(19Q13.33) WILD-TYPE                            2
                                 vv
clus                              LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 40(19Q13.33) MUTATED                               9
  DEL PEAK 40(19Q13.33) WILD-TYPE                            10
                                 vv
clus                              LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 40(19Q13.33) MUTATED                                 0
  DEL PEAK 40(19Q13.33) WILD-TYPE                               1
                                 vv
clus                              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 40(19Q13.33) MUTATED                                               3
  DEL PEAK 40(19Q13.33) WILD-TYPE                                             2
                                 vv
clus                              MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 40(19Q13.33) MUTATED                              1
  DEL PEAK 40(19Q13.33) WILD-TYPE                            6
D69V9, multiclass
                                                    clus
vv                                                   DEL PEAK 40(19Q13.33) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                     4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             42
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           113
  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                                  3
  MUCINOUS (COLLOID) CARCINOMA                                                   1
                                                    clus
vv                                                   DEL PEAK 40(19Q13.33) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                               52
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             190
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                       5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                   14
  LUNG CLEAR CELL ADENOCARCINOMA                                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                               2
  LUNG MUCINOUS ADENOCARCINOMA                                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                                   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"
D69V10, binary
                                 cls
clus                                0   1
  DEL PEAK 40(19Q13.33) MUTATED     6 173
  DEL PEAK 40(19Q13.33) WILD-TYPE  15 282
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 40(19Q13.33) MUTATED      6  173
  DEL PEAK 40(19Q13.33) WILD-TYPE   15  282
     clus
vv    DEL PEAK 40(19Q13.33) MUTATED DEL PEAK 40(19Q13.33) WILD-TYPE
  NO                              6                              15
  YES                           173                             282
[1] 2 2
[1] FALSE
D69V11, continuous
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 40(19Q13.33) MUTATED   119   4   3   8
  DEL PEAK 40(19Q13.33) WILD-TYPE 208   8   1  13
D69V12, multiclass
    clus
vv   DEL PEAK 40(19Q13.33) MUTATED DEL PEAK 40(19Q13.33) WILD-TYPE
  R0                           119                             208
  R1                             4                               8
  R2                             3                               1
  RX                             8                              13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 40(19Q13.33) MUTATED                                  0     4
  DEL PEAK 40(19Q13.33) WILD-TYPE                                1     2
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 40(19Q13.33) MUTATED                          10   137
  DEL PEAK 40(19Q13.33) WILD-TYPE                        25   230
D69V13, multiclass
                                  clus
vv                                 DEL PEAK 40(19Q13.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   10
  WHITE                                                      137
                                  clus
vv                                 DEL PEAK 40(19Q13.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          2
  BLACK OR AFRICAN AMERICAN                                     25
  WHITE                                                        230
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V14, binary
                                 cls
clus                                0   1
  DEL PEAK 40(19Q13.33) MUTATED     2 124
  DEL PEAK 40(19Q13.33) WILD-TYPE   5 221
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 40(19Q13.33) MUTATED      2  124
  DEL PEAK 40(19Q13.33) WILD-TYPE    5  221
                        clus
vv                       DEL PEAK 40(19Q13.33) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           124
                        clus
vv                       DEL PEAK 40(19Q13.33) WILD-TYPE
  HISPANIC OR LATINO                                   5
  NOT HISPANIC OR LATINO                             221
[1] 2 2
[1] FALSE

Clustering(70) Variable = DEL PEAK 41(20P13) MUTATION ANALYSIS
D70V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 41(20P13) MUTATED    79  27
  DEL PEAK 41(20P13) WILD-TYPE 250  60
  DEL PEAK 41(20P13) MUTATED DEL PEAK 41(20P13) WILD-TYPE 
                         106                          310 
  DEL PEAK 41(20P13) MUTATED DEL PEAK 41(20P13) WILD-TYPE 
                          27                           60 
$`DEL PEAK 41(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-49-AARQ TCGA-50-5051 TCGA-50-5072 TCGA-50-5933 TCGA-50-5944 
         522         6443          455          246         2370          764 
TCGA-50-6597 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-55-1594 TCGA-55-1595 
        1015          105         1986         1971         1178         1479 
TCGA-55-6712 TCGA-55-6980 TCGA-55-7283 TCGA-55-7576 TCGA-55-7725 TCGA-55-7727 
          24           67           35           40           39           34 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7994 TCGA-55-8090 TCGA-55-8092 TCGA-55-8094 
          19           16           31            6           26            4 
TCGA-55-8207 TCGA-55-8506 TCGA-55-8616 TCGA-55-A491 TCGA-55-A493 TCGA-62-8397 
          66           11           48         1952           28         1289 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 
        2067         2199         1246          910         1728         1189 
TCGA-64-1681 TCGA-64-5781 TCGA-67-3773 TCGA-67-6216 TCGA-69-7761 TCGA-69-7974 
        1968         1559          427          141          186          184 
TCGA-69-A59K TCGA-73-4662 TCGA-73-4666 TCGA-73-4670 TCGA-73-7499 TCGA-75-6214 
         214          912          800          131          519         1970 
TCGA-75-7031 TCGA-78-7145 TCGA-78-7148 TCGA-78-7158 TCGA-78-7159 TCGA-78-7535 
        1965         1973         1944         1963         1221         1972 
TCGA-78-8660 TCGA-78-8662 TCGA-80-5608 TCGA-86-6851 TCGA-86-7953 TCGA-86-7955 
        1954         1964         1972         1959          591          508 
TCGA-86-8278 TCGA-86-8280 TCGA-86-8673 TCGA-91-6828 TCGA-91-6835 TCGA-93-7347 
         476           16          455          323           79          297 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-A4VN TCGA-97-7554 
          34            2         1973          568          553          775 
TCGA-99-7458 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-A4AD TCGA-L4-A4E5 TCGA-L9-A444 
         392          170          154          287          578            6 
TCGA-L9-A7SV TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T8 
         111          827         1175         1946         1967         1957 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TI TCGA-MP-A4TK 
        1951         1944         1955         1971 

$`DEL PEAK 41(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          705           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          462 
TCGA-55-8089 TCGA-55-8091 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 
         100          600           47           15           33           46 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 
         674          216           44           23           29            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-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
         536           15           49           66          106           33 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A492 TCGA-55-A494 TCGA-55-A4DF 
          42           29           48            1            5           47 
TCGA-55-A4DG TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-64-1677 
         162         1216         1970         2696         1445          628 
TCGA-64-1679 TCGA-64-1680 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
        1686         1126         1959           62         1305          864 
TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3774 TCGA-67-6215 
         866           31          610          573          385          174 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
         422          202          690          414          165          230 
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-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 
          61         1600          711          467           40          164 
TCGA-73-4677 TCGA-73-7498 TCGA-73-A9RS TCGA-75-7025 TCGA-75-7027 TCGA-78-7146 
          38          621          305         1967         1956         1988 
TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
        1950         1093         1963         1202          760         1948 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        1957         1961          678          215         1940         1950 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
        1934         1937         1965         1949         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-80-5607 TCGA-83-5908 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
        1965          824           11          630          422         1968 
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-86-8279 TCGA-86-8281 TCGA-86-8358 TCGA-86-8359 
         479          489          482         1955           19           26 
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-A4P7 TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 
          10           30           14           39         1940           60 
TCGA-91-6831 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
         310          417          372          842          224           35 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
         492          505          174           36           44          218 
TCGA-93-7348 TCGA-93-8067 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
         127          186          377          477          476          830 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
          84          121          605          964         1965         1932 
TCGA-97-7553 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        1332          181           22          107          182         1965 
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-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-J2-8194 TCGA-J2-A4AE 
         271          427          459           44          114          282 
TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A50W TCGA-L9-A743 TCGA-L9-A8F4 
         238          435          116          266          312          102 
TCGA-MN-A4N5 TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE 
          84         1951         1954         1954         1980         1970 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A5C7 TCGA-S2-AA1A 
        1970          142         1490          121 

  DEL PEAK 41(20P13) MUTATED DEL PEAK 41(20P13) WILD-TYPE 
                           2                            1 
  DEL PEAK 41(20P13) MUTATED DEL PEAK 41(20P13) WILD-TYPE 
                        6443                         2696 
  DEL PEAK 41(20P13) MUTATED DEL PEAK 41(20P13) WILD-TYPE 
                       560.5                        456.0 
[1] "2.0 - 6443.0 (560.5)" "1.0 - 2696.0 (456.0)"
[1] "hr=" "1.5"
D70V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 41(20P13) MUTATED         2       26       26        15        23
  DEL PEAK 41(20P13) WILD-TYPE       3       90      106        34        47
                              vv
clus                           STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 41(20P13) MUTATED           21          5        6
  DEL PEAK 41(20P13) WILD-TYPE         47          6       18
D70V3, multiclass
            clus
vv           DEL PEAK 41(20P13) MUTATED DEL PEAK 41(20P13) WILD-TYPE
  STAGE I                             2                            3
  STAGE IA                           26                           90
  STAGE IB                           26                          106
  STAGE IIA                          15                           34
  STAGE IIB                          23                           47
  STAGE IIIA                         21                           47
  STAGE IIIB                          5                            6
  STAGE IV                            6                           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 41(20P13) MUTATED    33  71  11   7
  DEL PEAK 41(20P13) WILD-TYPE 114 196  31  11
D70V4, multiclass
    clus
vv   DEL PEAK 41(20P13) MUTATED DEL PEAK 41(20P13) WILD-TYPE
  T1                         33                          114
  T2                         71                          196
  T3                         11                           31
  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 41(20P13) MUTATED    69  28    25
  DEL PEAK 41(20P13) WILD-TYPE 232  63    49
D70V5, multiclass
       clus
vv      DEL PEAK 41(20P13) MUTATED DEL PEAK 41(20P13) WILD-TYPE
  N0                            69                          232
  N1                            28                           63
  N2+N3                         25                           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 41(20P13) MUTATED    91   5   0   1  26
  DEL PEAK 41(20P13) WILD-TYPE 235  13   1   3  97
D70V6, multiclass
     clus
vv    DEL PEAK 41(20P13) MUTATED DEL PEAK 41(20P13) WILD-TYPE
  M0                          91                          235
  M1                           5                           13
  M1A                          0                            1
  M1B                          1                            3
  MX                          26                           97
[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 41(20P13) MUTATED    74  50
  DEL PEAK 41(20P13) WILD-TYPE 181 171
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 41(20P13) MUTATED     74   50
  DEL PEAK 41(20P13) WILD-TYPE  181  171
        clus
vv       DEL PEAK 41(20P13) MUTATED DEL PEAK 41(20P13) WILD-TYPE
  FEMALE                         74                          181
  MALE                           50                          171
[1] 2 2
[1] FALSE
D70V8, continuous
                              vv
clus                           LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 41(20P13) MUTATED                            3
  DEL PEAK 41(20P13) WILD-TYPE                         12
                              vv
clus                           LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 41(20P13) MUTATED                                  23
  DEL PEAK 41(20P13) WILD-TYPE                                71
                              vv
clus                           LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 41(20P13) MUTATED                                                   83
  DEL PEAK 41(20P13) WILD-TYPE                                                220
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 41(20P13) MUTATED                                            0
  DEL PEAK 41(20P13) WILD-TYPE                                          5
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 41(20P13) MUTATED                                               6
  DEL PEAK 41(20P13) WILD-TYPE                                            13
                              vv
clus                           LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 41(20P13) MUTATED                                2
  DEL PEAK 41(20P13) WILD-TYPE                              0
                              vv
clus                           LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 41(20P13) MUTATED                                    1
  DEL PEAK 41(20P13) WILD-TYPE                                  3
                              vv
clus                           LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 41(20P13) MUTATED                              0
  DEL PEAK 41(20P13) WILD-TYPE                            2
                              vv
clus                           LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 41(20P13) MUTATED                               3
  DEL PEAK 41(20P13) WILD-TYPE                            16
                              vv
clus                           LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 41(20P13) MUTATED                                 1
  DEL PEAK 41(20P13) WILD-TYPE                               0
                              vv
clus                           LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 41(20P13) MUTATED                                               1
  DEL PEAK 41(20P13) WILD-TYPE                                             4
                              vv
clus                           MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 41(20P13) MUTATED                              1
  DEL PEAK 41(20P13) WILD-TYPE                            6
D70V9, multiclass
                                                    clus
vv                                                   DEL PEAK 41(20P13) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                  3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                          23
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         83
  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                               1
  MUCINOUS (COLLOID) CARCINOMA                                                1
                                                    clus
vv                                                   DEL PEAK 41(20P13) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                   12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            71
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          220
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    5
  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"
D70V10, binary
                              cls
clus                             0   1
  DEL PEAK 41(20P13) MUTATED     4 120
  DEL PEAK 41(20P13) WILD-TYPE  17 335
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 41(20P13) MUTATED      4  120
  DEL PEAK 41(20P13) WILD-TYPE   17  335
     clus
vv    DEL PEAK 41(20P13) MUTATED DEL PEAK 41(20P13) WILD-TYPE
  NO                           4                           17
  YES                        120                          335
[1] 2 2
[1] FALSE
D70V11, continuous
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 41(20P13) MUTATED    91   4   1   4
  DEL PEAK 41(20P13) WILD-TYPE 236   8   3  17
D70V12, multiclass
    clus
vv   DEL PEAK 41(20P13) MUTATED DEL PEAK 41(20P13) WILD-TYPE
  R0                         91                          236
  R1                          4                            8
  R2                          1                            3
  RX                          4                           17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 41(20P13) MUTATED                                  0     1
  DEL PEAK 41(20P13) WILD-TYPE                                1     5
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 41(20P13) MUTATED                           7    98
  DEL PEAK 41(20P13) WILD-TYPE                        28   269
D70V13, multiclass
                                  clus
vv                                 DEL PEAK 41(20P13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     1
  BLACK OR AFRICAN AMERICAN                                 7
  WHITE                                                    98
                                  clus
vv                                 DEL PEAK 41(20P13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  28
  WHITE                                                     269
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V14, binary
                              cls
clus                             0   1
  DEL PEAK 41(20P13) MUTATED     1  92
  DEL PEAK 41(20P13) WILD-TYPE   6 253
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 41(20P13) MUTATED      1   92
  DEL PEAK 41(20P13) WILD-TYPE    6  253
                        clus
vv                       DEL PEAK 41(20P13) MUTATED
  HISPANIC OR LATINO                              1
  NOT HISPANIC OR LATINO                         92
                        clus
vv                       DEL PEAK 41(20P13) WILD-TYPE
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          253
[1] 2 2
[1] FALSE

Clustering(71) Variable = DEL PEAK 42(20Q13.12) MUTATION ANALYSIS
D71V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 42(20Q13.12) MUTATED    51  16
  DEL PEAK 42(20Q13.12) WILD-TYPE 278  71
  DEL PEAK 42(20Q13.12) MUTATED DEL PEAK 42(20Q13.12) WILD-TYPE 
                             67                             349 
  DEL PEAK 42(20Q13.12) MUTATED DEL PEAK 42(20Q13.12) WILD-TYPE 
                             16                              71 
$`DEL PEAK 42(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          462            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 42(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-49-AARQ TCGA-50-5045 TCGA-50-5049 
         445          890          354         6443         2174         2146 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
         785          944         1499          282          267         1091 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        2370          653          567          883          764          686 
TCGA-50-6597 TCGA-50-7109 TCGA-53-7626 TCGA-53-7813 TCGA-55-1592 TCGA-55-1594 
        1015          255         1971          424          701         1178 
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-55-6980 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-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
          95           40          705           39           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-55-8089 TCGA-55-8091 
           3           31            5           33          100          600 
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-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
          66          674          216           44           23           29 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 TCGA-55-8511 TCGA-55-8513 TCGA-55-8514 
          11            8          228            9          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-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
          42           29           48         1952            1           28 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
          47          162         1216         1970         2696         1445 
TCGA-62-A46V TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 
        2199         1728          628         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-67-3771 TCGA-67-3772 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
         866          610          573          422          202          186 
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-69-7980 TCGA-69-8254 TCGA-69-8255 TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 
         382           77          129           61         1600          711 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 
         912          800          467          131          164           38 
TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 
         621          519          305         1970         1967         1956 
TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7153 
        1973         1950         1944         1093         1963          760 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7159 TCGA-78-7161 TCGA-78-7162 
        1948         1957         1961         1221          215         1940 
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-78-7540 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-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7954 TCGA-86-7955 
          11          630          422         1968         1963          508 
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-86-8280 TCGA-86-8281 TCGA-86-8359 TCGA-86-8585 
         476          482           16         1955           26           35 
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-91-6829 TCGA-91-6830 
          10           30           14           39         1940           60 
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-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
         492          505          174           36           44          218 
TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
         127          186           34            2         1973          568 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VN 
         377          477          476          830           84          553 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
         605          964         1965         1932         1332          775 
TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 
         181           22          107           87          147           15 
TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-8028 TCGA-99-8032 TCGA-J2-8192 
         115          197          271          459           44          154 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
         114          287          238          435          116            6 
TCGA-L9-A50W TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 
         266          312          111          102          827         1175 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 
          84         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 
TCGA-S2-AA1A 
         121 

  DEL PEAK 42(20Q13.12) MUTATED DEL PEAK 42(20Q13.12) WILD-TYPE 
                              3                               1 
  DEL PEAK 42(20Q13.12) MUTATED DEL PEAK 42(20Q13.12) WILD-TYPE 
                           2067                            6443 
  DEL PEAK 42(20Q13.12) MUTATED DEL PEAK 42(20Q13.12) WILD-TYPE 
                            427                             482 
[1] "3.0 - 2067.0 (427.0)" "1.0 - 6443.0 (482.0)"
[1] "hr=" "1"  
D71V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 42(20Q13.12) MUTATED         1       14       23         5        11
  DEL PEAK 42(20Q13.12) WILD-TYPE       4      102      109        44        59
                                 vv
clus                              STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 42(20Q13.12) MUTATED           16          2        7
  DEL PEAK 42(20Q13.12) WILD-TYPE         52          9       17
D71V3, multiclass
            clus
vv           DEL PEAK 42(20Q13.12) MUTATED DEL PEAK 42(20Q13.12) WILD-TYPE
  STAGE I                                1                               4
  STAGE IA                              14                             102
  STAGE IB                              23                             109
  STAGE IIA                              5                              44
  STAGE IIB                             11                              59
  STAGE IIIA                            16                              52
  STAGE IIIB                             2                               9
  STAGE IV                               7                              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 42(20Q13.12) MUTATED    20  47   7   4
  DEL PEAK 42(20Q13.12) WILD-TYPE 127 220  35  14
D71V4, multiclass
    clus
vv   DEL PEAK 42(20Q13.12) MUTATED DEL PEAK 42(20Q13.12) WILD-TYPE
  T1                            20                             127
  T2                            47                             220
  T3                             7                              35
  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 42(20Q13.12) MUTATED    45  14    18
  DEL PEAK 42(20Q13.12) WILD-TYPE 256  77    56
D71V5, multiclass
       clus
vv      DEL PEAK 42(20Q13.12) MUTATED DEL PEAK 42(20Q13.12) WILD-TYPE
  N0                               45                             256
  N1                               14                              77
  N2+N3                            18                              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
  DEL PEAK 42(20Q13.12) MUTATED    60   6   0   1  12
  DEL PEAK 42(20Q13.12) WILD-TYPE 266  12   1   3 111
D71V6, multiclass
     clus
vv    DEL PEAK 42(20Q13.12) MUTATED DEL PEAK 42(20Q13.12) WILD-TYPE
  M0                             60                             266
  M1                              6                              12
  M1A                             0                               1
  M1B                             1                               3
  MX                             12                             111
[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 42(20Q13.12) MUTATED    46  33
  DEL PEAK 42(20Q13.12) WILD-TYPE 209 188
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 42(20Q13.12) MUTATED     46   33
  DEL PEAK 42(20Q13.12) WILD-TYPE  209  188
        clus
vv       DEL PEAK 42(20Q13.12) MUTATED DEL PEAK 42(20Q13.12) WILD-TYPE
  FEMALE                            46                             209
  MALE                              33                             188
[1] 2 2
[1] FALSE
D71V8, continuous
                                 vv
clus                              LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 42(20Q13.12) MUTATED                            3
  DEL PEAK 42(20Q13.12) WILD-TYPE                         12
                                 vv
clus                              LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 42(20Q13.12) MUTATED                                  20
  DEL PEAK 42(20Q13.12) WILD-TYPE                                74
                                 vv
clus                              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 42(20Q13.12) MUTATED                                                   43
  DEL PEAK 42(20Q13.12) WILD-TYPE                                                260
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 42(20Q13.12) MUTATED                                            0
  DEL PEAK 42(20Q13.12) WILD-TYPE                                          5
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 42(20Q13.12) MUTATED                                               3
  DEL PEAK 42(20Q13.12) WILD-TYPE                                            16
                                 vv
clus                              LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 42(20Q13.12) MUTATED                                2
  DEL PEAK 42(20Q13.12) WILD-TYPE                              0
                                 vv
clus                              LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 42(20Q13.12) MUTATED                                    2
  DEL PEAK 42(20Q13.12) WILD-TYPE                                  2
                                 vv
clus                              LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 42(20Q13.12) MUTATED                              0
  DEL PEAK 42(20Q13.12) WILD-TYPE                            2
                                 vv
clus                              LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 42(20Q13.12) MUTATED                               4
  DEL PEAK 42(20Q13.12) WILD-TYPE                            15
                                 vv
clus                              LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 42(20Q13.12) MUTATED                                 0
  DEL PEAK 42(20Q13.12) WILD-TYPE                               1
                                 vv
clus                              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 42(20Q13.12) MUTATED                                               0
  DEL PEAK 42(20Q13.12) WILD-TYPE                                             5
                                 vv
clus                              MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 42(20Q13.12) MUTATED                              2
  DEL PEAK 42(20Q13.12) WILD-TYPE                            5
D71V9, multiclass
                                                    clus
vv                                                   DEL PEAK 42(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 42(20Q13.12) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                               74
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             260
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                       5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                   16
  LUNG CLEAR CELL ADENOCARCINOMA                                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                               2
  LUNG MUCINOUS ADENOCARCINOMA                                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                                   15
  LUNG SIGNET RING ADENOCARCINOMA                                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                    5
  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"
D71V10, binary
                                 cls
clus                                0   1
  DEL PEAK 42(20Q13.12) MUTATED     1  78
  DEL PEAK 42(20Q13.12) WILD-TYPE  20 377
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 42(20Q13.12) MUTATED      1   78
  DEL PEAK 42(20Q13.12) WILD-TYPE   20  377
     clus
vv    DEL PEAK 42(20Q13.12) MUTATED DEL PEAK 42(20Q13.12) WILD-TYPE
  NO                              1                              20
  YES                            78                             377
[1] 2 2
[1] FALSE
D71V11, continuous
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 42(20Q13.12) MUTATED    56   2   1   6
  DEL PEAK 42(20Q13.12) WILD-TYPE 271  10   3  15
D71V12, multiclass
    clus
vv   DEL PEAK 42(20Q13.12) MUTATED DEL PEAK 42(20Q13.12) WILD-TYPE
  R0                            56                             271
  R1                             2                              10
  R2                             1                               3
  RX                             6                              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 42(20Q13.12) MUTATED                                  0     1
  DEL PEAK 42(20Q13.12) WILD-TYPE                                1     5
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 42(20Q13.12) MUTATED                           4    59
  DEL PEAK 42(20Q13.12) WILD-TYPE                        31   308
D71V13, multiclass
                                  clus
vv                                 DEL PEAK 42(20Q13.12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                    4
  WHITE                                                       59
                                  clus
vv                                 DEL PEAK 42(20Q13.12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          5
  BLACK OR AFRICAN AMERICAN                                     31
  WHITE                                                        308
[1] 4 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 42(20Q13.12) MUTATED     2  52
  DEL PEAK 42(20Q13.12) WILD-TYPE   5 293
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 42(20Q13.12) MUTATED      2   52
  DEL PEAK 42(20Q13.12) WILD-TYPE    5  293
                        clus
vv                       DEL PEAK 42(20Q13.12) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            52
                        clus
vv                       DEL PEAK 42(20Q13.12) WILD-TYPE
  HISPANIC OR LATINO                                   5
  NOT HISPANIC OR LATINO                             293
[1] 2 2
[1] FALSE

Clustering(72) Variable = DEL PEAK 43(21Q11.2) MUTATION ANALYSIS
D72V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 43(21Q11.2) MUTATED   115  34
  DEL PEAK 43(21Q11.2) WILD-TYPE 214  53
  DEL PEAK 43(21Q11.2) MUTATED DEL PEAK 43(21Q11.2) WILD-TYPE 
                           149                            267 
  DEL PEAK 43(21Q11.2) MUTATED DEL PEAK 43(21Q11.2) WILD-TYPE 
                            34                             53 
$`DEL PEAK 43(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          705           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-73-A9RS TCGA-75-7027 TCGA-75-7031 
         467          131           40          305         1956         1965 
TCGA-78-7146 TCGA-78-7148 TCGA-78-7153 TCGA-78-7154 TCGA-78-7167 TCGA-78-7220 
        1988         1944          760         1948         1937         1965 
TCGA-78-7536 TCGA-78-8640 TCGA-78-8660 TCGA-80-5608 TCGA-86-7701 TCGA-86-7711 
        1949         1949         1954         1972           11          630 
TCGA-86-7953 TCGA-86-8054 TCGA-86-8278 TCGA-86-8359 TCGA-86-8585 TCGA-86-8669 
         591          745          476           26           35           34 
TCGA-91-6828 TCGA-91-6831 TCGA-91-6836 TCGA-91-6840 TCGA-91-7771 TCGA-95-7043 
         323          310          417          372          492            2 
TCGA-95-7562 TCGA-95-7948 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7547 TCGA-97-8172 
        1973          476           84          605         1965          182 
TCGA-97-8175 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AE 
          87          427          459           44          170          282 
TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MP-A4SV TCGA-MP-A4T8 TCGA-MP-A4TE 
         111          102         1946         1957         1970 

$`DEL PEAK 43(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-49-AARQ TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5930 
         890         6443         2146          785          944          282 
TCGA-50-5931 TCGA-50-5941 TCGA-50-5942 TCGA-50-6597 TCGA-50-8460 TCGA-53-7624 
         267          567          883         1015          105         1986 
TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1595 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
        1971          280         1479            2          993           24 
TCGA-55-6969 TCGA-55-6971 TCGA-55-6980 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 
        1239           25           67         1170           18           35 
TCGA-55-7284 TCGA-55-7573 TCGA-55-7574 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
         121            4           95           39           39           34 
TCGA-55-7903 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8091 
          19            3            5           33          462          600 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
          47           15           46           66          674          216 
TCGA-55-8301 TCGA-55-8505 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 
          44           29            9            3          146          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-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8395 
          29            1           28            5          162         1216 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-A46U TCGA-62-A46V TCGA-62-A472 
        1289         1970         2696         2067         2199          910 
TCGA-64-1676 TCGA-64-1678 TCGA-64-1680 TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 
        1728         1189         1126         1305          864          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-67-6217 TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 TCGA-69-7978 
         141          422          690          414          230           70 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-73-4662 
         100           77          129          214           61          912 
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-78-7145 TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7155 
        1973         1950         1093         1963         1202         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-78-7535 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
        1950         1934         1972         1944          327          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-83-5908 TCGA-86-6851 TCGA-86-7713 TCGA-86-7714 TCGA-86-7954 TCGA-86-7955 
         824         1959          422         1968         1963          508 
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-86-8280 TCGA-86-8281 TCGA-86-8358 TCGA-86-8668 TCGA-86-8671 
         482           16         1955           19           45           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-91-6847 TCGA-91-6848 
          39         1940           60           79          842          224 
TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
          35          505          174           36           44          218 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 
         297          127          186           34          568          377 
TCGA-95-7947 TCGA-95-8039 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-7546 TCGA-97-7552 
         477          830          121          553          964         1932 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 
        1332          775          181           22          107         1965 
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-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L4-A4E5 
         392          154          114          287          238          578 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A743 TCGA-MN-A4N1 
         435          116            6          266          312          827 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 
        1175           84         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 TCGA-S2-AA1A 
        1971         1490          121 

  DEL PEAK 43(21Q11.2) MUTATED DEL PEAK 43(21Q11.2) WILD-TYPE 
                             2                              1 
  DEL PEAK 43(21Q11.2) MUTATED DEL PEAK 43(21Q11.2) WILD-TYPE 
                          2370                           6443 
  DEL PEAK 43(21Q11.2) MUTATED DEL PEAK 43(21Q11.2) WILD-TYPE 
                           492                            455 
[1] "2.0 - 2370.0 (492.0)" "1.0 - 6443.0 (455.0)"
[1] "hr=" "1.2"
D72V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 43(21Q11.2) MUTATED         2       33       45        13        31
  DEL PEAK 43(21Q11.2) WILD-TYPE       3       83       87        36        39
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 43(21Q11.2) MUTATED           26          5        9
  DEL PEAK 43(21Q11.2) WILD-TYPE         42          6       15
D72V3, multiclass
            clus
vv           DEL PEAK 43(21Q11.2) MUTATED DEL PEAK 43(21Q11.2) WILD-TYPE
  STAGE I                               2                              3
  STAGE IA                             33                             83
  STAGE IB                             45                             87
  STAGE IIA                            13                             36
  STAGE IIB                            31                             39
  STAGE IIIA                           26                             42
  STAGE IIIB                            5                              6
  STAGE IV                              9                             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 43(21Q11.2) MUTATED    40  98  17   7
  DEL PEAK 43(21Q11.2) WILD-TYPE 107 169  25  11
D72V4, multiclass
    clus
vv   DEL PEAK 43(21Q11.2) MUTATED DEL PEAK 43(21Q11.2) WILD-TYPE
  T1                           40                            107
  T2                           98                            169
  T3                           17                             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 43(21Q11.2) MUTATED   102  34    26
  DEL PEAK 43(21Q11.2) WILD-TYPE 199  57    48
D72V5, multiclass
       clus
vv      DEL PEAK 43(21Q11.2) MUTATED DEL PEAK 43(21Q11.2) WILD-TYPE
  N0                             102                            199
  N1                              34                             57
  N2+N3                           26                             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
  DEL PEAK 43(21Q11.2) MUTATED   113   7   0   1  42
  DEL PEAK 43(21Q11.2) WILD-TYPE 213  11   1   3  81
D72V6, multiclass
     clus
vv    DEL PEAK 43(21Q11.2) MUTATED DEL PEAK 43(21Q11.2) WILD-TYPE
  M0                           113                            213
  M1                             7                             11
  M1A                            0                              1
  M1B                            1                              3
  MX                            42                             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"
D72V7, binary
                                cls
clus                               0   1
  DEL PEAK 43(21Q11.2) MUTATED    80  84
  DEL PEAK 43(21Q11.2) WILD-TYPE 175 137
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(21Q11.2) MUTATED     80   84
  DEL PEAK 43(21Q11.2) WILD-TYPE  175  137
        clus
vv       DEL PEAK 43(21Q11.2) MUTATED DEL PEAK 43(21Q11.2) WILD-TYPE
  FEMALE                           80                            175
  MALE                             84                            137
[1] 2 2
[1] FALSE
D72V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 43(21Q11.2) MUTATED                            8
  DEL PEAK 43(21Q11.2) WILD-TYPE                          7
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 43(21Q11.2) MUTATED                                  26
  DEL PEAK 43(21Q11.2) WILD-TYPE                                68
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 43(21Q11.2) MUTATED                                                  115
  DEL PEAK 43(21Q11.2) WILD-TYPE                                                188
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 43(21Q11.2) MUTATED                                            0
  DEL PEAK 43(21Q11.2) WILD-TYPE                                          5
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 43(21Q11.2) MUTATED                                               2
  DEL PEAK 43(21Q11.2) WILD-TYPE                                            17
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 43(21Q11.2) MUTATED                                0
  DEL PEAK 43(21Q11.2) WILD-TYPE                              2
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 43(21Q11.2) MUTATED                                    1
  DEL PEAK 43(21Q11.2) WILD-TYPE                                  3
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 43(21Q11.2) MUTATED                              0
  DEL PEAK 43(21Q11.2) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 43(21Q11.2) MUTATED                               6
  DEL PEAK 43(21Q11.2) WILD-TYPE                            13
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 43(21Q11.2) MUTATED                                 1
  DEL PEAK 43(21Q11.2) WILD-TYPE                               0
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 43(21Q11.2) MUTATED                                               2
  DEL PEAK 43(21Q11.2) WILD-TYPE                                             3
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 43(21Q11.2) MUTATED                              3
  DEL PEAK 43(21Q11.2) WILD-TYPE                            4
D72V9, multiclass
                                                    clus
vv                                                   DEL PEAK 43(21Q11.2) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            26
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          115
  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 43(21Q11.2) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              68
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            188
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  17
  LUNG CLEAR CELL ADENOCARCINOMA                                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              3
  LUNG MUCINOUS ADENOCARCINOMA                                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                                  13
  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"
D72V10, binary
                                cls
clus                               0   1
  DEL PEAK 43(21Q11.2) MUTATED    10 154
  DEL PEAK 43(21Q11.2) WILD-TYPE  11 301
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(21Q11.2) MUTATED     10  154
  DEL PEAK 43(21Q11.2) WILD-TYPE   11  301
     clus
vv    DEL PEAK 43(21Q11.2) MUTATED DEL PEAK 43(21Q11.2) WILD-TYPE
  NO                            10                             11
  YES                          154                            301
[1] 2 2
[1] FALSE
D72V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 43(21Q11.2) MUTATED   112   3   1   5
  DEL PEAK 43(21Q11.2) WILD-TYPE 215   9   3  16
D72V12, multiclass
    clus
vv   DEL PEAK 43(21Q11.2) MUTATED DEL PEAK 43(21Q11.2) WILD-TYPE
  R0                          112                            215
  R1                            3                              9
  R2                            1                              3
  RX                            5                             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 43(21Q11.2) MUTATED                                  1     1
  DEL PEAK 43(21Q11.2) WILD-TYPE                                0     5
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 43(21Q11.2) MUTATED                          17   116
  DEL PEAK 43(21Q11.2) WILD-TYPE                        18   251
D72V13, multiclass
                                  clus
vv                                 DEL PEAK 43(21Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                  17
  WHITE                                                     116
                                  clus
vv                                 DEL PEAK 43(21Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         5
  BLACK OR AFRICAN AMERICAN                                    18
  WHITE                                                       251
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V14, binary
                                cls
clus                               0   1
  DEL PEAK 43(21Q11.2) MUTATED     2 114
  DEL PEAK 43(21Q11.2) WILD-TYPE   5 231
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(21Q11.2) MUTATED      2  114
  DEL PEAK 43(21Q11.2) WILD-TYPE    5  231
                        clus
vv                       DEL PEAK 43(21Q11.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          114
                        clus
vv                       DEL PEAK 43(21Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            231
[1] 2 2
[1] FALSE

Clustering(73) Variable = DEL PEAK 44(22Q13.32) MUTATION ANALYSIS
D73V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 44(22Q13.32) MUTATED   163  42
  DEL PEAK 44(22Q13.32) WILD-TYPE 166  45
  DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE 
                            205                             211 
  DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE 
                             42                              45 
$`DEL PEAK 44(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-73-A9RS TCGA-75-6214 
         711          912          467          131          305         1970 
TCGA-75-7027 TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 TCGA-78-7152 TCGA-78-7159 
        1956         1965         1973         1988         1202         1221 
TCGA-78-7163 TCGA-78-7167 TCGA-78-7535 TCGA-78-7536 TCGA-78-8640 TCGA-78-8660 
        1950         1937         1972         1949         1949         1954 
TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
        1964         1972          824         1959           11          630 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8056 TCGA-86-8074 
         591         1963          508          745         1963           24 
TCGA-86-8279 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8672 TCGA-86-A4D0 
         482           19           26           35           15           30 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6836 TCGA-91-6840 
         323         1940           60          310          417          372 
TCGA-91-6847 TCGA-91-7771 TCGA-91-8499 TCGA-91-A4BC TCGA-93-8067 TCGA-95-7039 
         842          492           36           44          186           34 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VN 
        1973          568          377          830           84          553 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7552 TCGA-97-7554 TCGA-97-7937 TCGA-99-7458 
         605          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-L9-A50W TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV 
         266          111          102          827           84         1946 
TCGA-MP-A4T2 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
        1951         1957         1951         1970         1970          142 
TCGA-MP-A4TK 
        1971 

$`DEL PEAK 44(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-49-AARQ 
         157         1700          445          369          522         6443 
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-50-5931 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-8460 TCGA-53-7626 
         267          883          764          686          105         1971 
TCGA-55-1592 TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6983 
         701         1479         1375           87            2         1826 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 
        2151         1170          121            4          705           39 
TCGA-55-7726 TCGA-55-7728 TCGA-55-7815 TCGA-55-7907 TCGA-55-7914 TCGA-55-7995 
          39           24           54           16            3            5 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8096 
          33          462          100            6          600           47 
TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
          15           46          674          216           44           23 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
         146          202          536           49          106           33 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A494 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
        1952            1            5         1216         1289         1970 
TCGA-62-8402 TCGA-62-A46V TCGA-62-A471 TCGA-64-1680 TCGA-64-5815 TCGA-67-3770 
        1445         2199         1246         1126          866           31 
TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-69-7765 
         573          427          385          174          141          165 
TCGA-69-7974 TCGA-69-8254 TCGA-73-4658 TCGA-73-4666 TCGA-73-4675 TCGA-73-4676 
         184           77         1600          800           40          164 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-75-7025 TCGA-78-7147 TCGA-78-7148 
          38          621          519         1967         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-78-7158 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7166 TCGA-78-7220 
        1963          678          215         1940         1934         1965 
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-86-7713 TCGA-86-7714 TCGA-86-8055 TCGA-86-8073 
        1981         1965          422         1968           10           13 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8281 TCGA-86-8668 
         479          489          476           16         1955           45 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 
          34           18          455          405           10           14 
TCGA-86-A4P8 TCGA-91-6835 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 
          39           79          224           35          505          174 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-95-7043 TCGA-95-7947 TCGA-95-7948 
         218          297          127            2          477          476 
TCGA-95-A4VK TCGA-97-7547 TCGA-97-7553 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
         121         1965         1332           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-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
         197          271          427          154          114          287 
TCGA-J2-A4AE TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A743 TCGA-MN-A4N4 TCGA-MP-A4SW 
         282          435          116          312         1175         1967 
TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TC TCGA-MP-A4TI TCGA-MP-A5C7 
        1954         1954         1980         1944         1955         1490 
TCGA-S2-AA1A 
         121 

  DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE 
                              3                               1 
  DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE 
                           2696                            6443 
  DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE 
                            508                             462 
[1] "3.0 - 2696.0 (508.0)" "1.0 - 6443.0 (462.0)"
[1] "hr=" "1"  
D73V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 44(22Q13.32) MUTATED         3       49       63        27        35
  DEL PEAK 44(22Q13.32) WILD-TYPE       2       67       69        22        35
                                 vv
clus                              STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 44(22Q13.32) MUTATED           36          6       13
  DEL PEAK 44(22Q13.32) WILD-TYPE         32          5       11
D73V3, multiclass
            clus
vv           DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE
  STAGE I                                3                               2
  STAGE IA                              49                              67
  STAGE IB                              63                              69
  STAGE IIA                             27                              22
  STAGE IIB                             35                              35
  STAGE IIIA                            36                              32
  STAGE IIIB                             6                               5
  STAGE IV                              13                              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 44(22Q13.32) MUTATED    71 131  20   9
  DEL PEAK 44(22Q13.32) WILD-TYPE  76 136  22   9
D73V4, multiclass
    clus
vv   DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE
  T1                            71                              76
  T2                           131                             136
  T3                            20                              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
  DEL PEAK 44(22Q13.32) MUTATED   147  45    37
  DEL PEAK 44(22Q13.32) WILD-TYPE 154  46    37
D73V5, multiclass
       clus
vv      DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE
  N0                              147                             154
  N1                               45                              46
  N2+N3                            37                              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 44(22Q13.32) MUTATED   158  10   0   3  59
  DEL PEAK 44(22Q13.32) WILD-TYPE 168   8   1   1  64
D73V6, multiclass
     clus
vv    DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE
  M0                            158                             168
  M1                             10                               8
  M1A                             0                               1
  M1B                             3                               1
  MX                             59                              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"
D73V7, binary
                                 cls
clus                                0   1
  DEL PEAK 44(22Q13.32) MUTATED   109 123
  DEL PEAK 44(22Q13.32) WILD-TYPE 146  98
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 44(22Q13.32) MUTATED    109  123
  DEL PEAK 44(22Q13.32) WILD-TYPE  146   98
        clus
vv       DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE
  FEMALE                           109                             146
  MALE                             123                              98
[1] 2 2
[1] FALSE
D73V8, continuous
                                 vv
clus                              LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 44(22Q13.32) MUTATED                           10
  DEL PEAK 44(22Q13.32) WILD-TYPE                          5
                                 vv
clus                              LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 44(22Q13.32) MUTATED                                  39
  DEL PEAK 44(22Q13.32) WILD-TYPE                                55
                                 vv
clus                              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 44(22Q13.32) MUTATED                                                  155
  DEL PEAK 44(22Q13.32) WILD-TYPE                                                148
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 44(22Q13.32) MUTATED                                            1
  DEL PEAK 44(22Q13.32) WILD-TYPE                                          4
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 44(22Q13.32) MUTATED                                              10
  DEL PEAK 44(22Q13.32) WILD-TYPE                                             9
                                 vv
clus                              LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 44(22Q13.32) MUTATED                                0
  DEL PEAK 44(22Q13.32) WILD-TYPE                              2
                                 vv
clus                              LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 44(22Q13.32) MUTATED                                    2
  DEL PEAK 44(22Q13.32) WILD-TYPE                                  2
                                 vv
clus                              LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 44(22Q13.32) MUTATED                              0
  DEL PEAK 44(22Q13.32) WILD-TYPE                            2
                                 vv
clus                              LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 44(22Q13.32) MUTATED                               8
  DEL PEAK 44(22Q13.32) WILD-TYPE                            11
                                 vv
clus                              LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 44(22Q13.32) MUTATED                                 1
  DEL PEAK 44(22Q13.32) WILD-TYPE                               0
                                 vv
clus                              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 44(22Q13.32) MUTATED                                               4
  DEL PEAK 44(22Q13.32) WILD-TYPE                                             1
                                 vv
clus                              MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 44(22Q13.32) MUTATED                              2
  DEL PEAK 44(22Q13.32) WILD-TYPE                            5
D73V9, multiclass
                                                    clus
vv                                                   DEL PEAK 44(22Q13.32) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             39
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           155
  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                                                   2
                                                    clus
vv                                                   DEL PEAK 44(22Q13.32) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                       5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                               55
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             148
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                       4
  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"
D73V10, binary
                                 cls
clus                                0   1
  DEL PEAK 44(22Q13.32) MUTATED     9 223
  DEL PEAK 44(22Q13.32) WILD-TYPE  12 232
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 44(22Q13.32) MUTATED      9  223
  DEL PEAK 44(22Q13.32) WILD-TYPE   12  232
     clus
vv    DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE
  NO                              9                              12
  YES                           223                             232
[1] 2 2
[1] FALSE
D73V11, continuous
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 44(22Q13.32) MUTATED   159   6   1  10
  DEL PEAK 44(22Q13.32) WILD-TYPE 168   6   3  11
D73V12, multiclass
    clus
vv   DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE
  R0                           159                             168
  R1                             6                               6
  R2                             1                               3
  RX                            10                              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 44(22Q13.32) MUTATED                                  1     2
  DEL PEAK 44(22Q13.32) WILD-TYPE                                0     4
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 44(22Q13.32) MUTATED                          21   174
  DEL PEAK 44(22Q13.32) WILD-TYPE                        14   193
D73V13, multiclass
                                  clus
vv                                 DEL PEAK 44(22Q13.32) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   21
  WHITE                                                      174
                                  clus
vv                                 DEL PEAK 44(22Q13.32) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          4
  BLACK OR AFRICAN AMERICAN                                     14
  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"
D73V14, binary
                                 cls
clus                                0   1
  DEL PEAK 44(22Q13.32) MUTATED     4 172
  DEL PEAK 44(22Q13.32) WILD-TYPE   3 173
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 44(22Q13.32) MUTATED      4  172
  DEL PEAK 44(22Q13.32) WILD-TYPE    3  173
                        clus
vv                       DEL PEAK 44(22Q13.32) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           172
                        clus
vv                       DEL PEAK 44(22Q13.32) WILD-TYPE
  HISPANIC OR LATINO                                   3
  NOT HISPANIC OR LATINO                             173
[1] 2 2
[1] FALSE

Clustering(74) Variable = DEL PEAK 45(XP22.2) MUTATION ANALYSIS
D74V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 45(XP22.2) MUTATED    96  23
  DEL PEAK 45(XP22.2) WILD-TYPE 233  64
  DEL PEAK 45(XP22.2) MUTATED DEL PEAK 45(XP22.2) WILD-TYPE 
                          119                           297 
  DEL PEAK 45(XP22.2) MUTATED DEL PEAK 45(XP22.2) WILD-TYPE 
                           23                            64 
$`DEL PEAK 45(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-49-AARQ TCGA-50-5066 
         385          260          428          157         6443          944 
TCGA-50-5068 TCGA-50-5932 TCGA-50-5933 TCGA-50-5941 TCGA-50-5946 TCGA-50-6597 
        1499         1091         2370          567          686         1015 
TCGA-50-7109 TCGA-53-7624 TCGA-53-7626 TCGA-55-1592 TCGA-55-1596 TCGA-55-5899 
         255         1986         1971          701         1375           87 
TCGA-55-6543 TCGA-55-6712 TCGA-55-6987 TCGA-55-7281 TCGA-55-7570 TCGA-55-7726 
           2           24         1170           18            6           39 
TCGA-55-7903 TCGA-55-7994 TCGA-55-8090 TCGA-55-8094 TCGA-55-8301 TCGA-55-8510 
          19           31            6            4           44          228 
TCGA-55-8616 TCGA-55-A48X TCGA-55-A48Z TCGA-55-A492 TCGA-55-A4DG TCGA-62-8397 
          48           33           29            1          162         1289 
TCGA-62-A46U TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 TCGA-64-5778 TCGA-64-5815 
        2067          910         1728         1189         1305          866 
TCGA-67-3770 TCGA-67-3772 TCGA-67-3773 TCGA-67-6217 TCGA-69-7764 TCGA-69-7765 
          31          573          427          422          414          165 
TCGA-69-7979 TCGA-69-A59K TCGA-71-6725 TCGA-73-4666 TCGA-73-4668 TCGA-73-7499 
          89          214           61          800          467          519 
TCGA-73-A9RS TCGA-75-7025 TCGA-75-7031 TCGA-78-7146 TCGA-78-7154 TCGA-78-7160 
         305         1967         1965         1988         1948          678 
TCGA-78-7166 TCGA-78-7535 TCGA-78-7542 TCGA-78-8640 TCGA-78-8655 TCGA-78-8660 
        1934         1972         1952         1949         1981         1954 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8075 TCGA-86-8281 
        1963          508          745           10          479         1955 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8673 TCGA-86-A4P7 TCGA-91-6848 TCGA-91-7771 
          19           26          455           14          224          492 
TCGA-91-8496 TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-95-8039 TCGA-95-8494 
         505           34            2          568          830           84 
TCGA-97-7554 TCGA-97-7937 TCGA-97-8172 TCGA-97-8179 TCGA-97-8547 TCGA-97-A4M7 
         775          181          182           15          148          271 
TCGA-L4-A4E5 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A7SV TCGA-MN-A4N5 TCGA-MP-A4SV 
         578            6          266          111           84         1946 
TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4TI TCGA-S2-AA1A 
        1967         1951         1954         1955          121 

$`DEL PEAK 45(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-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 TCGA-55-6983 
         993         1239           25         1475           67         1826 
TCGA-55-6985 TCGA-55-6986 TCGA-55-7283 TCGA-55-7284 TCGA-55-7573 TCGA-55-7574 
        1233         2151           35          121            4           95 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
          40          705           39           34           24           54 
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-55-8091 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 
         462          100          600           26           47           15 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8302 
          33           46           66          674          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-95-7562 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK 
         186         1973          377          477          476          121 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
         553          605          964         1965         1932         1332 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 TCGA-97-8552 
          22          107         1965           87          147          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-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 
         154          114          287          282          238          435 
TCGA-L9-A443 TCGA-L9-A743 TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4T7 
         116          312          102          827         1175         1954 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TF 
        1957         1980         1951         1944         1970         1970 
TCGA-MP-A4TH TCGA-MP-A4TK TCGA-MP-A5C7 
         142         1971         1490 

  DEL PEAK 45(XP22.2) MUTATED DEL PEAK 45(XP22.2) WILD-TYPE 
                            1                             3 
  DEL PEAK 45(XP22.2) MUTATED DEL PEAK 45(XP22.2) WILD-TYPE 
                         6443                          2696 
  DEL PEAK 45(XP22.2) MUTATED DEL PEAK 45(XP22.2) WILD-TYPE 
                          508                           459 
[1] "1.0 - 6443.0 (508.0)" "3.0 - 2696.0 (459.0)"
[1] "hr=" "1.4"
D74V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 45(XP22.2) MUTATED         3       29       36        12        28
  DEL PEAK 45(XP22.2) WILD-TYPE       2       87       96        37        42
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 45(XP22.2) MUTATED           15          3        8
  DEL PEAK 45(XP22.2) WILD-TYPE         53          8       16
D74V3, multiclass
            clus
vv           DEL PEAK 45(XP22.2) MUTATED DEL PEAK 45(XP22.2) WILD-TYPE
  STAGE I                              3                             2
  STAGE IA                            29                            87
  STAGE IB                            36                            96
  STAGE IIA                           12                            37
  STAGE IIB                           28                            42
  STAGE IIIA                          15                            53
  STAGE IIIB                           3                             8
  STAGE IV                             8                            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 45(XP22.2) MUTATED    39  75  14   5
  DEL PEAK 45(XP22.2) WILD-TYPE 108 192  28  13
D74V4, multiclass
    clus
vv   DEL PEAK 45(XP22.2) MUTATED DEL PEAK 45(XP22.2) WILD-TYPE
  T1                          39                           108
  T2                          75                           192
  T3                          14                            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
  DEL PEAK 45(XP22.2) MUTATED    80  33    19
  DEL PEAK 45(XP22.2) WILD-TYPE 221  58    55
D74V5, multiclass
       clus
vv      DEL PEAK 45(XP22.2) MUTATED DEL PEAK 45(XP22.2) WILD-TYPE
  N0                             80                           221
  N1                             33                            58
  N2+N3                          19                            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 45(XP22.2) MUTATED    93   6   0   1  32
  DEL PEAK 45(XP22.2) WILD-TYPE 233  12   1   3  91
D74V6, multiclass
     clus
vv    DEL PEAK 45(XP22.2) MUTATED DEL PEAK 45(XP22.2) WILD-TYPE
  M0                           93                           233
  M1                            6                            12
  M1A                           0                             1
  M1B                           1                             3
  MX                           32                            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"
D74V7, binary
                               cls
clus                              0   1
  DEL PEAK 45(XP22.2) MUTATED    60  74
  DEL PEAK 45(XP22.2) WILD-TYPE 195 147
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 45(XP22.2) MUTATED     60   74
  DEL PEAK 45(XP22.2) WILD-TYPE  195  147
        clus
vv       DEL PEAK 45(XP22.2) MUTATED DEL PEAK 45(XP22.2) WILD-TYPE
  FEMALE                          60                           195
  MALE                            74                           147
[1] 2 2
[1] FALSE
D74V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 45(XP22.2) MUTATED                            5
  DEL PEAK 45(XP22.2) WILD-TYPE                         10
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 45(XP22.2) MUTATED                                  29
  DEL PEAK 45(XP22.2) WILD-TYPE                                65
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 45(XP22.2) MUTATED                                                   87
  DEL PEAK 45(XP22.2) WILD-TYPE                                                216
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 45(XP22.2) MUTATED                                            2
  DEL PEAK 45(XP22.2) WILD-TYPE                                          3
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 45(XP22.2) MUTATED                                               4
  DEL PEAK 45(XP22.2) WILD-TYPE                                            15
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 45(XP22.2) MUTATED                                0
  DEL PEAK 45(XP22.2) WILD-TYPE                              2
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 45(XP22.2) MUTATED                                    3
  DEL PEAK 45(XP22.2) WILD-TYPE                                  1
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 45(XP22.2) MUTATED                              1
  DEL PEAK 45(XP22.2) WILD-TYPE                            1
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 45(XP22.2) MUTATED                               2
  DEL PEAK 45(XP22.2) WILD-TYPE                            17
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 45(XP22.2) MUTATED                                 0
  DEL PEAK 45(XP22.2) WILD-TYPE                               1
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 45(XP22.2) MUTATED                                               0
  DEL PEAK 45(XP22.2) WILD-TYPE                                             5
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 45(XP22.2) MUTATED                              1
  DEL PEAK 45(XP22.2) WILD-TYPE                            6
D74V9, multiclass
                                                    clus
vv                                                   DEL PEAK 45(XP22.2) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           29
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          87
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                   2
  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 45(XP22.2) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                    10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             65
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           216
  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                                  5
  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"
D74V10, binary
                               cls
clus                              0   1
  DEL PEAK 45(XP22.2) MUTATED     4 130
  DEL PEAK 45(XP22.2) WILD-TYPE  17 325
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 45(XP22.2) MUTATED      4  130
  DEL PEAK 45(XP22.2) WILD-TYPE   17  325
     clus
vv    DEL PEAK 45(XP22.2) MUTATED DEL PEAK 45(XP22.2) WILD-TYPE
  NO                            4                            17
  YES                         130                           325
[1] 2 2
[1] FALSE
D74V11, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 45(XP22.2) MUTATED    88   2   1   4
  DEL PEAK 45(XP22.2) WILD-TYPE 239  10   3  17
D74V12, multiclass
    clus
vv   DEL PEAK 45(XP22.2) MUTATED DEL PEAK 45(XP22.2) WILD-TYPE
  R0                          88                           239
  R1                           2                            10
  R2                           1                             3
  RX                           4                            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 45(XP22.2) MUTATED                                  1     2
  DEL PEAK 45(XP22.2) WILD-TYPE                                0     4
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 45(XP22.2) MUTATED                          13    97
  DEL PEAK 45(XP22.2) WILD-TYPE                        22   270
D74V13, multiclass
                                  clus
vv                                 DEL PEAK 45(XP22.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 13
  WHITE                                                     97
                                  clus
vv                                 DEL PEAK 45(XP22.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   22
  WHITE                                                      270
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V14, binary
                               cls
clus                              0   1
  DEL PEAK 45(XP22.2) MUTATED     1  95
  DEL PEAK 45(XP22.2) WILD-TYPE   6 250
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 45(XP22.2) MUTATED      1   95
  DEL PEAK 45(XP22.2) WILD-TYPE    6  250
                        clus
vv                       DEL PEAK 45(XP22.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          95
                        clus
vv                       DEL PEAK 45(XP22.2) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           250
[1] 2 2
[1] FALSE
