[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"        "-oTLUSC-TP"
[1] "opt"       "-OPMUTSIG"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/LUSC-TP/11541613/LUSC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LUSC-TP/11545692/transformed.cor.cli.txt"

nPatients in clinical file=422, in cluster file=501, common to both=420
[1]  83 420
[1] "AMP PEAK  1(1Q21.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE 
                          223                           197 
  AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE 
                          223                           197 
[1] "AMP PEAK  2(2P16.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE 
                          227                           193 
  AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE 
                          227                           193 
[1] "AMP PEAK  3(2Q31.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(2Q31.2) MUTATED AMP PEAK  3(2Q31.2) WILD-TYPE 
                          143                           277 
  AMP PEAK  3(2Q31.2) MUTATED AMP PEAK  3(2Q31.2) WILD-TYPE 
                          143                           277 
[1] "AMP PEAK  4(3Q26.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE 
                           383                             37 
  AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE 
                           383                             37 
[1] "AMP PEAK  5(4Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                        103                         317 
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                        103                         317 
[1] "AMP PEAK  6(5P15.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                           332                             88 
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                           332                             88 
[1] "AMP PEAK  7(5P12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(5P12) MUTATED AMP PEAK  7(5P12) WILD-TYPE 
                        305                         115 
  AMP PEAK  7(5P12) MUTATED AMP PEAK  7(5P12) WILD-TYPE 
                        305                         115 
[1] "AMP PEAK  8(6P12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(6P12.1) MUTATED AMP PEAK  8(6P12.1) WILD-TYPE 
                          138                           282 
  AMP PEAK  8(6P12.1) MUTATED AMP PEAK  8(6P12.1) WILD-TYPE 
                          138                           282 
[1] "AMP PEAK  9(6Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE 
                        126                         294 
  AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE 
                        126                         294 
[1] "AMP PEAK 10(7P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE 
                          216                           204 
  AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE 
                          216                           204 
[1] "AMP PEAK 11(7Q21.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(7Q21.2) MUTATED AMP PEAK 11(7Q21.2) WILD-TYPE 
                          227                           193 
  AMP PEAK 11(7Q21.2) MUTATED AMP PEAK 11(7Q21.2) WILD-TYPE 
                          227                           193 
[1] "AMP PEAK 12(8P11.23) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(8P11.23) MUTATED AMP PEAK 12(8P11.23) WILD-TYPE 
                           201                            219 
  AMP PEAK 12(8P11.23) MUTATED AMP PEAK 12(8P11.23) WILD-TYPE 
                           201                            219 
[1] "AMP PEAK 13(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                           302                            118 
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                           302                            118 
[1] "AMP PEAK 14(9P13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE 
                          112                           308 
  AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE 
                          112                           308 
[1] "AMP PEAK 15(11Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE 
                           158                            262 
  AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE 
                           158                            262 
[1] "AMP PEAK 16(12P13.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(12P13.33) MUTATED AMP PEAK 16(12P13.33) WILD-TYPE 
                            216                             204 
  AMP PEAK 16(12P13.33) MUTATED AMP PEAK 16(12P13.33) WILD-TYPE 
                            216                             204 
[1] "AMP PEAK 17(12Q15) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE 
                         155                          265 
  AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE 
                         155                          265 
[1] "AMP PEAK 18(13Q34) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE 
                          75                          345 
  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE 
                          75                          345 
[1] "AMP PEAK 19(14Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(14Q13.3) MUTATED AMP PEAK 19(14Q13.3) WILD-TYPE 
                           130                            290 
  AMP PEAK 19(14Q13.3) MUTATED AMP PEAK 19(14Q13.3) WILD-TYPE 
                           130                            290 
[1] "AMP PEAK 20(14Q32.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(14Q32.33) MUTATED AMP PEAK 20(14Q32.33) WILD-TYPE 
                            131                             289 
  AMP PEAK 20(14Q32.33) MUTATED AMP PEAK 20(14Q32.33) WILD-TYPE 
                            131                             289 
[1] "AMP PEAK 21(15Q26.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE 
                           147                            273 
  AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE 
                           147                            273 
[1] "AMP PEAK 22(17Q25.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE 
                           201                            219 
  AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE 
                           201                            219 
[1] "AMP PEAK 23(18P11.32) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(18P11.32) MUTATED AMP PEAK 23(18P11.32) WILD-TYPE 
                            153                             267 
  AMP PEAK 23(18P11.32) MUTATED AMP PEAK 23(18P11.32) WILD-TYPE 
                            153                             267 
[1] "AMP PEAK 24(18Q11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE 
                           135                            285 
  AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE 
                           135                            285 
[1] "AMP PEAK 25(19Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE 
                         186                          234 
  AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE 
                         186                          234 
[1] "AMP PEAK 26(19Q13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 26(19Q13.2) MUTATED AMP PEAK 26(19Q13.2) WILD-TYPE 
                           196                            224 
  AMP PEAK 26(19Q13.2) MUTATED AMP PEAK 26(19Q13.2) WILD-TYPE 
                           196                            224 
[1] "AMP PEAK 27(20P12.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE 
                           234                            186 
  AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE 
                           234                            186 
[1] "AMP PEAK 28(20Q11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 28(20Q11.21) MUTATED AMP PEAK 28(20Q11.21) WILD-TYPE 
                            256                             164 
  AMP PEAK 28(20Q11.21) MUTATED AMP PEAK 28(20Q11.21) WILD-TYPE 
                            256                             164 
[1] "AMP PEAK 29(22Q11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 29(22Q11.21) MUTATED AMP PEAK 29(22Q11.21) WILD-TYPE 
                            218                             202 
  AMP PEAK 29(22Q11.21) MUTATED AMP PEAK 29(22Q11.21) WILD-TYPE 
                            218                             202 
[1] "AMP PEAK 30(XQ28) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 30(XQ28) MUTATED AMP PEAK 30(XQ28) WILD-TYPE 
                        103                         317 
  AMP PEAK 30(XQ28) MUTATED AMP PEAK 30(XQ28) WILD-TYPE 
                        103                         317 
[1] "DEL PEAK  1(1P36.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           189                            231 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           189                            231 
[1] "DEL PEAK  2(1P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                          187                           233 
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                          187                           233 
[1] "DEL PEAK  3(2P25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                           41                           379 
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                           41                           379 
[1] "DEL PEAK  4(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                          107                           313 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                          107                           313 
[1] "DEL PEAK  5(2Q37.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE 
                          132                           288 
  DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE 
                          132                           288 
[1] "DEL PEAK  6(3P25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(3P25.3) MUTATED DEL PEAK  6(3P25.3) WILD-TYPE 
                          334                            86 
  DEL PEAK  6(3P25.3) MUTATED DEL PEAK  6(3P25.3) WILD-TYPE 
                          334                            86 
[1] "DEL PEAK  7(3P13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(3P13) MUTATED DEL PEAK  7(3P13) WILD-TYPE 
                        364                          56 
  DEL PEAK  7(3P13) MUTATED DEL PEAK  7(3P13) WILD-TYPE 
                        364                          56 
[1] "DEL PEAK  8(3P12.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(3P12.3) MUTATED DEL PEAK  8(3P12.3) WILD-TYPE 
                          358                            62 
  DEL PEAK  8(3P12.3) MUTATED DEL PEAK  8(3P12.3) WILD-TYPE 
                          358                            62 
[1] "DEL PEAK  9(3P12.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(3P12.3) MUTATED DEL PEAK  9(3P12.3) WILD-TYPE 
                          353                            67 
  DEL PEAK  9(3P12.3) MUTATED DEL PEAK  9(3P12.3) WILD-TYPE 
                          353                            67 
[1] "DEL PEAK 10(3Q11.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(3Q11.1) MUTATED DEL PEAK 10(3Q11.1) WILD-TYPE 
                           63                           357 
  DEL PEAK 10(3Q11.1) MUTATED DEL PEAK 10(3Q11.1) WILD-TYPE 
                           63                           357 
[1] "DEL PEAK 11(4P15.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                          262                           158 
  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                          262                           158 
[1] "DEL PEAK 12(4Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                          238                           182 
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                          238                           182 
[1] "DEL PEAK 13(4Q32.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(4Q32.3) MUTATED DEL PEAK 13(4Q32.3) WILD-TYPE 
                          271                           149 
  DEL PEAK 13(4Q32.3) MUTATED DEL PEAK 13(4Q32.3) WILD-TYPE 
                          271                           149 
[1] "DEL PEAK 14(4Q35.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE 
                          275                           145 
  DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE 
                          275                           145 
[1] "DEL PEAK 15(5Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE 
                          313                           107 
  DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE 
                          313                           107 
[1] "DEL PEAK 16(5Q31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(5Q31.1) MUTATED DEL PEAK 16(5Q31.1) WILD-TYPE 
                          326                            94 
  DEL PEAK 16(5Q31.1) MUTATED DEL PEAK 16(5Q31.1) WILD-TYPE 
                          326                            94 
[1] "DEL PEAK 17(6P25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(6P25.3) MUTATED DEL PEAK 17(6P25.3) WILD-TYPE 
                          113                           307 
  DEL PEAK 17(6P25.3) MUTATED DEL PEAK 17(6P25.3) WILD-TYPE 
                          113                           307 
[1] "DEL PEAK 18(6Q22.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(6Q22.31) MUTATED DEL PEAK 18(6Q22.31) WILD-TYPE 
                           103                            317 
  DEL PEAK 18(6Q22.31) MUTATED DEL PEAK 18(6Q22.31) WILD-TYPE 
                           103                            317 
[1] "DEL PEAK 19(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE 
                        113                         307 
  DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE 
                        113                         307 
[1] "DEL PEAK 20(7Q11.22) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(7Q11.22) MUTATED DEL PEAK 20(7Q11.22) WILD-TYPE 
                            38                            382 
  DEL PEAK 20(7Q11.22) MUTATED DEL PEAK 20(7Q11.22) WILD-TYPE 
                            38                            382 
[1] "DEL PEAK 21(7Q36.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE 
                           87                           333 
  DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE 
                           87                           333 
[1] "DEL PEAK 22(8P23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE 
                          291                           129 
  DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE 
                          291                           129 
[1] "DEL PEAK 23(9P23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE 
                        277                         143 
  DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE 
                        277                         143 
[1] "DEL PEAK 24(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE 
                          323                            97 
  DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE 
                          323                            97 
[1] "DEL PEAK 25(9P21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(9P21.1) MUTATED DEL PEAK 25(9P21.1) WILD-TYPE 
                          275                           145 
  DEL PEAK 25(9P21.1) MUTATED DEL PEAK 25(9P21.1) WILD-TYPE 
                          275                           145 
[1] "DEL PEAK 26(9Q21.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(9Q21.11) MUTATED DEL PEAK 26(9Q21.11) WILD-TYPE 
                           210                            210 
  DEL PEAK 26(9Q21.11) MUTATED DEL PEAK 26(9Q21.11) WILD-TYPE 
                           210                            210 
[1] "DEL PEAK 27(10P15.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(10P15.2) MUTATED DEL PEAK 27(10P15.2) WILD-TYPE 
                           186                            234 
  DEL PEAK 27(10P15.2) MUTATED DEL PEAK 27(10P15.2) WILD-TYPE 
                           186                            234 
[1] "DEL PEAK 28(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE 
                            222                             198 
  DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE 
                            222                             198 
[1] "DEL PEAK 29(11P15.5) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE 
                           205                            215 
  DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE 
                           205                            215 
[1] "DEL PEAK 30(11Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(11Q22.1) MUTATED DEL PEAK 30(11Q22.1) WILD-TYPE 
                           136                            284 
  DEL PEAK 30(11Q22.1) MUTATED DEL PEAK 30(11Q22.1) WILD-TYPE 
                           136                            284 
[1] "DEL PEAK 31(11Q25) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(11Q25) MUTATED DEL PEAK 31(11Q25) WILD-TYPE 
                         155                          265 
  DEL PEAK 31(11Q25) MUTATED DEL PEAK 31(11Q25) WILD-TYPE 
                         155                          265 
[1] "DEL PEAK 32(12Q24.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(12Q24.31) MUTATED DEL PEAK 32(12Q24.31) WILD-TYPE 
                             71                             349 
  DEL PEAK 32(12Q24.31) MUTATED DEL PEAK 32(12Q24.31) WILD-TYPE 
                             71                             349 
[1] "DEL PEAK 33(13Q12.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE 
                            275                             145 
  DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE 
                            275                             145 
[1] "DEL PEAK 34(13Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE 
                           284                            136 
  DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE 
                           284                            136 
[1] "DEL PEAK 35(14Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 35(14Q11.2) MUTATED DEL PEAK 35(14Q11.2) WILD-TYPE 
                           148                            272 
  DEL PEAK 35(14Q11.2) MUTATED DEL PEAK 35(14Q11.2) WILD-TYPE 
                           148                            272 
[1] "DEL PEAK 36(15Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE 
                           131                            289 
  DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE 
                           131                            289 
[1] "DEL PEAK 37(15Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 37(15Q21.1) MUTATED DEL PEAK 37(15Q21.1) WILD-TYPE 
                           133                            287 
  DEL PEAK 37(15Q21.1) MUTATED DEL PEAK 37(15Q21.1) WILD-TYPE 
                           133                            287 
[1] "DEL PEAK 38(16P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE 
                           155                            265 
  DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE 
                           155                            265 
[1] "DEL PEAK 39(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE 
                           170                            250 
  DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE 
                           170                            250 
[1] "DEL PEAK 40(17P11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE 
                           221                            199 
  DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE 
                           221                            199 
[1] "DEL PEAK 41(17Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 41(17Q11.2) MUTATED DEL PEAK 41(17Q11.2) WILD-TYPE 
                           113                            307 
  DEL PEAK 41(17Q11.2) MUTATED DEL PEAK 41(17Q11.2) WILD-TYPE 
                           113                            307 
[1] "DEL PEAK 42(17Q25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 42(17Q25.3) MUTATED DEL PEAK 42(17Q25.3) WILD-TYPE 
                            86                            334 
  DEL PEAK 42(17Q25.3) MUTATED DEL PEAK 42(17Q25.3) WILD-TYPE 
                            86                            334 
[1] "DEL PEAK 43(18Q23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 43(18Q23) MUTATED DEL PEAK 43(18Q23) WILD-TYPE 
                         191                          229 
  DEL PEAK 43(18Q23) MUTATED DEL PEAK 43(18Q23) WILD-TYPE 
                         191                          229 
[1] "DEL PEAK 44(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                           193                            227 
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                           193                            227 
[1] "DEL PEAK 45(19Q13.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 45(19Q13.32) MUTATED DEL PEAK 45(19Q13.32) WILD-TYPE 
                            121                             299 
  DEL PEAK 45(19Q13.32) MUTATED DEL PEAK 45(19Q13.32) WILD-TYPE 
                            121                             299 
[1] "DEL PEAK 46(21Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 46(21Q11.2) MUTATED DEL PEAK 46(21Q11.2) WILD-TYPE 
                           201                            219 
  DEL PEAK 46(21Q11.2) MUTATED DEL PEAK 46(21Q11.2) WILD-TYPE 
                           201                            219 
[1] "DEL PEAK 47(21Q22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 47(21Q22.3) MUTATED DEL PEAK 47(21Q22.3) WILD-TYPE 
                           235                            185 
  DEL PEAK 47(21Q22.3) MUTATED DEL PEAK 47(21Q22.3) WILD-TYPE 
                           235                            185 
[1] "DEL PEAK 48(22Q11.21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 48(22Q11.21) MUTATED DEL PEAK 48(22Q11.21) WILD-TYPE 
                             74                             346 
  DEL PEAK 48(22Q11.21) MUTATED DEL PEAK 48(22Q11.21) WILD-TYPE 
                             74                             346 
[1] "DEL PEAK 49(22Q13.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 49(22Q13.32) MUTATED DEL PEAK 49(22Q13.32) WILD-TYPE 
                             98                             322 
  DEL PEAK 49(22Q13.32) MUTATED DEL PEAK 49(22Q13.32) WILD-TYPE 
                             98                             322 
[1] "DEL PEAK 50(XP22.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE 
                          124                           296 
  DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE 
                          124                           296 
[1] "DEL PEAK 51(XP21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE 
                          124                           296 
  DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE 
                          124                           296 
[1] "DEL PEAK 52(XP11.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE 
                          119                           301 
  DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE 
                          119                           301 
[1] "DEL PEAK 53(XQ22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 53(XQ22.3) MUTATED DEL PEAK 53(XQ22.3) WILD-TYPE 
                           87                           333 
  DEL PEAK 53(XQ22.3) MUTATED DEL PEAK 53(XQ22.3) WILD-TYPE 
                           87                           333 
[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 420 columns.

[1] "Batch" "23"   
[1] "Last Follow UP"
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
         370          136         2464         2417          146         1415 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 
         345          396         1810          862          758           50 
TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 
        1331          187           85         2754           92          827 
TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 
        3636         1426         3016         2134         1852         1058 
TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 
         474          965         3724          284         3644          267 
TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI 
         962           NA         1268         1032          329          979 
TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 
         608          223           NA          131         1953           53 
TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 
         429          822         1485          623         1067         1470 
TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 
         734           17         1161         1057          399           NA 
TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 
         587           NA          358          965         1975         1933 
TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 
         445         1346           24         1651         2170           NA 
TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 
         357          573          916         1912         1713          506 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 
          29         2524         3469         2979         1311         5287 
TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-33-6737 
        3149         4299          428           NA           NA           NA 
TCGA-33-6738 TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 
         822           80         1874          958          881         1000 
TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 
         951         1528         2062         1715           NA          707 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 
         365          428          941          552           NA           NA 
TCGA-34-8454 TCGA-34-8455 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 
         166           NA          120           13           12          200 
TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 
         247          227          238          207           12          103 
TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 
        1454         2253         1361         2086           NA         2130 
TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 
        1849           52          740           59          833         1107 
TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 
         474         1084         1086          544           NA         1223 
TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 
         684         1176          822         1007          349          849 
TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 
         376          757          310           NA           NA          212 
TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 
         236         2023          407          358           NA          353 
TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 
         296          432          366           NA           NA           NA 
TCGA-46-3768 TCGA-46-3769 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 
          NA           NA          324          423           12           12 
TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 
         911          541           NA          923           NA           NA 
TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 
         881            3          555           62           26           30 
TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 
          13           30           44           40           26            6 
TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 
          NA            1           41          178           55           36 
TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW 
          63           17           16           34           38            2 
TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS 
          46           30           25            4            4            8 
TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 
          NA           NA          378          911         2167           NA 
TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N 
        1058         2589           NA         1723         1072          910 
TCGA-60-2695 TCGA-60-2696 TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 
         642          109           NA          311           NA           NA 
TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 
        2820          661         2447         1505         2024         1260 
TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 
         274         1731         1531         1075         1475         1297 
TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 
          97          983          908         1092          717          816 
TCGA-60-2726 TCGA-63-5128 TCGA-63-5131 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 
         358           NA           NA           NA           NA           NA 
TCGA-63-7022 TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 
          NA           NA           NA         1311           61          641 
TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 
          30           31           61           28           30           30 
TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 
         639          762           30           61           31           61 
TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 
          61           NA          700          578           NA           61 
TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 
         578           NA          121           NA          759           60 
TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 
         790         1217          699           NA          699           NA 
TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 
         913           NA         1645          122         1492           83 
TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J 
         202          211          244           96          121          104 
TCGA-70-6722 TCGA-70-6723 TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 
          NA           NA           NA           NA           NA           NA 
TCGA-77-7138 TCGA-77-7139 TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 
          NA         2737           NA           15         1286           NA 
TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 
          NA           NA           NA          479           NA           NA 
TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 
        1641           NA         2522           NA           NA           NA 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-8145 
          NA         3166           NA           NA          833           NA 
TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ 
         293           NA         1684         1092           10           NA 
TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA 
        4026         3576           NA           NA         1290         1280 
TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-79-5596 TCGA-85-6175 TCGA-85-6560 
          NA          839          713           NA           NA          364 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 
         395           34           18           10           49            1 
TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 
          NA           35          911           60           26           60 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 
          16          960          428          513           13           11 
TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 
          13           54           60           55           67           54 
TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 
          61           61           22           21          445          424 
TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB 
          NA            3          475           15           NA           NA 
TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z 
          NA           NA           NA           25           19           NA 
TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 
          NA           NA           NA           24           13          111 
TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED 
         758          289           89          358          428          244 
TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 
         331          269           82          106          122          160 
TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7544 
          70           87           NA          356          430         1213 
TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 
        1344          189          211          273          183          256 
TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A4E7 
          NA          413          224          308          222           35 
TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HI 
         449           36           83         1722         1548         1135 
Variable 1:'AGE':	nDistinctValues=45,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=138,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=269,	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=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=19,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=123,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'HISTOLOGICAL.TYPE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'NUMBERPACKYEARSSMOKED':	nDistinctValues=97,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=55,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 23:'BATCH.NUMBER':	nDistinctValues=30,	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 420 columns, 1 survival variables, and 13 non-survival variables.
AGE, nv=45, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=9, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
 98 254  48  20 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
 98 254  48  20 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
 98 254  48  20 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
 98 254  48  20 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
261 113  35   5 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
261 113  35   5 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
 N0  N1  N2  N3 
261 113  35   5 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
261 113  35   5 
PATHOLOGY.M.STAGE, nv=4, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=8, binary=FALSE, numeric=TRUE
HISTOLOGICAL.TYPE, nv=4, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
NUMBERPACKYEARSSMOKED, nv=97, binary=FALSE, numeric=TRUE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK  1(1Q21.2) MUTATION ANALYSIS
D1V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  1(1Q21.2) MUTATED   145  65
  AMP PEAK  1(1Q21.2) WILD-TYPE 120  58
  AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE 
                          210                           178 
  AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE 
                           65                            58 
$`AMP PEAK  1(1Q21.2) MUTATED`
TCGA-18-3408 TCGA-18-3411 TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 
        2464         1415          396         1810          862          758 
TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 
        2754           92         3636         1426         3016         2134 
TCGA-21-1077 TCGA-21-1081 TCGA-21-1082 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 
        1058          284         3644         1268         1032          329 
TCGA-22-0940 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 
         608           53          429          822         1485          623 
TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4607 
        1470          734           17         1161         1057          587 
TCGA-22-5471 TCGA-22-5473 TCGA-22-5474 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 
         965         1933          445         1651         1952         1952 
TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4538 
         573          916         1912           29         1940         2979 
TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-6738 
        5287         1966         1941          428         1970          822 
TCGA-34-2596 TCGA-34-2600 TCGA-34-2605 TCGA-34-2608 TCGA-34-5231 TCGA-34-5239 
          80         1874          881         1000         1528          707 
TCGA-34-5240 TCGA-34-5928 TCGA-37-3783 TCGA-37-3792 TCGA-37-4130 TCGA-37-4132 
         365          552          120           12          247          227 
TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5016 TCGA-39-5021 
         238          207           12          103         2253         1947 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5034 TCGA-39-5035 TCGA-39-5037 TCGA-39-5040 
        1996         1964         1107          474         1086         1964 
TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-6143 TCGA-43-7657 
        1223         1176          822         1007          376          236 
TCGA-43-7658 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56V TCGA-46-6025 TCGA-51-4079 
        1970          353          296          366          324           12 
TCGA-51-4080 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 
          12          541         1948          923         1958         1967 
TCGA-56-5898 TCGA-56-6545 TCGA-56-7223 TCGA-56-7730 TCGA-56-8504 TCGA-56-8622 
         555           62           30            6          178           55 
TCGA-56-A4BX TCGA-58-8388 TCGA-58-8393 TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N 
          46          378         1058         1723         1072          910 
TCGA-60-2695 TCGA-60-2698 TCGA-60-2706 TCGA-60-2708 TCGA-60-2711 TCGA-60-2715 
         642          311         1958         1963         1260         1075 
TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 
         983          908         1092          816          358         1973 
TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2755 TCGA-66-2756 
        1967         1311           61          641           28           30 
TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2770 TCGA-66-2773 TCGA-66-2777 
         639          762           30          700         1946           61 
TCGA-66-2781 TCGA-66-2782 TCGA-66-2785 TCGA-66-2787 TCGA-66-2791 TCGA-66-2793 
         121         1954           60         1217         1977         1952 
TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J 
         122         1492           83           96          121          104 
TCGA-77-6843 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7337 
        1941         1952         1959         1968           15         1942 
TCGA-77-7338 TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8133 
        1952          479         1945         1641         1953         1941 
TCGA-77-8136 TCGA-77-8139 TCGA-77-8145 TCGA-77-8148 TCGA-77-8156 TCGA-77-A5G3 
        1947         1951         1943          293           10         1959 
TCGA-77-A5G6 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH 
        1955         1290         1280         1939          839          713 
TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7699 TCGA-85-7710 
         364          395           34           18            1         1965 
TCGA-85-7844 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8072 
         911           26           60           16          960          513 
TCGA-85-8277 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8479 TCGA-85-8664 
          11           55           67           54           22            3 
TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A511 TCGA-85-A512 
         475           15         1960           19         1972         1987 
TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7767 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE 
          13          111           89          428          244          331 
TCGA-90-A59Q TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7943 
         269          106          122          160           70          356 
TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8169 TCGA-96-A4JK TCGA-98-8021 TCGA-98-8022 
         430         1213          189          273          413          224 
TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A524 TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HG 
         308          222          449           83         1722         1548 

$`AMP PEAK  1(1Q21.2) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3412 TCGA-18-3419 
         370          136         2417          146          345           50 
TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-5595 TCGA-21-1076 TCGA-21-1078 
        1331          187           85          827         1852          474 
TCGA-21-1079 TCGA-21-1080 TCGA-21-1083 TCGA-21-5782 TCGA-21-A5DI TCGA-22-0944 
         965         3724          267          962          979          223 
TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-4593 TCGA-22-4604 TCGA-22-4605 
        1945          131         1952         1067          399         1946 
TCGA-22-4613 TCGA-22-5472 TCGA-22-5477 TCGA-22-5478 TCGA-22-5482 TCGA-22-5491 
         358         1964         1346           24          357         1713 
TCGA-22-5492 TCGA-33-4532 TCGA-33-4547 TCGA-33-4589 TCGA-34-2604 TCGA-34-2609 
         506         2524         1311         1948          958          951 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5241 TCGA-34-5927 TCGA-34-8454 TCGA-37-3789 
        2062         1715          428          941          166           13 
TCGA-37-4129 TCGA-39-5011 TCGA-39-5019 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 
         200         1454         1361         1849           52          740 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5036 TCGA-39-5039 TCGA-43-2578 TCGA-43-5668 
          59          833         1084          544          684          349 
TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 TCGA-43-8115 
         849          757          310         1936          212          407 
TCGA-43-8116 TCGA-43-8118 TCGA-43-A56U TCGA-46-6026 TCGA-51-4081 TCGA-56-1622 
         358         1971          432          423          911          881 
TCGA-56-5897 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7579 TCGA-56-7580 
           3           26           30           13           44           40 
TCGA-56-7582 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 TCGA-56-8624 TCGA-56-8625 
          26         1961            1           41           36           63 
TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BY 
          17           16           34           38            2           30 
TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8390 TCGA-58-8391 
          25            4            4            8          911         2167 
TCGA-58-A46J TCGA-60-2696 TCGA-60-2703 TCGA-60-2704 TCGA-60-2707 TCGA-60-2709 
        2589          109         1950         1943          661         1505 
TCGA-60-2710 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 TCGA-60-2719 
        1963          274         1731         1531         1475         1297 
TCGA-60-2720 TCGA-60-2724 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 
          97          717         1957         1955         1947         1952 
TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2757 TCGA-66-2765 TCGA-66-2766 
          30           31           61           30           61           31 
TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2771 TCGA-66-2778 TCGA-66-2780 
          61           61         1947          578          578         1956 
TCGA-66-2783 TCGA-66-2786 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2792 
         759          790          699         1955          699          913 
TCGA-66-2794 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-77-6842 TCGA-77-6844 
        1645          202          211          244         1950         1942 
TCGA-77-7142 TCGA-77-7335 TCGA-77-7463 TCGA-77-8007 TCGA-77-8130 TCGA-77-8131 
        1286         1954         1954         1960         1945         1941 
TCGA-77-8138 TCGA-77-8140 TCGA-77-8144 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 
        1946         1962          833         1961         1684         1092 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G7 TCGA-85-7697 TCGA-85-7698 TCGA-85-7843 
        1953         1942         1963           10           49           35 
TCGA-85-7950 TCGA-85-8071 TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 
          60          428           13           13           54           60 
TCGA-85-8354 TCGA-85-8355 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-A4PA 
          61           61           21          445          424         1972 
TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A510 TCGA-85-A513 TCGA-90-6837 TCGA-90-7766 
          25         1973         1967           24          758          289 
TCGA-90-7769 TCGA-92-7340 TCGA-94-7033 TCGA-96-7545 TCGA-96-8170 TCGA-96-A4JL 
         358           82           87         1344          211          183 
TCGA-98-7454 TCGA-L3-A4E7 TCGA-LA-A446 TCGA-NC-A5HI 
         256           35           36         1135 

  AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE 
                            1                             1 
  AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE 
                         5287                          3724 
  AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE 
                          710                           525 
[1] "1.0 - 5287.0 (710.0)" "1.0 - 3724.0 (525.0)"
[1] "hr=" "1.2"
D1V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  1(1Q21.2) MUTATED         0       29       77        1        27
  AMP PEAK  1(1Q21.2) WILD-TYPE       1       43       60        0        25
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK  1(1Q21.2) MUTATED          38         34         12        5
  AMP PEAK  1(1Q21.2) WILD-TYPE        33         23          8        1
D1V3, multiclass
            clus
vv           AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE
  STAGE I                              0                             1
  STAGE IA                            29                            43
  STAGE IB                            77                            60
  STAGE II                             1                             0
  STAGE IIA                           27                            25
  STAGE IIB                           38                            33
  STAGE IIIA                          34                            23
  STAGE IIIB                          12                             8
  STAGE IV                             5                             1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK  1(1Q21.2) MUTATED    41 140  28  14
  AMP PEAK  1(1Q21.2) WILD-TYPE  57 114  20   6
D1V4, multiclass
    clus
vv   AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE
  T1                          41                            57
  T2                         140                           114
  T3                          28                            20
  T4                          14                             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  1(1Q21.2) MUTATED   136  61  22   1
  AMP PEAK  1(1Q21.2) WILD-TYPE 125  52  13   4
D1V5, multiclass
    clus
vv   AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE
  N0                         136                           125
  N1                          61                            52
  N2                          22                            13
  N3                           1                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A  MX
  AMP PEAK  1(1Q21.2) MUTATED   195   4   1  20
  AMP PEAK  1(1Q21.2) WILD-TYPE 163   1   0  30
D1V6, multiclass
     clus
vv    AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE
  M0                          195                           163
  M1                            4                             1
  M1A                           1                             0
  MX                           20                            30
[1] 4 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(1Q21.2) MUTATED    52 171
  AMP PEAK  1(1Q21.2) WILD-TYPE  55 142
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q21.2) MUTATED     52  171
  AMP PEAK  1(1Q21.2) WILD-TYPE   55  142
        clus
vv       AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE
  FEMALE                          52                            55
  MALE                           171                           142
[1] 2 2
[1] FALSE
D1V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK  1(1Q21.2) MUTATED                                      11
  AMP PEAK  1(1Q21.2) WILD-TYPE                                     1
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK  1(1Q21.2) MUTATED                                        2
  AMP PEAK  1(1Q21.2) WILD-TYPE                                      4
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK  1(1Q21.2) MUTATED                                         1
  AMP PEAK  1(1Q21.2) WILD-TYPE                                       0
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  1(1Q21.2) MUTATED                                                           209
  AMP PEAK  1(1Q21.2) WILD-TYPE                                                         192
D1V9, multiclass
                                                             clus
vv                                                            AMP PEAK  1(1Q21.2) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                11
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         209
                                                             clus
vv                                                            AMP PEAK  1(1Q21.2) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           192
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V10, binary
                               cls
clus                              0   1
  AMP PEAK  1(1Q21.2) MUTATED     8 215
  AMP PEAK  1(1Q21.2) WILD-TYPE   5 192
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q21.2) MUTATED      8  215
  AMP PEAK  1(1Q21.2) WILD-TYPE    5  192
     clus
vv    AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE
  NO                            8                             5
  YES                         215                           192
[1] 2 2
[1] FALSE
D1V11, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  1(1Q21.2) MUTATED   185   5   1   8
  AMP PEAK  1(1Q21.2) WILD-TYPE 157   3   3  10
D1V12, multiclass
    clus
vv   AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE
  R0                         185                           157
  R1                           5                             3
  R2                           1                             3
  RX                           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                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  1(1Q21.2) MUTATED       4                         9   163
  AMP PEAK  1(1Q21.2) WILD-TYPE     5                         8   135
D1V13, multiclass
                           clus
vv                          AMP PEAK  1(1Q21.2) MUTATED
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                           9
  WHITE                                             163
                           clus
vv                          AMP PEAK  1(1Q21.2) WILD-TYPE
  ASIAN                                                 5
  BLACK OR AFRICAN AMERICAN                             8
  WHITE                                               135
[1] 3 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(1Q21.2) MUTATED     5 143
  AMP PEAK  1(1Q21.2) WILD-TYPE   3 124
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q21.2) MUTATED      5  143
  AMP PEAK  1(1Q21.2) WILD-TYPE    3  124
                        clus
vv                       AMP PEAK  1(1Q21.2) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         143
                        clus
vv                       AMP PEAK  1(1Q21.2) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           124
[1] 2 2
[1] FALSE

Clustering(2) Variable = AMP PEAK  2(2P16.1) MUTATION ANALYSIS
D2V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  2(2P16.1) MUTATED   143  63
  AMP PEAK  2(2P16.1) WILD-TYPE 122  60
  AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE 
                          206                           182 
  AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE 
                           63                            60 
$`AMP PEAK  2(2P16.1) MUTATED`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 
         136         2417         1415          345          396         1810 
TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-21-1071 TCGA-21-1072 
         862          758           50         1331         1426         3016 
TCGA-21-1076 TCGA-21-1077 TCGA-21-1079 TCGA-21-1081 TCGA-21-1083 TCGA-21-5786 
        1852         1058          965          284          267         1032 
TCGA-21-A5DI TCGA-22-4591 TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 
         979          623          734         1161         1057          399 
TCGA-22-4605 TCGA-22-4613 TCGA-22-5471 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 
        1946          358          965         1933          445         1346 
TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5483 TCGA-22-5489 TCGA-22-5491 
          24         1651         1952          573         1912         1713 
TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4566 TCGA-33-4582 TCGA-33-6738 
         506           29         2524         5287         1966          822 
TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-5231 TCGA-34-5240 
          80         1874          958          881         1528          365 
TCGA-34-5241 TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 TCGA-37-3792 TCGA-37-4130 
         428          552          166          120           12          247 
TCGA-37-4133 TCGA-37-4141 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5027 
         238           12         1454         2253         1361         1849 
TCGA-39-5028 TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5040 
          52          833          474         1084         1086         1964 
TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 
        1223         1176          822         1007          349          849 
TCGA-43-6143 TCGA-43-6647 TCGA-43-7658 TCGA-43-8115 TCGA-43-8118 TCGA-46-6025 
         376          757         1970          407         1971          324 
TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 
          12           12          911         1948          923         1958 
TCGA-56-1622 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7222 TCGA-56-7223 
         881          555           62           26           13           30 
TCGA-56-7579 TCGA-56-7582 TCGA-56-7730 TCGA-56-8503 TCGA-56-8504 TCGA-56-8628 
          44           26            6           41          178           16 
TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A5DS TCGA-58-8391 
          34            2           46           30            8         2167 
TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2698 TCGA-60-2703 TCGA-60-2708 
        1723         1072          910          311         1950         1963 
TCGA-60-2711 TCGA-60-2712 TCGA-60-2715 TCGA-60-2719 TCGA-60-2722 TCGA-60-2723 
        1260          274         1075         1297          908         1092 
TCGA-60-2724 TCGA-60-2726 TCGA-63-6202 TCGA-63-7023 TCGA-66-2737 TCGA-66-2755 
         717          358         1973         1952           61           28 
TCGA-66-2758 TCGA-66-2763 TCGA-66-2766 TCGA-66-2767 TCGA-66-2769 TCGA-66-2770 
         639           30           31           61         1947          700 
TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2781 TCGA-66-2787 TCGA-66-2789 
         578         1946           61          121         1217         1955 
TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 
        1977          913         1952         1645          122         1492 
TCGA-68-7755 TCGA-68-7756 TCGA-68-8250 TCGA-68-A59I TCGA-77-6842 TCGA-77-6845 
          83          202          244          121         1950         1952 
TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 
        1959         1968           15         1286         1954         1942 
TCGA-77-7465 TCGA-77-8009 TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 TCGA-77-8139 
         479         1641         1945         1941         1947         1951 
TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8156 TCGA-77-A5G1 TCGA-77-A5G3 
        1943          293         1961           10         1942         1959 
TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 TCGA-85-6798 
        1290         1280          839          713          364           34 
TCGA-85-7696 TCGA-85-7843 TCGA-85-7844 TCGA-85-8052 TCGA-85-8070 TCGA-85-8072 
          18           35          911           16          960          513 
TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8350 TCGA-85-8352 TCGA-85-8354 
          13           11           13           60           67           61 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4QR TCGA-85-A50M TCGA-85-A510 TCGA-85-A511 
           3          475           25           19         1967         1972 
TCGA-85-A5B5 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4EE TCGA-92-7341 TCGA-92-8064 
         111           89          358          331          106          160 
TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7545 TCGA-96-8169 TCGA-96-A4JK TCGA-98-7454 
         356          430         1344          189          273          256 
TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A524 TCGA-LA-A446 
         413          224          308          222          449           36 
TCGA-MF-A522 TCGA-NC-A5HG 
          83         1548 

$`AMP PEAK  2(2P16.1) WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3410 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 
         370         2464          146          187           85         2754 
TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1075 TCGA-21-1078 TCGA-21-1080 
          92          827         3636         2134          474         3724 
TCGA-21-1082 TCGA-21-5782 TCGA-21-5784 TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 
        3644          962         1268          329          608          223 
TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 
        1945          131         1952           53          429          822 
TCGA-22-1017 TCGA-22-4593 TCGA-22-4594 TCGA-22-4596 TCGA-22-4607 TCGA-22-5472 
        1485         1067         1470           17          587         1964 
TCGA-22-5481 TCGA-22-5482 TCGA-22-5485 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 
        1952          357          916         1940         2979         1311 
TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-34-2608 TCGA-34-2609 
        1941          428         1970         1948         1000          951 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5927 TCGA-37-3789 TCGA-37-4129 
        2062         1715          707          941           13          200 
TCGA-37-4132 TCGA-37-4135 TCGA-37-5819 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 
         227          207          103         1947         1996         1964 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5034 TCGA-39-5039 TCGA-43-2578 TCGA-43-6770 
         740           59         1107          544          684          310 
TCGA-43-6771 TCGA-43-7656 TCGA-43-7657 TCGA-43-8116 TCGA-43-A474 TCGA-43-A475 
        1936          212          236          358          353          296 
TCGA-43-A56U TCGA-43-A56V TCGA-46-6026 TCGA-52-7622 TCGA-52-7812 TCGA-56-5897 
         432          366          423          541         1967            3 
TCGA-56-7221 TCGA-56-7580 TCGA-56-7731 TCGA-56-7822 TCGA-56-8622 TCGA-56-8624 
          30           40         1961            1           55           36 
TCGA-56-8625 TCGA-56-8626 TCGA-56-A49D TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR 
          63           17           38           25            4            4 
TCGA-58-8388 TCGA-58-8390 TCGA-58-8393 TCGA-58-A46J TCGA-60-2695 TCGA-60-2696 
         378          911         1058         2589          642          109 
TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 
        1943         1958          661         1505         1963         1731 
TCGA-60-2714 TCGA-60-2716 TCGA-60-2720 TCGA-60-2721 TCGA-60-2725 TCGA-63-7020 
        1531         1475           97          983          816         1957 
TCGA-63-7021 TCGA-63-7022 TCGA-66-2727 TCGA-66-2734 TCGA-66-2742 TCGA-66-2744 
        1955         1947         1967         1311          641           30 
TCGA-66-2753 TCGA-66-2754 TCGA-66-2756 TCGA-66-2757 TCGA-66-2759 TCGA-66-2765 
          31           61           30           30          762           61 
TCGA-66-2768 TCGA-66-2778 TCGA-66-2780 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 
          61          578         1956         1954          759           60 
TCGA-66-2786 TCGA-66-2788 TCGA-66-2790 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59J 
         790          699          699          211           96          104 
TCGA-77-6843 TCGA-77-6844 TCGA-77-7338 TCGA-77-7463 TCGA-77-8007 TCGA-77-8008 
        1941         1942         1952         1954         1960         1945 
TCGA-77-8128 TCGA-77-8131 TCGA-77-8138 TCGA-77-8140 TCGA-77-8144 TCGA-77-8153 
        1953         1941         1946         1962          833         1684 
TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5GB TCGA-85-6561 
        1092         1953         1955         1963         1939          395 
TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7950 TCGA-85-8048 
          10           49            1         1965           60           26 
TCGA-85-8049 TCGA-85-8071 TCGA-85-8288 TCGA-85-8351 TCGA-85-8353 TCGA-85-8355 
          60          428           54           55           54           61 
TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-A4CL TCGA-85-A4PA 
          22           21          445          424           15         1972 
TCGA-85-A4QQ TCGA-85-A50Z TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 
        1960         1973         1987           24           13          758 
TCGA-90-7766 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A59Q TCGA-92-7340 TCGA-92-8063 
         289          428          244          269           82          122 
TCGA-92-8065 TCGA-94-7033 TCGA-96-7544 TCGA-96-8170 TCGA-96-A4JL TCGA-L3-A4E7 
          70           87         1213          211          183           35 
TCGA-NC-A5HE TCGA-NC-A5HI 
        1722         1135 

  AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE 
                            2                             1 
  AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE 
                         5287                          3724 
  AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE 
                        669.5                         641.5 
[1] "2.0 - 5287.0 (669.5)" "1.0 - 3724.0 (641.5)"
[1] "hr=" "1.1"
D2V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  2(2P16.1) MUTATED         1       33       66        1        30
  AMP PEAK  2(2P16.1) WILD-TYPE       0       39       71        0        22
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK  2(2P16.1) MUTATED          44         33         14        3
  AMP PEAK  2(2P16.1) WILD-TYPE        27         24          6        3
D2V3, multiclass
            clus
vv           AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE
  STAGE I                              1                             0
  STAGE IA                            33                            39
  STAGE IB                            66                            71
  STAGE II                             1                             0
  STAGE IIA                           30                            22
  STAGE IIB                           44                            27
  STAGE IIIA                          33                            24
  STAGE IIIB                          14                             6
  STAGE IV                             3                             3
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK  2(2P16.1) MUTATED    48 132  31  16
  AMP PEAK  2(2P16.1) WILD-TYPE  50 122  17   4
D2V4, multiclass
    clus
vv   AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE
  T1                          48                            50
  T2                         132                           122
  T3                          31                            17
  T4                          16                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  AMP PEAK  2(2P16.1) MUTATED   131  76  16   3
  AMP PEAK  2(2P16.1) WILD-TYPE 130  37  19   2
D2V5, multiclass
    clus
vv   AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE
  N0                         131                           130
  N1                          76                            37
  N2                          16                            19
  N3                           3                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A  MX
  AMP PEAK  2(2P16.1) MUTATED   197   2   1  23
  AMP PEAK  2(2P16.1) WILD-TYPE 161   3   0  27
D2V6, multiclass
     clus
vv    AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE
  M0                          197                           161
  M1                            2                             3
  M1A                           1                             0
  MX                           23                            27
[1] 4 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(2P16.1) MUTATED    49 178
  AMP PEAK  2(2P16.1) WILD-TYPE  58 135
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2P16.1) MUTATED     49  178
  AMP PEAK  2(2P16.1) WILD-TYPE   58  135
        clus
vv       AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE
  FEMALE                          49                            58
  MALE                           178                           135
[1] 2 2
[1] FALSE
D2V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK  2(2P16.1) MUTATED                                      10
  AMP PEAK  2(2P16.1) WILD-TYPE                                     2
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK  2(2P16.1) MUTATED                                        1
  AMP PEAK  2(2P16.1) WILD-TYPE                                      5
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK  2(2P16.1) MUTATED                                         0
  AMP PEAK  2(2P16.1) WILD-TYPE                                       1
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  2(2P16.1) MUTATED                                                           216
  AMP PEAK  2(2P16.1) WILD-TYPE                                                         185
D2V9, multiclass
                                                             clus
vv                                                            AMP PEAK  2(2P16.1) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                10
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         216
                                                             clus
vv                                                            AMP PEAK  2(2P16.1) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           185
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V10, binary
                               cls
clus                              0   1
  AMP PEAK  2(2P16.1) MUTATED     8 219
  AMP PEAK  2(2P16.1) WILD-TYPE   5 188
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2P16.1) MUTATED      8  219
  AMP PEAK  2(2P16.1) WILD-TYPE    5  188
     clus
vv    AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE
  NO                            8                             5
  YES                         219                           188
[1] 2 2
[1] FALSE
D2V11, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  2(2P16.1) MUTATED   189   4   1   8
  AMP PEAK  2(2P16.1) WILD-TYPE 153   4   3  10
D2V12, multiclass
    clus
vv   AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE
  R0                         189                           153
  R1                           4                             4
  R2                           1                             3
  RX                           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                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  2(2P16.1) MUTATED       5                         6   166
  AMP PEAK  2(2P16.1) WILD-TYPE     4                        11   132
D2V13, multiclass
                           clus
vv                          AMP PEAK  2(2P16.1) MUTATED
  ASIAN                                               5
  BLACK OR AFRICAN AMERICAN                           6
  WHITE                                             166
                           clus
vv                          AMP PEAK  2(2P16.1) WILD-TYPE
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                            11
  WHITE                                               132
[1] 3 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(2P16.1) MUTATED     1 146
  AMP PEAK  2(2P16.1) WILD-TYPE   7 121
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2P16.1) MUTATED      1  146
  AMP PEAK  2(2P16.1) WILD-TYPE    7  121
                        clus
vv                       AMP PEAK  2(2P16.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                         146
                        clus
vv                       AMP PEAK  2(2P16.1) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           121
[1] 2 2
[1] FALSE

Clustering(3) Variable = AMP PEAK  3(2Q31.2) MUTATION ANALYSIS
D3V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  3(2Q31.2) MUTATED    87  42
  AMP PEAK  3(2Q31.2) WILD-TYPE 178  81
  AMP PEAK  3(2Q31.2) MUTATED AMP PEAK  3(2Q31.2) WILD-TYPE 
                          129                           259 
  AMP PEAK  3(2Q31.2) MUTATED AMP PEAK  3(2Q31.2) WILD-TYPE 
                           42                            81 
$`AMP PEAK  3(2Q31.2) MUTATED`
TCGA-18-3409 TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 
        2417         1415          345         1810          862          758 
TCGA-18-3421 TCGA-18-4721 TCGA-21-1072 TCGA-21-1081 TCGA-21-1083 TCGA-21-A5DI 
        1331         2754         3016          284          267          979 
TCGA-22-0944 TCGA-22-1012 TCGA-22-1017 TCGA-22-4594 TCGA-22-4601 TCGA-22-4605 
         223          429         1485         1470         1057         1946 
TCGA-22-4613 TCGA-22-5474 TCGA-22-5483 TCGA-22-5489 TCGA-22-5491 TCGA-33-4532 
         358          445          573         1912         1713         2524 
TCGA-33-4538 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4587 TCGA-33-6738 
        2979         5287         1966         1941         1970          822 
TCGA-34-2596 TCGA-34-2600 TCGA-34-2605 TCGA-34-5240 TCGA-34-5241 TCGA-37-3792 
          80         1874          881          365          428           12 
TCGA-37-4130 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5029 
         247         1454         2253         1361         1947          740 
TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5040 TCGA-43-2581 TCGA-43-3394 
         474         1084         1086         1964         1176          822 
TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-A474 TCGA-46-6025 
        1007          349          849          376          353          324 
TCGA-52-7810 TCGA-52-7811 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6546 
         923         1958          881            3          555           26 
TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7582 TCGA-56-8504 TCGA-56-8629 
          13           30           44           26          178           34 
TCGA-56-A5DS TCGA-58-8391 TCGA-58-A46N TCGA-60-2703 TCGA-60-2708 TCGA-60-2712 
           8         2167          910         1950         1963          274 
TCGA-60-2719 TCGA-60-2726 TCGA-66-2727 TCGA-66-2754 TCGA-66-2758 TCGA-66-2759 
        1297          358         1967           61          639          762 
TCGA-66-2766 TCGA-66-2770 TCGA-66-2773 TCGA-66-2785 TCGA-66-2791 TCGA-66-2792 
          31          700         1946           60         1977          913 
TCGA-68-7755 TCGA-68-7756 TCGA-68-A59J TCGA-77-6842 TCGA-77-6845 TCGA-77-7142 
          83          202          104         1950         1952         1286 
TCGA-77-7338 TCGA-77-8009 TCGA-77-8130 TCGA-77-8139 TCGA-77-8145 TCGA-77-8150 
        1952         1641         1945         1951         1943         1961 
TCGA-77-8153 TCGA-77-8156 TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5GA TCGA-77-A5GH 
        1684           10         1942         1959         1280          713 
TCGA-85-6560 TCGA-85-6798 TCGA-85-7698 TCGA-85-7844 TCGA-85-8070 TCGA-85-8072 
         364           34           49          911          960          513 
TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8352 TCGA-85-8354 TCGA-85-8666 
          13           11           13           67           61          475 
TCGA-85-A4QR TCGA-85-A50M TCGA-85-A510 TCGA-85-A511 TCGA-85-A5B5 TCGA-90-7769 
          25           19         1967         1972          111          358 
TCGA-90-7964 TCGA-92-7341 TCGA-96-7545 TCGA-96-A4JK TCGA-L3-A524 TCGA-LA-A446 
         428          106         1344          273          449           36 
TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HG 
          83         1722         1548 

$`AMP PEAK  3(2Q31.2) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3410 TCGA-18-3414 TCGA-18-3419 
         370          136         2464          146          396           50 
TCGA-18-4083 TCGA-18-4086 TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 
         187           85           92          827         3636         1426 
TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 
        2134         1852         1058          474          965         3724 
TCGA-21-1082 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-22-0940 
        3644          962         1268         1032          329          608 
TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1016 TCGA-22-4591 
        1945          131         1952           53          822          623 
TCGA-22-4593 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4604 TCGA-22-4607 
        1067          734           17         1161          399          587 
TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 
         965         1964         1933         1346           24         1651 
TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5485 TCGA-22-5492 TCGA-22-A5C4 
        1952         1952          357          916          506           29 
TCGA-33-4533 TCGA-33-4547 TCGA-33-4586 TCGA-33-4589 TCGA-34-2604 TCGA-34-2608 
        1940         1311          428         1948          958         1000 
TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5927 
         951         1528         2062         1715          707          941 
TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 TCGA-37-4132 
         552          166          120           13          200          227 
TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5022 TCGA-39-5024 
         238          207           12          103         1996         1964 
TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5039 
        1849           52           59          833         1107          544 
TCGA-43-2576 TCGA-43-2578 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 
        1223          684          757          310         1936          212 
TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A475 
         236         1970          407          358         1971          296 
TCGA-43-A56U TCGA-43-A56V TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 
         432          366          423           12           12          911 
TCGA-52-7622 TCGA-52-7809 TCGA-52-7812 TCGA-56-6545 TCGA-56-7221 TCGA-56-7580 
         541         1948         1967           62           30           40 
TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 TCGA-56-8622 TCGA-56-8624 
           6         1961            1           41           55           36 
TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX 
          63           17           16           38            2           46 
TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-58-8388 TCGA-58-8390 
          30           25            4            4          378          911 
TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-60-2695 TCGA-60-2696 
        1058         2589         1723         1072          642          109 
TCGA-60-2698 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2709 TCGA-60-2710 
         311         1943         1958          661         1505         1963 
TCGA-60-2711 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2720 
        1260         1731         1531         1075         1475           97 
TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-63-6202 
         983          908         1092          717          816         1973 
TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-66-2734 TCGA-66-2737 
        1957         1955         1947         1952         1311           61 
TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 
         641           30           31           28           30           30 
TCGA-66-2763 TCGA-66-2765 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2771 
          30           61           61           61         1947          578 
TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 
          61          578         1956          121         1954          759 
TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2793 
         790         1217          699         1955          699         1952 
TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 
        1645          122         1492          211          244           96 
TCGA-68-A59I TCGA-77-6843 TCGA-77-6844 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 
         121         1941         1942         1959         1968           15 
TCGA-77-7335 TCGA-77-7337 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 
        1954         1942         1954          479         1960         1945 
TCGA-77-8128 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8140 
        1953         1941         1941         1947         1946         1962 
TCGA-77-8144 TCGA-77-8148 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G6 TCGA-77-A5G7 
         833          293         1092         1953         1955         1963 
TCGA-77-A5G8 TCGA-77-A5GB TCGA-77-A5GF TCGA-85-6561 TCGA-85-7696 TCGA-85-7697 
        1290         1939          839          395           18           10 
TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 
           1         1965           35           60           26           60 
TCGA-85-8052 TCGA-85-8071 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 
          16          428           54           60           55           54 
TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 
          61           22           21          445          424            3 
TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50Z TCGA-85-A512 TCGA-85-A513 
          15         1972         1960         1973         1987           24 
TCGA-85-A53L TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-A4ED TCGA-90-A4EE 
          13          758          289           89          244          331 
TCGA-90-A59Q TCGA-92-7340 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 
         269           82          122          160           70           87 
TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL 
         356          430         1213          189          211          183 
TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A4E7 
         256          413          224          308          222           35 
TCGA-NC-A5HI 
        1135 

  AMP PEAK  3(2Q31.2) MUTATED AMP PEAK  3(2Q31.2) WILD-TYPE 
                            3                             1 
  AMP PEAK  3(2Q31.2) MUTATED AMP PEAK  3(2Q31.2) WILD-TYPE 
                         5287                          3724 
  AMP PEAK  3(2Q31.2) MUTATED AMP PEAK  3(2Q31.2) WILD-TYPE 
                          822                           552 
[1] "3.0 - 5287.0 (822.0)" "1.0 - 3724.0 (552.0)"
[1] "hr=" "1.2"
D3V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  3(2Q31.2) MUTATED         1       19       49        1        15
  AMP PEAK  3(2Q31.2) WILD-TYPE       0       53       88        0        37
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK  3(2Q31.2) MUTATED          26         24          4        2
  AMP PEAK  3(2Q31.2) WILD-TYPE        45         33         16        4
D3V3, multiclass
            clus
vv           AMP PEAK  3(2Q31.2) MUTATED AMP PEAK  3(2Q31.2) WILD-TYPE
  STAGE I                              1                             0
  STAGE IA                            19                            53
  STAGE IB                            49                            88
  STAGE II                             1                             0
  STAGE IIA                           15                            37
  STAGE IIB                           26                            45
  STAGE IIIA                          24                            33
  STAGE IIIB                           4                            16
  STAGE IV                             2                             4
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK  3(2Q31.2) MUTATED    32  88  17   6
  AMP PEAK  3(2Q31.2) WILD-TYPE  66 166  31  14
D3V4, multiclass
    clus
vv   AMP PEAK  3(2Q31.2) MUTATED AMP PEAK  3(2Q31.2) WILD-TYPE
  T1                          32                            66
  T2                          88                           166
  T3                          17                            31
  T4                           6                            14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  AMP PEAK  3(2Q31.2) MUTATED    87  41  14   1
  AMP PEAK  3(2Q31.2) WILD-TYPE 174  72  21   4
D3V5, multiclass
    clus
vv   AMP PEAK  3(2Q31.2) MUTATED AMP PEAK  3(2Q31.2) WILD-TYPE
  N0                          87                           174
  N1                          41                            72
  N2                          14                            21
  N3                           1                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A  MX
  AMP PEAK  3(2Q31.2) MUTATED   124   1   1  16
  AMP PEAK  3(2Q31.2) WILD-TYPE 234   4   0  34
D3V6, multiclass
     clus
vv    AMP PEAK  3(2Q31.2) MUTATED AMP PEAK  3(2Q31.2) WILD-TYPE
  M0                          124                           234
  M1                            1                             4
  M1A                           1                             0
  MX                           16                            34
[1] 4 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(2Q31.2) MUTATED    30 113
  AMP PEAK  3(2Q31.2) WILD-TYPE  77 200
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(2Q31.2) MUTATED     30  113
  AMP PEAK  3(2Q31.2) WILD-TYPE   77  200
        clus
vv       AMP PEAK  3(2Q31.2) MUTATED AMP PEAK  3(2Q31.2) WILD-TYPE
  FEMALE                          30                            77
  MALE                           113                           200
[1] 2 2
[1] FALSE
D3V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK  3(2Q31.2) MUTATED                                       7
  AMP PEAK  3(2Q31.2) WILD-TYPE                                     5
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK  3(2Q31.2) MUTATED                                        1
  AMP PEAK  3(2Q31.2) WILD-TYPE                                      5
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK  3(2Q31.2) MUTATED                                         1
  AMP PEAK  3(2Q31.2) WILD-TYPE                                       0
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  3(2Q31.2) MUTATED                                                           134
  AMP PEAK  3(2Q31.2) WILD-TYPE                                                         267
D3V9, multiclass
                                                             clus
vv                                                            AMP PEAK  3(2Q31.2) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         134
                                                             clus
vv                                                            AMP PEAK  3(2Q31.2) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           267
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V10, binary
                               cls
clus                              0   1
  AMP PEAK  3(2Q31.2) MUTATED     3 140
  AMP PEAK  3(2Q31.2) WILD-TYPE  10 267
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(2Q31.2) MUTATED      3  140
  AMP PEAK  3(2Q31.2) WILD-TYPE   10  267
     clus
vv    AMP PEAK  3(2Q31.2) MUTATED AMP PEAK  3(2Q31.2) WILD-TYPE
  NO                            3                            10
  YES                         140                           267
[1] 2 2
[1] FALSE
D3V11, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  3(2Q31.2) MUTATED   119   4   0   3
  AMP PEAK  3(2Q31.2) WILD-TYPE 223   4   4  15
D3V12, multiclass
    clus
vv   AMP PEAK  3(2Q31.2) MUTATED AMP PEAK  3(2Q31.2) WILD-TYPE
  R0                         119                           223
  R1                           4                             4
  R2                           0                             4
  RX                           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                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  3(2Q31.2) MUTATED       2                         3   109
  AMP PEAK  3(2Q31.2) WILD-TYPE     7                        14   189
D3V13, multiclass
                           clus
vv                          AMP PEAK  3(2Q31.2) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           3
  WHITE                                             109
                           clus
vv                          AMP PEAK  3(2Q31.2) WILD-TYPE
  ASIAN                                                 7
  BLACK OR AFRICAN AMERICAN                            14
  WHITE                                               189
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V14, binary
                               cls
clus                              0   1
  AMP PEAK  3(2Q31.2) MUTATED     3  94
  AMP PEAK  3(2Q31.2) WILD-TYPE   5 173
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(2Q31.2) MUTATED      3   94
  AMP PEAK  3(2Q31.2) WILD-TYPE    5  173
                        clus
vv                       AMP PEAK  3(2Q31.2) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          94
                        clus
vv                       AMP PEAK  3(2Q31.2) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           173
[1] 2 2
[1] FALSE

Clustering(4) Variable = AMP PEAK  4(3Q26.33) MUTATION ANALYSIS
D4V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  4(3Q26.33) MUTATED   249 106
  AMP PEAK  4(3Q26.33) WILD-TYPE  16  17
  AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE 
                           355                             33 
  AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE 
                           106                             17 
$`AMP PEAK  4(3Q26.33) MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
         370          136         2464         2417          146         1415 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 
         345          396         1810          862          758           50 
TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 
        1331          187           85         2754           92          827 
TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 
        3636         1426         3016         2134         1852         1058 
TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 
         965         3724          284         3644          267          962 
TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 
        1268         1032          329          979          608          223 
TCGA-22-1000 TCGA-22-1002 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 
        1945          131          429          822          623         1067 
TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 
         734         1161         1057          399         1946          587 
TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 
         358          965         1964         1933          445         1346 
TCGA-22-5479 TCGA-22-5480 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 
        1651         1952          357          573          916         1912 
TCGA-22-5491 TCGA-22-5492 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 
        1713          506         2524         1940         2979         1311 
TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 
        5287         1966         1941          428         1970         1948 
TCGA-33-6738 TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 
         822           80         1874          958          881         1000 
TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 
         951         1528         2062          365          428          941 
TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4130 
         552          166          120           13           12          247 
TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5016 
         227          238          207           12          103         2253 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 
        1361         1947         1996         1964         1849           52 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 
         740           59          833          474         1084         1086 
TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 
        1964         1223          684          822         1007          849 
TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 TCGA-43-7657 
         376          757          310         1936          212          236 
TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 
        1970          407          358         1971          353          296 
TCGA-43-A56U TCGA-43-A56V TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 
         432          366          324          423           12           12 
TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-56-1622 
         911          541         1948          923         1958          881 
TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 
           3          555           62           30           13           30 
TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 
          44           40           26            6         1961            1 
TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 
          41          178           55           36           63           17 
TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY 
          16           34           38            2           46           30 
TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 
          25            4            4            8          378          911 
TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N 
        2167         1058         2589         1723         1072          910 
TCGA-60-2695 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 
         642          311         1950         1943         1958          661 
TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 
        1963         1505         1963         1260          274         1731 
TCGA-60-2714 TCGA-60-2715 TCGA-60-2719 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 
        1531         1075         1297          983          908         1092 
TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 
         717          816          358         1957         1955         1947 
TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 
        1952         1967         1311           61          641           30 
TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 
          31           61           28           30           30          639 
TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 
         762           30           61           31           61           61 
TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 
        1947          700          578         1946           61          578 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2786 TCGA-66-2787 
        1956          121         1954          759          790         1217 
TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 
         699         1955          699         1977          913         1952 
TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 
        1645          122         1492           83          202          211 
TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 
         244           96          121          104         1950         1941 
TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 
        1942         1952         1959         1968           15         1286 
TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8008 
        1954         1942         1952         1954          479         1945 
TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 
        1641         1953         1945         1941         1947         1946 
TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 
        1951         1962          833         1943          293         1961 
TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 
        1684         1092           10         1942         1959         1955 
TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH 
        1963         1290         1280         1939          839          713 
TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 
         364          395           34           18           10           49 
TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 
           1         1965           35          911           60           26 
TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 
          60           16          960          428          513           13 
TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 
          11           13           54           60           55           67 
TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 
          54           61           61           22           21          445 
TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4QQ TCGA-85-A4QR 
         424            3          475           15         1960           25 
TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A53L TCGA-85-A5B5 
        1973         1967         1972         1987           13          111 
TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4EE TCGA-90-A59Q 
         289           89          358          428          331          269 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 
          82          106          122          160           70           87 
TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 
         356          430         1213         1344          189          211 
TCGA-96-A4JK TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-J1-A4AH 
         273          256          413          224          308          222 
TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HG 
          35          449           36           83         1722         1548 
TCGA-NC-A5HI 
        1135 

$`AMP PEAK  4(3Q26.33) WILD-TYPE`
TCGA-21-1078 TCGA-22-1005 TCGA-22-1011 TCGA-22-1017 TCGA-22-4594 TCGA-22-4596 
         474         1952           53         1485         1470           17 
TCGA-22-5478 TCGA-22-5481 TCGA-22-A5C4 TCGA-34-5234 TCGA-34-5239 TCGA-37-4129 
          24         1952           29         1715          707          200 
TCGA-39-5011 TCGA-39-5034 TCGA-39-5039 TCGA-43-2581 TCGA-43-5668 TCGA-52-7812 
        1454         1107          544         1176          349         1967 
TCGA-56-6546 TCGA-60-2696 TCGA-60-2716 TCGA-60-2720 TCGA-63-6202 TCGA-66-2785 
          26          109         1475           97         1973           60 
TCGA-77-8007 TCGA-77-8131 TCGA-77-A5FZ TCGA-85-A4PA TCGA-85-A50M TCGA-85-A513 
        1960         1941         1953         1972           19           24 
TCGA-90-6837 TCGA-90-A4ED TCGA-96-A4JL 
         758          244          183 

  AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE 
                             1                             17 
  AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE 
                          5287                           1973 
  AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE 
                           641                            707 
[1] "1.0 - 5287.0 (641.0)"  "17.0 - 1973.0 (707.0)"
[1] "hr=" "1.7"
D4V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  4(3Q26.33) MUTATED         1       67      127        1        41
  AMP PEAK  4(3Q26.33) WILD-TYPE       0        5       10        0        11
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK  4(3Q26.33) MUTATED          65         54         18        6
  AMP PEAK  4(3Q26.33) WILD-TYPE         6          3          2        0
D4V3, multiclass
            clus
vv           AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE
  STAGE I                               1                              0
  STAGE IA                             67                              5
  STAGE IB                            127                             10
  STAGE II                              1                              0
  STAGE IIA                            41                             11
  STAGE IIB                            65                              6
  STAGE IIIA                           54                              3
  STAGE IIIB                           18                              2
  STAGE IV                              6                              0
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK  4(3Q26.33) MUTATED    90 231  44  18
  AMP PEAK  4(3Q26.33) WILD-TYPE   8  23   4   2
D4V4, multiclass
    clus
vv   AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE
  T1                           90                              8
  T2                          231                             23
  T3                           44                              4
  T4                           18                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK  4(3Q26.33) MUTATED   238 105  31   5
  AMP PEAK  4(3Q26.33) WILD-TYPE  23   8   4   0
D4V5, multiclass
    clus
vv   AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE
  N0                          238                             23
  N1                          105                              8
  N2                           31                              4
  N3                            5                              0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A  MX
  AMP PEAK  4(3Q26.33) MUTATED   325   5   1  46
  AMP PEAK  4(3Q26.33) WILD-TYPE  33   0   0   4
D4V6, multiclass
     clus
vv    AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE
  M0                           325                             33
  M1                             5                              0
  M1A                            1                              0
  MX                            46                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
                                cls
clus                               0   1
  AMP PEAK  4(3Q26.33) MUTATED    95 288
  AMP PEAK  4(3Q26.33) WILD-TYPE  12  25
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(3Q26.33) MUTATED     95  288
  AMP PEAK  4(3Q26.33) WILD-TYPE   12   25
        clus
vv       AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE
  FEMALE                           95                             12
  MALE                            288                             25
[1] 2 2
[1] FALSE
D4V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK  4(3Q26.33) MUTATED                                      12
  AMP PEAK  4(3Q26.33) WILD-TYPE                                     0
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK  4(3Q26.33) MUTATED                                        3
  AMP PEAK  4(3Q26.33) WILD-TYPE                                      3
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK  4(3Q26.33) MUTATED                                         1
  AMP PEAK  4(3Q26.33) WILD-TYPE                                       0
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  4(3Q26.33) MUTATED                                                           367
  AMP PEAK  4(3Q26.33) WILD-TYPE                                                          34
D4V9, multiclass
                                                             clus
vv                                                            AMP PEAK  4(3Q26.33) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 12
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          367
                                                             clus
vv                                                            AMP PEAK  4(3Q26.33) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             34
[1] 4 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(3Q26.33) MUTATED    13 370
  AMP PEAK  4(3Q26.33) WILD-TYPE   0  37
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(3Q26.33) MUTATED     13  370
  AMP PEAK  4(3Q26.33) WILD-TYPE    0   37
     clus
vv    AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE
  NO                            13                              0
  YES                          370                             37
[1] 2 2
[1] FALSE
D4V11, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK  4(3Q26.33) MUTATED   313   8   4  16
  AMP PEAK  4(3Q26.33) WILD-TYPE  29   0   0   2
D4V12, multiclass
    clus
vv   AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE
  R0                          313                             29
  R1                            8                              0
  R2                            4                              0
  RX                           16                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  4(3Q26.33) MUTATED       6                        16   273
  AMP PEAK  4(3Q26.33) WILD-TYPE     3                         1    25
D4V13, multiclass
                           clus
vv                          AMP PEAK  4(3Q26.33) MUTATED
  ASIAN                                                6
  BLACK OR AFRICAN AMERICAN                           16
  WHITE                                              273
                           clus
vv                          AMP PEAK  4(3Q26.33) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 25
[1] 3 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(3Q26.33) MUTATED     7 244
  AMP PEAK  4(3Q26.33) WILD-TYPE   1  23
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(3Q26.33) MUTATED      7  244
  AMP PEAK  4(3Q26.33) WILD-TYPE    1   23
                        clus
vv                       AMP PEAK  4(3Q26.33) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                          244
                        clus
vv                       AMP PEAK  4(3Q26.33) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                             23
[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  31
  AMP PEAK  5(4Q12) WILD-TYPE 203  92
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                         93                         295 
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                         31                          92 
$`AMP PEAK  5(4Q12) MUTATED`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 TCGA-18-3416 
         136         2417          146         1415          345          862 
TCGA-21-1075 TCGA-21-1082 TCGA-21-5782 TCGA-21-5786 TCGA-22-1017 TCGA-22-4591 
        2134         3644          962         1032         1485          623 
TCGA-22-4593 TCGA-22-4595 TCGA-22-4601 TCGA-22-4604 TCGA-22-5478 TCGA-22-5481 
        1067          734         1057          399           24         1952 
TCGA-22-A5C4 TCGA-33-4566 TCGA-33-4582 TCGA-33-6738 TCGA-34-2596 TCGA-34-2605 
          29         5287         1966          822           80          881 
TCGA-34-2609 TCGA-34-5241 TCGA-34-5928 TCGA-37-3789 TCGA-37-4130 TCGA-37-4135 
         951          428          552           13          247          207 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5031 TCGA-43-2576 TCGA-43-2578 TCGA-43-3920 
        2253         1361          833         1223          684         1007 
TCGA-43-6647 TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 TCGA-43-A56U TCGA-43-A56V 
         757          236         1970         1971          432          366 
TCGA-46-6025 TCGA-52-7809 TCGA-52-7810 TCGA-56-1622 TCGA-56-7579 TCGA-56-8629 
         324         1948          923          881           44           34 
TCGA-56-A49D TCGA-56-A4ZJ TCGA-58-A46L TCGA-58-A46M TCGA-60-2703 TCGA-60-2711 
          38           25         1723         1072         1950         1260 
TCGA-60-2715 TCGA-60-2721 TCGA-60-2722 TCGA-60-2726 TCGA-66-2737 TCGA-66-2744 
        1075          983          908          358           61           30 
TCGA-66-2758 TCGA-66-2763 TCGA-66-2769 TCGA-66-2778 TCGA-66-2781 TCGA-66-2786 
         639           30         1947          578          121          790 
TCGA-66-2787 TCGA-66-2793 TCGA-66-2800 TCGA-68-A59I TCGA-77-7465 TCGA-77-8007 
        1217         1952         1492          121          479         1960 
TCGA-77-8009 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-85-6561 TCGA-85-7843 
        1641         1959         1955         1963          395           35 
TCGA-85-8072 TCGA-85-8287 TCGA-85-8351 TCGA-85-8354 TCGA-85-8580 TCGA-85-A53L 
         513           13           55           61          445           13 
TCGA-85-A5B5 TCGA-90-7767 TCGA-90-7769 TCGA-92-7340 TCGA-92-7341 TCGA-92-8064 
         111           89          358           82          106          160 
TCGA-94-A4VJ TCGA-96-7545 TCGA-J1-A4AH 
         430         1344          222 

$`AMP PEAK  5(4Q12) WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 
         370         2464          396         1810          758           50 
TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 
        1331          187           85         2754           92          827 
TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 
        3636         1426         3016         1852         1058          474 
TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1083 TCGA-21-5784 TCGA-21-5787 
         965         3724          284          267         1268          329 
TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 
         979          608          223         1945          131         1952 
TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4594 TCGA-22-4596 TCGA-22-4599 
          53          429          822         1470           17         1161 
TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 
        1946          587          358          965         1964         1933 
TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 TCGA-22-5480 TCGA-22-5482 TCGA-22-5483 
         445         1346         1651         1952          357          573 
TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4532 TCGA-33-4533 
         916         1912         1713          506         2524         1940 
TCGA-33-4538 TCGA-33-4547 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 
        2979         1311         1941          428         1970         1948 
TCGA-34-2600 TCGA-34-2604 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 
        1874          958         1000         1528         2062         1715 
TCGA-34-5239 TCGA-34-5240 TCGA-34-5927 TCGA-34-8454 TCGA-37-3783 TCGA-37-3792 
         707          365          941          166          120           12 
TCGA-37-4129 TCGA-37-4132 TCGA-37-4133 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 
         200          227          238           12          103         1454 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 
        1947         1996         1964         1849           52          740 
TCGA-39-5030 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 
          59         1107          474         1084         1086          544 
TCGA-39-5040 TCGA-43-2581 TCGA-43-3394 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 
        1964         1176          822          349          849          376 
TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 TCGA-43-A474 
         310         1936          212          407          358          353 
TCGA-43-A475 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 
         296          423           12           12          911          541 
TCGA-52-7811 TCGA-52-7812 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 
        1958         1967            3          555           62           26 
TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 
          30           13           30           40           26            6 
TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 
        1961            1           41          178           55           36 
TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY 
          63           17           16            2           46           30 
TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 
           4            4            8          378          911         2167 
TCGA-58-8393 TCGA-58-A46J TCGA-58-A46N TCGA-60-2695 TCGA-60-2696 TCGA-60-2698 
        1058         2589          910          642          109          311 
TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 
        1943         1958          661         1963         1505         1963 
TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 
         274         1731         1531         1475         1297           97 
TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 
        1092          717          816         1973         1957         1955 
TCGA-63-7022 TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 TCGA-66-2742 TCGA-66-2753 
        1947         1952         1967         1311          641           31 
TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2759 TCGA-66-2765 
          61           28           30           30          762           61 
TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 
          31           61           61          700          578         1946 
TCGA-66-2777 TCGA-66-2780 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2788 
          61         1956         1954          759           60          699 
TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 
        1955          699         1977          913         1645          122 
TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59J 
          83          202          211          244           96          104 
TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 
        1950         1941         1942         1952         1959         1968 
TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 
          15         1286         1954         1942         1952         1954 
TCGA-77-8008 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 
        1945         1953         1945         1941         1941         1947 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 
        1946         1951         1962          833         1943          293 
TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 
        1961         1684         1092           10         1953         1942 
TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 
        1290         1280         1939          839          713          364 
TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 
          34           18           10           49            1         1965 
TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 
         911           60           26           60           16          960 
TCGA-85-8071 TCGA-85-8276 TCGA-85-8277 TCGA-85-8288 TCGA-85-8350 TCGA-85-8352 
         428           13           11           54           60           67 
TCGA-85-8353 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8582 TCGA-85-8664 
          54           61           22           21          424            3 
TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M 
         475           15         1972         1960           25           19 
TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-90-6837 
        1973         1967         1972         1987           24          758 
TCGA-90-7766 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-8063 
         289          428          244          331          269          122 
TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 
          70           87          356         1213          189          211 
TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 
         273          183          256          413          224          308 
TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HG 
          35          449           36           83         1722         1548 
TCGA-NC-A5HI 
        1135 

  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                         13                           1 
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                       5287                        3724 
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                        684                         641 
[1] "13.0 - 5287.0 (684.0)" "1.0 - 3724.0 (641.0)" 
[1] "hr=" "1.1"
D5V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  5(4Q12) MUTATED         0       19       25        0        14
  AMP PEAK  5(4Q12) WILD-TYPE       1       53      112        1        38
                             vv
clus                          STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK  5(4Q12) MUTATED          24         14          6        0
  AMP PEAK  5(4Q12) WILD-TYPE        47         43         14        6
D5V3, multiclass
            clus
vv           AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  STAGE I                            0                           1
  STAGE IA                          19                          53
  STAGE IB                          25                         112
  STAGE II                           0                           1
  STAGE IIA                         14                          38
  STAGE IIB                         24                          47
  STAGE IIIA                        14                          43
  STAGE IIIB                         6                          14
  STAGE IV                           0                           6
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2  T3  T4
  AMP PEAK  5(4Q12) MUTATED    22  67   8   6
  AMP PEAK  5(4Q12) WILD-TYPE  76 187  40  14
D5V4, multiclass
    clus
vv   AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  T1                        22                          76
  T2                        67                         187
  T3                         8                          40
  T4                         6                          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  5(4Q12) MUTATED    60  31  10   1
  AMP PEAK  5(4Q12) WILD-TYPE 201  82  25   4
D5V5, multiclass
    clus
vv   AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  N0                        60                         201
  N1                        31                          82
  N2                        10                          25
  N3                         1                           4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           M0  M1 M1A  MX
  AMP PEAK  5(4Q12) MUTATED    88   0   0  13
  AMP PEAK  5(4Q12) WILD-TYPE 270   5   1  37
D5V6, multiclass
     clus
vv    AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  M0                         88                         270
  M1                          0                           5
  M1A                         0                           1
  MX                         13                          37
[1] 4 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    26  77
  AMP PEAK  5(4Q12) WILD-TYPE  81 236
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(4Q12) MUTATED     26   77
  AMP PEAK  5(4Q12) WILD-TYPE   81  236
        clus
vv       AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  FEMALE                        26                          81
  MALE                          77                         236
[1] 2 2
[1] FALSE
D5V8, continuous
                             vv
clus                          LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK  5(4Q12) MUTATED                                       4
  AMP PEAK  5(4Q12) WILD-TYPE                                     8
                             vv
clus                          LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK  5(4Q12) MUTATED                                        0
  AMP PEAK  5(4Q12) WILD-TYPE                                      6
                             vv
clus                          LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK  5(4Q12) MUTATED                                         0
  AMP PEAK  5(4Q12) WILD-TYPE                                       1
                             vv
clus                          LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  5(4Q12) MUTATED                                                            99
  AMP PEAK  5(4Q12) WILD-TYPE                                                         302
D5V9, multiclass
                                                             clus
vv                                                            AMP PEAK  5(4Q12) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                               4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                              0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                             0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                        99
                                                             clus
vv                                                            AMP PEAK  5(4Q12) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         302
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V10, binary
                             cls
clus                            0   1
  AMP PEAK  5(4Q12) MUTATED     3 100
  AMP PEAK  5(4Q12) WILD-TYPE  10 307
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(4Q12) MUTATED      3  100
  AMP PEAK  5(4Q12) WILD-TYPE   10  307
     clus
vv    AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  NO                          3                          10
  YES                       100                         307
[1] 2 2
[1] FALSE
D5V11, continuous
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK  5(4Q12) MUTATED    84   3   1   3
  AMP PEAK  5(4Q12) WILD-TYPE 258   5   3  15
D5V12, multiclass
    clus
vv   AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  R0                        84                         258
  R1                         3                           5
  R2                         1                           3
  RX                         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                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  5(4Q12) MUTATED       2                         4    74
  AMP PEAK  5(4Q12) WILD-TYPE     7                        13   224
D5V13, multiclass
                           clus
vv                          AMP PEAK  5(4Q12) MUTATED
  ASIAN                                             2
  BLACK OR AFRICAN AMERICAN                         4
  WHITE                                            74
                           clus
vv                          AMP PEAK  5(4Q12) WILD-TYPE
  ASIAN                                               7
  BLACK OR AFRICAN AMERICAN                          13
  WHITE                                             224
[1] 3 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     0  68
  AMP PEAK  5(4Q12) WILD-TYPE   8 199
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(4Q12) MUTATED      0   68
  AMP PEAK  5(4Q12) WILD-TYPE    8  199
                        clus
vv                       AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  HISPANIC OR LATINO                             0                           8
  NOT HISPANIC OR LATINO                        68                         199
[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   205  98
  AMP PEAK  6(5P15.33) WILD-TYPE  60  25
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                           303                             85 
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                            98                             25 
$`AMP PEAK  6(5P15.33) MUTATED`
TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 
         146         1415          345          396         1810          758 
TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 
        1331          187           85           92         3636         1426 
TCGA-21-1072 TCGA-21-1075 TCGA-21-1077 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 
        3016         2134         1058          965         3724          284 
TCGA-21-1082 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI 
        3644          962         1268         1032          329          979 
TCGA-22-0940 TCGA-22-0944 TCGA-22-1002 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 
         608          223          131           53          429          822 
TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 
        1485          623         1067         1470          734           17 
TCGA-22-4599 TCGA-22-4601 TCGA-22-4605 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 
        1161         1057         1946          358          965         1964 
TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 
        1933          445         1346           24         1651         1952 
TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5492 TCGA-22-A5C4 
        1952          357          573          916          506           29 
TCGA-33-4532 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4586 
        2524         2979         1311         5287         1966          428 
TCGA-33-4587 TCGA-33-6738 TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 
        1970          822           80         1874          958          881 
TCGA-34-2608 TCGA-34-2609 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5928 
        1000          951          707          365          428          552 
TCGA-37-3783 TCGA-37-3792 TCGA-37-4130 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 
         120           12          247          238          207           12 
TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 
         103         1454         2253         1947         1996         1964 
TCGA-39-5027 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 
        1849          740           59          833         1107          474 
TCGA-39-5036 TCGA-39-5039 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 
        1084          544         1223          684         1176          822 
TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-7656 
        1007          349          849          376          757          212 
TCGA-43-7657 TCGA-43-7658 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56U 
         236         1970          358         1971          353          432 
TCGA-43-A56V TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4081 TCGA-52-7622 
         366          324          423           12          911          541 
TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5898 
        1948          923         1958         1967          881          555 
TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7580 TCGA-56-7582 
          62           26           30           13           40           26 
TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 
        1961            1           41          178           55           36 
TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW 
          63           17           16           34           38            2 
TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS 
          46           30           25            4            4            8 
TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-A46J TCGA-58-A46M TCGA-58-A46N 
         378          911         2167         2589         1072          910 
TCGA-60-2695 TCGA-60-2703 TCGA-60-2704 TCGA-60-2707 TCGA-60-2710 TCGA-60-2711 
         642         1950         1943          661         1963         1260 
TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 TCGA-60-2719 TCGA-60-2720 
         274         1731         1531         1075         1297           97 
TCGA-60-2721 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 
         983         1092          717          816          358         1973 
TCGA-63-7020 TCGA-63-7022 TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 
        1957         1947         1967         1311           61          641 
TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 
          30           31           61           28           30           30 
TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2766 TCGA-66-2768 TCGA-66-2769 
         639          762           30           31           61         1947 
TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 
         700          578         1946           61          578         1956 
TCGA-66-2781 TCGA-66-2782 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 
         121         1954           60          790         1217          699 
TCGA-66-2789 TCGA-66-2790 TCGA-66-2792 TCGA-66-2794 TCGA-66-2800 TCGA-68-7756 
        1955          699          913         1645         1492          202 
TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 
         211          244           96          121          104         1950 
TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 
        1942         1952         1959         1968           15         1286 
TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 
        1954         1942         1952         1954          479         1960 
TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 
        1945         1641         1953         1945         1941         1947 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 
        1946         1951         1962         1943          293         1961 
TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 
        1684         1092           10         1942         1955         1963 
TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 TCGA-85-6798 
        1290         1280          839          713          364           34 
TCGA-85-7696 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 
          18           49            1         1965           35          911 
TCGA-85-7950 TCGA-85-8048 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 
          60           26          960          428          513           13 
TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 
          11           13           54           60           55           67 
TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 
          22           21          445          424            3          475 
TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 
        1960           25           19         1973         1967         1972 
TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4EE TCGA-90-A59Q 
         289           89          358          428          331          269 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 
          82          106          160           70           87          356 
TCGA-94-A4VJ TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK 
         430         1213         1344          189          211          273 
TCGA-98-8022 TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 
         224          308          222           35          449           36 
TCGA-MF-A522 TCGA-NC-A5HG TCGA-NC-A5HI 
          83         1548         1135 

$`AMP PEAK  6(5P15.33) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3416 TCGA-18-3419 
         370          136         2464         2417          862           50 
TCGA-18-4721 TCGA-18-5595 TCGA-21-1076 TCGA-21-1078 TCGA-21-1083 TCGA-22-1000 
        2754          827         1852          474          267         1945 
TCGA-22-1005 TCGA-22-4604 TCGA-22-4607 TCGA-22-5489 TCGA-22-5491 TCGA-33-4533 
        1952          399          587         1912         1713         1940 
TCGA-33-4583 TCGA-33-4589 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5927 
        1941         1948         1528         2062         1715          941 
TCGA-34-8454 TCGA-37-3789 TCGA-37-4129 TCGA-37-4132 TCGA-39-5019 TCGA-39-5028 
         166           13          200          227         1361           52 
TCGA-39-5037 TCGA-39-5040 TCGA-43-6770 TCGA-43-6771 TCGA-43-8115 TCGA-43-A475 
        1086         1964          310         1936          407          296 
TCGA-51-4080 TCGA-56-5897 TCGA-56-7223 TCGA-56-7579 TCGA-56-7730 TCGA-58-8393 
          12            3           30           44            6         1058 
TCGA-58-A46L TCGA-60-2696 TCGA-60-2698 TCGA-60-2706 TCGA-60-2708 TCGA-60-2709 
        1723          109          311         1958         1963         1505 
TCGA-60-2716 TCGA-60-2722 TCGA-63-7021 TCGA-63-7023 TCGA-66-2765 TCGA-66-2767 
        1475          908         1955         1952           61           61 
TCGA-66-2783 TCGA-66-2791 TCGA-66-2793 TCGA-66-2795 TCGA-68-7755 TCGA-77-6843 
         759         1977         1952          122           83         1941 
TCGA-77-8131 TCGA-77-8144 TCGA-77-A5FZ TCGA-77-A5G3 TCGA-77-A5GB TCGA-85-6561 
        1941          833         1953         1959         1939          395 
TCGA-85-7697 TCGA-85-8049 TCGA-85-8052 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 
          10           60           16           54           61           61 
TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 
          15         1972         1987           24           13          111 
TCGA-90-6837 TCGA-90-A4ED TCGA-92-8063 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 
         758          244          122          183          256          413 
TCGA-NC-A5HE 
        1722 

  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                             1                              3 
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                          5287                           2754 
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                           641                            758 
[1] "1.0 - 5287.0 (641.0)" "3.0 - 2754.0 (758.0)"
[1] "hr=" "1.2"
D6V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  6(5P15.33) MUTATED         1       54      112        1        39
  AMP PEAK  6(5P15.33) WILD-TYPE       0       18       25        0        13
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK  6(5P15.33) MUTATED          58         47         13        5
  AMP PEAK  6(5P15.33) WILD-TYPE        13         10          7        1
D6V3, multiclass
            clus
vv           AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE
  STAGE I                               1                              0
  STAGE IA                             54                             18
  STAGE IB                            112                             25
  STAGE II                              1                              0
  STAGE IIA                            39                             13
  STAGE IIB                            58                             13
  STAGE IIIA                           47                             10
  STAGE IIIB                           13                              7
  STAGE IV                              5                              1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK  6(5P15.33) MUTATED    72 206  39  15
  AMP PEAK  6(5P15.33) WILD-TYPE  26  48   9   5
D6V4, multiclass
    clus
vv   AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE
  T1                           72                             26
  T2                          206                             48
  T3                           39                              9
  T4                           15                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK  6(5P15.33) MUTATED   212  84  32   2
  AMP PEAK  6(5P15.33) WILD-TYPE  49  29   3   3
D6V5, multiclass
    clus
vv   AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE
  N0                          212                             49
  N1                           84                             29
  N2                           32                              3
  N3                            2                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A  MX
  AMP PEAK  6(5P15.33) MUTATED   283   4   1  40
  AMP PEAK  6(5P15.33) WILD-TYPE  75   1   0  10
D6V6, multiclass
     clus
vv    AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE
  M0                           283                             75
  M1                             4                              1
  M1A                            1                              0
  MX                            40                             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"
D6V7, binary
                                cls
clus                               0   1
  AMP PEAK  6(5P15.33) MUTATED    86 246
  AMP PEAK  6(5P15.33) WILD-TYPE  21  67
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(5P15.33) MUTATED     86  246
  AMP PEAK  6(5P15.33) WILD-TYPE   21   67
        clus
vv       AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE
  FEMALE                           86                             21
  MALE                            246                             67
[1] 2 2
[1] FALSE
D6V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK  6(5P15.33) MUTATED                                       9
  AMP PEAK  6(5P15.33) WILD-TYPE                                     3
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK  6(5P15.33) MUTATED                                        4
  AMP PEAK  6(5P15.33) WILD-TYPE                                      2
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK  6(5P15.33) MUTATED                                         1
  AMP PEAK  6(5P15.33) WILD-TYPE                                       0
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  6(5P15.33) MUTATED                                                           318
  AMP PEAK  6(5P15.33) WILD-TYPE                                                          83
D6V9, multiclass
                                                             clus
vv                                                            AMP PEAK  6(5P15.33) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          318
                                                             clus
vv                                                            AMP PEAK  6(5P15.33) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             83
[1] 4 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     9 323
  AMP PEAK  6(5P15.33) WILD-TYPE   4  84
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(5P15.33) MUTATED      9  323
  AMP PEAK  6(5P15.33) WILD-TYPE    4   84
     clus
vv    AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE
  NO                             9                              4
  YES                          323                             84
[1] 2 2
[1] FALSE
D6V11, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK  6(5P15.33) MUTATED   272   6   3  13
  AMP PEAK  6(5P15.33) WILD-TYPE  70   2   1   5
D6V12, multiclass
    clus
vv   AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE
  R0                          272                             70
  R1                            6                              2
  R2                            3                              1
  RX                           13                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  6(5P15.33) MUTATED       5                        11   239
  AMP PEAK  6(5P15.33) WILD-TYPE     4                         6    59
D6V13, multiclass
                           clus
vv                          AMP PEAK  6(5P15.33) MUTATED
  ASIAN                                                5
  BLACK OR AFRICAN AMERICAN                           11
  WHITE                                              239
                           clus
vv                          AMP PEAK  6(5P15.33) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                              6
  WHITE                                                 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"
D6V14, binary
                                cls
clus                               0   1
  AMP PEAK  6(5P15.33) MUTATED     7 209
  AMP PEAK  6(5P15.33) WILD-TYPE   1  58
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(5P15.33) MUTATED      7  209
  AMP PEAK  6(5P15.33) WILD-TYPE    1   58
                        clus
vv                       AMP PEAK  6(5P15.33) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                          209
                        clus
vv                       AMP PEAK  6(5P15.33) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                             58
[1] 2 2
[1] FALSE

Clustering(7) Variable = AMP PEAK  7(5P12) MUTATION ANALYSIS
D7V1, survival
                             sevent
clus2                           0   1
  AMP PEAK  7(5P12) MUTATED   190  88
  AMP PEAK  7(5P12) WILD-TYPE  75  35
  AMP PEAK  7(5P12) MUTATED AMP PEAK  7(5P12) WILD-TYPE 
                        278                         110 
  AMP PEAK  7(5P12) MUTATED AMP PEAK  7(5P12) WILD-TYPE 
                         88                          35 
$`AMP PEAK  7(5P12) MUTATED`
TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 
         146         1415          345          396         1810          758 
TCGA-18-3421 TCGA-18-4083 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1075 
        1331          187           92         3636         1426         2134 
TCGA-21-1077 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 
        1058          965         3724          284         3644          267 
TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 
         962         1268         1032          329          979          608 
TCGA-22-0944 TCGA-22-1002 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 
         223          131           53          429          822          623 
TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 
        1067         1470          734           17         1161         1057 
TCGA-22-4604 TCGA-22-4605 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 
         399         1946          358          965         1964         1933 
TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 
         445         1346           24         1952          357          573 
TCGA-22-5485 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 
         916          506           29         2524         1940         2979 
TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-6738 
        1311         5287         1966         1941          428          822 
TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 
          80         1874          958          881         1000          951 
TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5928 TCGA-37-3783 TCGA-37-3792 
         707          365          428          552          120           12 
TCGA-37-4130 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 
         247          238          207           12          103         1454 
TCGA-39-5016 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5029 TCGA-39-5030 
        2253         1947         1996         1964          740           59 
TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 TCGA-39-5039 TCGA-43-2576 TCGA-43-2581 
         833          474         1084          544         1223         1176 
TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-7656 
         822         1007          849          376          757          212 
TCGA-43-7657 TCGA-43-7658 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V 
         236         1970          358         1971          353          366 
TCGA-46-6025 TCGA-46-6026 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 
         324          423          911          541         1948          923 
TCGA-52-7811 TCGA-56-1622 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 
        1958          881          555           62           26           30 
TCGA-56-7222 TCGA-56-7580 TCGA-56-7582 TCGA-56-7822 TCGA-56-8503 TCGA-56-8504 
          13           40           26            1           41          178 
TCGA-56-8622 TCGA-56-8624 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D 
          55           36           17           16           34           38 
TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR TCGA-56-A5DS 
           2           46           30           25            4            8 
TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-A46J TCGA-58-A46M TCGA-58-A46N 
         378          911         2167         2589         1072          910 
TCGA-60-2695 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2709 
         642         1950         1943         1958          661         1505 
TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2719 
        1963         1260          274         1731         1531         1297 
TCGA-60-2720 TCGA-60-2721 TCGA-60-2723 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 
          97          983         1092          816          358         1973 
TCGA-63-7020 TCGA-63-7022 TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 
        1957         1947         1967         1311           61          641 
TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 
          30           31           61           28           30           30 
TCGA-66-2759 TCGA-66-2766 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 
         762           31           61         1947          700          578 
TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2782 TCGA-66-2785 TCGA-66-2786 
          61          578         1956         1954           60          790 
TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 
        1217          699         1955         1977          913         1645 
TCGA-66-2795 TCGA-66-2800 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 
         122         1492          202          211          244           96 
TCGA-68-A59J TCGA-77-6842 TCGA-77-6844 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 
         104         1950         1942         1959         1968           15 
TCGA-77-7142 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 
        1286         1942         1952         1954          479         1960 
TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 
        1945         1641         1953         1945         1941         1947 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 
        1946         1951         1962         1943          293         1961 
TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 
        1684         1092           10         1942         1959         1955 
TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 
        1963         1290         1280          839          713          364 
TCGA-85-6798 TCGA-85-7696 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 
          34           18           49            1         1965           35 
TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 
         911           60           26          428          513           13 
TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 
          11           13           54           60           55           67 
TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4QQ 
          21          445          424            3          475         1960 
TCGA-85-A4QR TCGA-85-A50M TCGA-85-A510 TCGA-85-A511 TCGA-85-A5B5 TCGA-90-7766 
          25           19         1967         1972          111          289 
TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-92-7340 TCGA-92-7341 TCGA-92-8064 
          89          358          428           82          106          160 
TCGA-94-7943 TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-98-8021 
         356         1213         1344          189          211          413 
TCGA-98-8022 TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 
         224          308          222           35          449           36 
TCGA-MF-A522 TCGA-NC-A5HG 
          83         1548 

$`AMP PEAK  7(5P12) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3416 TCGA-18-3419 
         370          136         2464         2417          862           50 
TCGA-18-4086 TCGA-18-4721 TCGA-18-5595 TCGA-21-1072 TCGA-21-1076 TCGA-21-1078 
          85         2754          827         3016         1852          474 
TCGA-22-1000 TCGA-22-1005 TCGA-22-1017 TCGA-22-4607 TCGA-22-5479 TCGA-22-5480 
        1945         1952         1485          587         1651         1952 
TCGA-22-5489 TCGA-22-5491 TCGA-33-4587 TCGA-33-4589 TCGA-34-5231 TCGA-34-5232 
        1912         1713         1970         1948         1528         2062 
TCGA-34-5234 TCGA-34-5927 TCGA-34-8454 TCGA-37-3789 TCGA-37-4129 TCGA-37-4132 
        1715          941          166           13          200          227 
TCGA-39-5019 TCGA-39-5027 TCGA-39-5028 TCGA-39-5034 TCGA-39-5037 TCGA-39-5040 
        1361         1849           52         1107         1086         1964 
TCGA-43-2578 TCGA-43-5668 TCGA-43-6770 TCGA-43-6771 TCGA-43-8115 TCGA-43-A475 
         684          349          310         1936          407          296 
TCGA-43-A56U TCGA-51-4079 TCGA-51-4080 TCGA-52-7812 TCGA-56-5897 TCGA-56-7223 
         432           12           12         1967            3           30 
TCGA-56-7579 TCGA-56-7730 TCGA-56-7731 TCGA-56-8625 TCGA-56-A4ZK TCGA-58-8393 
          44            6         1961           63            4         1058 
TCGA-58-A46L TCGA-60-2696 TCGA-60-2698 TCGA-60-2708 TCGA-60-2715 TCGA-60-2716 
        1723          109          311         1963         1075         1475 
TCGA-60-2722 TCGA-60-2724 TCGA-63-7021 TCGA-63-7023 TCGA-66-2758 TCGA-66-2763 
         908          717         1955         1952          639           30 
TCGA-66-2765 TCGA-66-2767 TCGA-66-2773 TCGA-66-2781 TCGA-66-2783 TCGA-66-2790 
          61           61         1946          121          759          699 
TCGA-66-2793 TCGA-68-7755 TCGA-68-A59I TCGA-77-6843 TCGA-77-6845 TCGA-77-7335 
        1952           83          121         1941         1952         1954 
TCGA-77-8131 TCGA-77-8144 TCGA-77-A5FZ TCGA-77-A5GB TCGA-85-6561 TCGA-85-7697 
        1941          833         1953         1939          395           10 
TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 
          60           16          960           54           61           61 
TCGA-85-8479 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A50Z TCGA-85-A512 TCGA-85-A513 
          22           15         1972         1973         1987           24 
TCGA-85-A53L TCGA-90-6837 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-8063 
          13          758          244          331          269          122 
TCGA-92-8065 TCGA-94-7033 TCGA-94-A4VJ TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 
          70           87          430          273          183          256 
TCGA-NC-A5HE TCGA-NC-A5HI 
        1722         1135 

  AMP PEAK  7(5P12) MUTATED AMP PEAK  7(5P12) WILD-TYPE 
                          1                           3 
  AMP PEAK  7(5P12) MUTATED AMP PEAK  7(5P12) WILD-TYPE 
                       5287                        3016 
  AMP PEAK  7(5P12) MUTATED AMP PEAK  7(5P12) WILD-TYPE 
                      632.0                       691.5 
[1] "1.0 - 5287.0 (632.0)" "3.0 - 3016.0 (691.5)"
[1] "hr=" "1.1"
D7V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  7(5P12) MUTATED         1       51       99        1        33
  AMP PEAK  7(5P12) WILD-TYPE       0       21       38        0        19
                             vv
clus                          STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK  7(5P12) MUTATED          56         43         14        5
  AMP PEAK  7(5P12) WILD-TYPE        15         14          6        1
D7V3, multiclass
            clus
vv           AMP PEAK  7(5P12) MUTATED AMP PEAK  7(5P12) WILD-TYPE
  STAGE I                            1                           0
  STAGE IA                          51                          21
  STAGE IB                          99                          38
  STAGE II                           1                           0
  STAGE IIA                         33                          19
  STAGE IIB                         56                          15
  STAGE IIIA                        43                          14
  STAGE IIIB                        14                           6
  STAGE IV                           5                           1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2  T3  T4
  AMP PEAK  7(5P12) MUTATED    68 191  31  15
  AMP PEAK  7(5P12) WILD-TYPE  30  63  17   5
D7V4, multiclass
    clus
vv   AMP PEAK  7(5P12) MUTATED AMP PEAK  7(5P12) WILD-TYPE
  T1                        68                          30
  T2                       191                          63
  T3                        31                          17
  T4                        15                           5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           N0  N1  N2  N3
  AMP PEAK  7(5P12) MUTATED   191  79  30   3
  AMP PEAK  7(5P12) WILD-TYPE  70  34   5   2
D7V5, multiclass
    clus
vv   AMP PEAK  7(5P12) MUTATED AMP PEAK  7(5P12) WILD-TYPE
  N0                       191                          70
  N1                        79                          34
  N2                        30                           5
  N3                         3                           2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           M0  M1 M1A  MX
  AMP PEAK  7(5P12) MUTATED   263   4   1  34
  AMP PEAK  7(5P12) WILD-TYPE  95   1   0  16
D7V6, multiclass
     clus
vv    AMP PEAK  7(5P12) MUTATED AMP PEAK  7(5P12) WILD-TYPE
  M0                        263                          95
  M1                          4                           1
  M1A                         1                           0
  MX                         34                          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"
D7V7, binary
                             cls
clus                            0   1
  AMP PEAK  7(5P12) MUTATED    72 233
  AMP PEAK  7(5P12) WILD-TYPE  35  80
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(5P12) MUTATED     72  233
  AMP PEAK  7(5P12) WILD-TYPE   35   80
        clus
vv       AMP PEAK  7(5P12) MUTATED AMP PEAK  7(5P12) WILD-TYPE
  FEMALE                        72                          35
  MALE                         233                          80
[1] 2 2
[1] FALSE
D7V8, continuous
                             vv
clus                          LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK  7(5P12) MUTATED                                       9
  AMP PEAK  7(5P12) WILD-TYPE                                     3
                             vv
clus                          LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK  7(5P12) MUTATED                                        2
  AMP PEAK  7(5P12) WILD-TYPE                                      4
                             vv
clus                          LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK  7(5P12) MUTATED                                         0
  AMP PEAK  7(5P12) WILD-TYPE                                       1
                             vv
clus                          LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  7(5P12) MUTATED                                                           294
  AMP PEAK  7(5P12) WILD-TYPE                                                         107
D7V9, multiclass
                                                             clus
vv                                                            AMP PEAK  7(5P12) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                               9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                              2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                             0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                       294
                                                             clus
vv                                                            AMP PEAK  7(5P12) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         107
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V10, binary
                             cls
clus                            0   1
  AMP PEAK  7(5P12) MUTATED     9 296
  AMP PEAK  7(5P12) WILD-TYPE   4 111
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(5P12) MUTATED      9  296
  AMP PEAK  7(5P12) WILD-TYPE    4  111
     clus
vv    AMP PEAK  7(5P12) MUTATED AMP PEAK  7(5P12) WILD-TYPE
  NO                          9                           4
  YES                       296                         111
[1] 2 2
[1] FALSE
D7V11, continuous
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK  7(5P12) MUTATED   252   6   3   9
  AMP PEAK  7(5P12) WILD-TYPE  90   2   1   9
D7V12, multiclass
    clus
vv   AMP PEAK  7(5P12) MUTATED AMP PEAK  7(5P12) WILD-TYPE
  R0                       252                          90
  R1                         6                           2
  R2                         3                           1
  RX                         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                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  7(5P12) MUTATED       4                        11   216
  AMP PEAK  7(5P12) WILD-TYPE     5                         6    82
D7V13, multiclass
                           clus
vv                          AMP PEAK  7(5P12) MUTATED
  ASIAN                                             4
  BLACK OR AFRICAN AMERICAN                        11
  WHITE                                           216
                           clus
vv                          AMP PEAK  7(5P12) WILD-TYPE
  ASIAN                                               5
  BLACK OR AFRICAN AMERICAN                           6
  WHITE                                              82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V14, binary
                             cls
clus                            0   1
  AMP PEAK  7(5P12) MUTATED     6 187
  AMP PEAK  7(5P12) WILD-TYPE   2  80
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(5P12) MUTATED      6  187
  AMP PEAK  7(5P12) WILD-TYPE    2   80
                        clus
vv                       AMP PEAK  7(5P12) MUTATED AMP PEAK  7(5P12) WILD-TYPE
  HISPANIC OR LATINO                             6                           2
  NOT HISPANIC OR LATINO                       187                          80
[1] 2 2
[1] FALSE

Clustering(8) Variable = AMP PEAK  8(6P12.1) MUTATION ANALYSIS
D8V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  8(6P12.1) MUTATED    90  35
  AMP PEAK  8(6P12.1) WILD-TYPE 175  88
  AMP PEAK  8(6P12.1) MUTATED AMP PEAK  8(6P12.1) WILD-TYPE 
                          125                           263 
  AMP PEAK  8(6P12.1) MUTATED AMP PEAK  8(6P12.1) WILD-TYPE 
                           35                            88 
$`AMP PEAK  8(6P12.1) MUTATED`
TCGA-18-3409 TCGA-18-3411 TCGA-18-3412 TCGA-18-3421 TCGA-21-1070 TCGA-21-1072 
        2417         1415          345         1331         3636         3016 
TCGA-21-1076 TCGA-21-1079 TCGA-21-1082 TCGA-21-1083 TCGA-21-5786 TCGA-21-5787 
        1852          965         3644          267         1032          329 
TCGA-22-1002 TCGA-22-1012 TCGA-22-1017 TCGA-22-4591 TCGA-22-4594 TCGA-22-4595 
         131          429         1485          623         1470          734 
TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-5471 TCGA-22-5482 
        1057          399         1946          587          965          357 
TCGA-22-5483 TCGA-33-4533 TCGA-33-4587 TCGA-34-2605 TCGA-34-2609 TCGA-34-5928 
         573         1940         1970          881          951          552 
TCGA-37-4133 TCGA-37-4141 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5027 
         238           12         1361         1947         1996         1849 
TCGA-39-5037 TCGA-43-2578 TCGA-43-3394 TCGA-43-5670 TCGA-43-6770 TCGA-46-6025 
        1086          684          822          849          310          324 
TCGA-46-6026 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-56-1622 TCGA-56-5898 
         423         1948          923         1958          881          555 
TCGA-56-6545 TCGA-56-6546 TCGA-56-7582 TCGA-56-7730 TCGA-56-8503 TCGA-56-8629 
          62           26           26            6           41           34 
TCGA-56-A49D TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46N TCGA-60-2695 
          38         2167         1058         2589          910          642 
TCGA-60-2698 TCGA-60-2703 TCGA-60-2706 TCGA-60-2711 TCGA-60-2714 TCGA-60-2715 
         311         1950         1958         1260         1531         1075 
TCGA-60-2719 TCGA-60-2722 TCGA-60-2726 TCGA-63-6202 TCGA-66-2734 TCGA-66-2744 
        1297          908          358         1973         1311           30 
TCGA-66-2754 TCGA-66-2757 TCGA-66-2765 TCGA-66-2766 TCGA-66-2769 TCGA-66-2781 
          61           30           61           31         1947          121 
TCGA-66-2785 TCGA-66-2786 TCGA-66-2791 TCGA-66-2793 TCGA-66-2795 TCGA-66-2800 
          60          790         1977         1952          122         1492 
TCGA-68-8251 TCGA-68-A59J TCGA-77-7138 TCGA-77-7141 TCGA-77-7142 TCGA-77-7465 
          96          104         1959           15         1286          479 
TCGA-77-8007 TCGA-77-8130 TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5GF TCGA-85-6798 
        1960         1945           10         1959          839           34 
TCGA-85-7699 TCGA-85-7843 TCGA-85-8052 TCGA-85-8070 TCGA-85-8072 TCGA-85-8276 
           1           35           16          960          513           13 
TCGA-85-8287 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8582 
          13           67           54           61           61          424 
TCGA-85-8664 TCGA-85-A4QR TCGA-85-A5B5 TCGA-90-7769 TCGA-90-A4EE TCGA-90-A59Q 
           3           25          111          358          331          269 
TCGA-92-8064 TCGA-94-7943 TCGA-98-7454 TCGA-98-8022 TCGA-98-8023 TCGA-J1-A4AH 
         160          356          256          224          308          222 
TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HG 
         449           36           83         1722         1548 

$`AMP PEAK  8(6P12.1) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3410 TCGA-18-3414 TCGA-18-3415 
         370          136         2464          146          396         1810 
TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 
         862          758           50          187           85         2754 
TCGA-18-5592 TCGA-18-5595 TCGA-21-1071 TCGA-21-1075 TCGA-21-1077 TCGA-21-1078 
          92          827         1426         2134         1058          474 
TCGA-21-1080 TCGA-21-1081 TCGA-21-5782 TCGA-21-5784 TCGA-21-A5DI TCGA-22-0940 
        3724          284          962         1268          979          608 
TCGA-22-0944 TCGA-22-1000 TCGA-22-1005 TCGA-22-1011 TCGA-22-1016 TCGA-22-4593 
         223         1945         1952           53          822         1067 
TCGA-22-4596 TCGA-22-4599 TCGA-22-4613 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 
          17         1161          358         1964         1933          445 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5485 
        1346           24         1651         1952         1952          916 
TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4538 
        1912         1713          506           29         2524         2979 
TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4589 
        1311         5287         1966         1941          428         1948 
TCGA-33-6738 TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2608 TCGA-34-5231 
         822           80         1874          958         1000         1528 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 
        2062         1715          707          365          428          941 
TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 
         166          120           13           12          200          247 
TCGA-37-4132 TCGA-37-4135 TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5024 
         227          207          103         1454         2253         1964 
TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 
          52          740           59          833         1107          474 
TCGA-39-5036 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-3920 
        1084          544         1964         1223         1176         1007 
TCGA-43-5668 TCGA-43-6143 TCGA-43-6647 TCGA-43-6771 TCGA-43-7656 TCGA-43-7657 
         349          376          757         1936          212          236 
TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 
        1970          407          358         1971          353          296 
TCGA-43-A56U TCGA-43-A56V TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 
         432          366           12           12          911          541 
TCGA-52-7812 TCGA-56-5897 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 
        1967            3           30           13           30           44 
TCGA-56-7580 TCGA-56-7731 TCGA-56-7822 TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 
          40         1961            1          178           55           36 
TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY 
          63           17           16            2           46           30 
TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 
          25            4            4            8          378          911 
TCGA-58-A46L TCGA-58-A46M TCGA-60-2696 TCGA-60-2704 TCGA-60-2707 TCGA-60-2708 
        1723         1072          109         1943          661         1963 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2712 TCGA-60-2713 TCGA-60-2716 TCGA-60-2720 
        1505         1963          274         1731         1475           97 
TCGA-60-2721 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-63-7020 TCGA-63-7021 
         983         1092          717          816         1957         1955 
TCGA-63-7022 TCGA-63-7023 TCGA-66-2727 TCGA-66-2737 TCGA-66-2742 TCGA-66-2753 
        1947         1952         1967           61          641           31 
TCGA-66-2755 TCGA-66-2756 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2767 
          28           30          639          762           30           61 
TCGA-66-2768 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 
          61          700          578         1946           61          578 
TCGA-66-2780 TCGA-66-2782 TCGA-66-2783 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 
        1956         1954          759         1217          699         1955 
TCGA-66-2790 TCGA-66-2792 TCGA-66-2794 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 
         699          913         1645           83          202          211 
TCGA-68-8250 TCGA-68-A59I TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 
         244          121         1950         1941         1942         1952 
TCGA-77-7139 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-8008 
        1968         1954         1942         1952         1954         1945 
TCGA-77-8009 TCGA-77-8128 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 
        1641         1953         1941         1941         1947         1946 
TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 
        1951         1962          833         1943          293         1961 
TCGA-77-8153 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 
        1684         1092         1953         1942         1955         1963 
TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6560 TCGA-85-6561 
        1290         1280         1939          713          364          395 
TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 
          18           10           49         1965          911           60 
TCGA-85-8048 TCGA-85-8049 TCGA-85-8071 TCGA-85-8277 TCGA-85-8288 TCGA-85-8350 
          26           60          428           11           54           60 
TCGA-85-8351 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8666 TCGA-85-A4CL 
          55           22           21          445          475           15 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 
        1972         1960           19         1973         1967         1972 
TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 
        1987           24           13          758          289           89 
TCGA-90-7964 TCGA-90-A4ED TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8065 
         428          244           82          106          122           70 
TCGA-94-7033 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 
          87          430         1213         1344          189          211 
TCGA-96-A4JK TCGA-96-A4JL TCGA-98-8021 TCGA-L3-A4E7 TCGA-NC-A5HI 
         273          183          413           35         1135 

  AMP PEAK  8(6P12.1) MUTATED AMP PEAK  8(6P12.1) WILD-TYPE 
                            1                             1 
  AMP PEAK  8(6P12.1) MUTATED AMP PEAK  8(6P12.1) WILD-TYPE 
                         3644                          5287 
  AMP PEAK  8(6P12.1) MUTATED AMP PEAK  8(6P12.1) WILD-TYPE 
                          555                           700 
[1] "1.0 - 3644.0 (555.0)" "1.0 - 5287.0 (700.0)"
[1] "hr=" "1.1"
D8V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  8(6P12.1) MUTATED         0       18       45        1        19
  AMP PEAK  8(6P12.1) WILD-TYPE       1       54       92        0        33
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK  8(6P12.1) MUTATED          23         22          8        1
  AMP PEAK  8(6P12.1) WILD-TYPE        48         35         12        5
D8V3, multiclass
            clus
vv           AMP PEAK  8(6P12.1) MUTATED AMP PEAK  8(6P12.1) WILD-TYPE
  STAGE I                              0                             1
  STAGE IA                            18                            54
  STAGE IB                            45                            92
  STAGE II                             1                             0
  STAGE IIA                           19                            33
  STAGE IIB                           23                            48
  STAGE IIIA                          22                            35
  STAGE IIIB                           8                            12
  STAGE IV                             1                             5
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK  8(6P12.1) MUTATED    23  88  18   9
  AMP PEAK  8(6P12.1) WILD-TYPE  75 166  30  11
D8V4, multiclass
    clus
vv   AMP PEAK  8(6P12.1) MUTATED AMP PEAK  8(6P12.1) WILD-TYPE
  T1                          23                            75
  T2                          88                           166
  T3                          18                            30
  T4                           9                            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(6P12.1) MUTATED    86  36  13   1
  AMP PEAK  8(6P12.1) WILD-TYPE 175  77  22   4
D8V5, multiclass
    clus
vv   AMP PEAK  8(6P12.1) MUTATED AMP PEAK  8(6P12.1) WILD-TYPE
  N0                          86                           175
  N1                          36                            77
  N2                          13                            22
  N3                           1                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A  MX
  AMP PEAK  8(6P12.1) MUTATED   122   1   0  14
  AMP PEAK  8(6P12.1) WILD-TYPE 236   4   1  36
D8V6, multiclass
     clus
vv    AMP PEAK  8(6P12.1) MUTATED AMP PEAK  8(6P12.1) WILD-TYPE
  M0                          122                           236
  M1                            1                             4
  M1A                           0                             1
  MX                           14                            36
[1] 4 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(6P12.1) MUTATED    32 106
  AMP PEAK  8(6P12.1) WILD-TYPE  75 207
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(6P12.1) MUTATED     32  106
  AMP PEAK  8(6P12.1) WILD-TYPE   75  207
        clus
vv       AMP PEAK  8(6P12.1) MUTATED AMP PEAK  8(6P12.1) WILD-TYPE
  FEMALE                          32                            75
  MALE                           106                           207
[1] 2 2
[1] FALSE
D8V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK  8(6P12.1) MUTATED                                       6
  AMP PEAK  8(6P12.1) WILD-TYPE                                     6
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK  8(6P12.1) MUTATED                                        2
  AMP PEAK  8(6P12.1) WILD-TYPE                                      4
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK  8(6P12.1) MUTATED                                         1
  AMP PEAK  8(6P12.1) WILD-TYPE                                       0
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  8(6P12.1) MUTATED                                                           129
  AMP PEAK  8(6P12.1) WILD-TYPE                                                         272
D8V9, multiclass
                                                             clus
vv                                                            AMP PEAK  8(6P12.1) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         129
                                                             clus
vv                                                            AMP PEAK  8(6P12.1) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           272
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V10, binary
                               cls
clus                              0   1
  AMP PEAK  8(6P12.1) MUTATED     5 133
  AMP PEAK  8(6P12.1) WILD-TYPE   8 274
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(6P12.1) MUTATED      5  133
  AMP PEAK  8(6P12.1) WILD-TYPE    8  274
     clus
vv    AMP PEAK  8(6P12.1) MUTATED AMP PEAK  8(6P12.1) WILD-TYPE
  NO                            5                             8
  YES                         133                           274
[1] 2 2
[1] FALSE
D8V11, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  8(6P12.1) MUTATED   118   3   2   5
  AMP PEAK  8(6P12.1) WILD-TYPE 224   5   2  13
D8V12, multiclass
    clus
vv   AMP PEAK  8(6P12.1) MUTATED AMP PEAK  8(6P12.1) WILD-TYPE
  R0                         118                           224
  R1                           3                             5
  R2                           2                             2
  RX                           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                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  8(6P12.1) MUTATED       1                         7   103
  AMP PEAK  8(6P12.1) WILD-TYPE     8                        10   195
D8V13, multiclass
                           clus
vv                          AMP PEAK  8(6P12.1) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           7
  WHITE                                             103
                           clus
vv                          AMP PEAK  8(6P12.1) WILD-TYPE
  ASIAN                                                 8
  BLACK OR AFRICAN AMERICAN                            10
  WHITE                                               195
[1] 3 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(6P12.1) MUTATED     2  92
  AMP PEAK  8(6P12.1) WILD-TYPE   6 175
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(6P12.1) MUTATED      2   92
  AMP PEAK  8(6P12.1) WILD-TYPE    6  175
                        clus
vv                       AMP PEAK  8(6P12.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          92
                        clus
vv                       AMP PEAK  8(6P12.1) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           175
[1] 2 2
[1] FALSE

Clustering(9) Variable = AMP PEAK  9(6Q12) MUTATION ANALYSIS
D9V1, survival
                             sevent
clus2                           0   1
  AMP PEAK  9(6Q12) MUTATED    86  29
  AMP PEAK  9(6Q12) WILD-TYPE 179  94
  AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE 
                        115                         273 
  AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE 
                         29                          94 
$`AMP PEAK  9(6Q12) MUTATED`
TCGA-18-3409 TCGA-18-3412 TCGA-18-3421 TCGA-18-4721 TCGA-21-1076 TCGA-21-1079 
        2417          345         1331         2754         1852          965 
TCGA-21-1082 TCGA-21-1083 TCGA-21-5786 TCGA-21-5787 TCGA-22-1002 TCGA-22-1012 
        3644          267         1032          329          131          429 
TCGA-22-1017 TCGA-22-4594 TCGA-22-4595 TCGA-22-4601 TCGA-22-4605 TCGA-22-5471 
        1485         1470          734         1057         1946          965 
TCGA-22-5477 TCGA-22-5482 TCGA-22-5483 TCGA-33-4533 TCGA-33-4547 TCGA-33-4582 
        1346          357          573         1940         1311         1966 
TCGA-33-4587 TCGA-34-2605 TCGA-34-2609 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 
        1970          881          951          238          207           12 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5037 TCGA-43-2578 TCGA-43-3394 
        1361         1947         1996         1086          684          822 
TCGA-43-3920 TCGA-43-6770 TCGA-46-6025 TCGA-46-6026 TCGA-52-7810 TCGA-52-7811 
        1007          310          324          423          923         1958 
TCGA-56-1622 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7582 TCGA-56-7730 
         881          555           62           26           26            6 
TCGA-56-7822 TCGA-56-8629 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46N TCGA-60-2703 
           1           34         1058         2589          910         1950 
TCGA-60-2711 TCGA-60-2714 TCGA-60-2719 TCGA-60-2723 TCGA-63-6202 TCGA-66-2734 
        1260         1531         1297         1092         1973         1311 
TCGA-66-2744 TCGA-66-2754 TCGA-66-2757 TCGA-66-2759 TCGA-66-2765 TCGA-66-2766 
          30           61           30          762           61           31 
TCGA-66-2769 TCGA-66-2781 TCGA-66-2785 TCGA-66-2786 TCGA-66-2789 TCGA-66-2791 
        1947          121           60          790         1955         1977 
TCGA-66-2792 TCGA-66-2793 TCGA-66-2795 TCGA-66-2800 TCGA-68-8251 TCGA-68-A59J 
         913         1952          122         1492           96          104 
TCGA-77-7142 TCGA-77-7465 TCGA-77-8009 TCGA-77-8130 TCGA-77-A5G3 TCGA-77-A5GF 
        1286          479         1641         1945         1959          839 
TCGA-85-6560 TCGA-85-6798 TCGA-85-7699 TCGA-85-7843 TCGA-85-7950 TCGA-85-8052 
         364           34            1           35           60           16 
TCGA-85-8072 TCGA-85-8276 TCGA-85-8287 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 
         513           13           13           67           54           61 
TCGA-85-8355 TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 TCGA-85-A5B5 TCGA-90-7769 
          61          424            3          475          111          358 
TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7341 TCGA-92-8064 TCGA-94-7943 TCGA-94-A4VJ 
         331          269          106          160          356          430 
TCGA-96-A4JK TCGA-98-7454 TCGA-98-8022 TCGA-J1-A4AH TCGA-LA-A446 TCGA-MF-A522 
         273          256          224          222           36           83 
TCGA-NC-A5HE 
        1722 

$`AMP PEAK  9(6Q12) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3410 TCGA-18-3411 TCGA-18-3414 
         370          136         2464          146         1415          396 
TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-4083 TCGA-18-4086 
        1810          862          758           50          187           85 
TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 
          92          827         3636         1426         3016         2134 
TCGA-21-1077 TCGA-21-1078 TCGA-21-1080 TCGA-21-1081 TCGA-21-5782 TCGA-21-5784 
        1058          474         3724          284          962         1268 
TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1005 TCGA-22-1011 
         979          608          223         1945         1952           53 
TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 TCGA-22-4596 TCGA-22-4599 TCGA-22-4604 
         822          623         1067           17         1161          399 
TCGA-22-4607 TCGA-22-4613 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5478 
         587          358         1964         1933          445           24 
TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 
        1651         1952         1952          916         1912         1713 
TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4538 TCGA-33-4566 TCGA-33-4583 
         506           29         2524         2979         5287         1941 
TCGA-33-4586 TCGA-33-4589 TCGA-33-6738 TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 
         428         1948          822           80         1874          958 
TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 
        1000         1528         2062         1715          707          365 
TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 
         428          941          552          166          120           13 
TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-5819 TCGA-39-5011 
          12          200          247          227          103         1454 
TCGA-39-5016 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 
        2253         1964         1849           52          740           59 
TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5039 TCGA-39-5040 
         833         1107          474         1084          544         1964 
TCGA-43-2576 TCGA-43-2581 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 
        1223         1176          349          849          376          757 
TCGA-43-6771 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 
        1936          212          236         1970          407          358 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-51-4079 
        1971          353          296          432          366           12 
TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7812 TCGA-56-5897 
          12          911          541         1948         1967            3 
TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7731 
          30           13           30           44           40         1961 
TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 
          41          178           55           36           63           17 
TCGA-56-8628 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ 
          16           38            2           46           30           25 
TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 
           4            4            8          378          911         2167 
TCGA-58-A46L TCGA-58-A46M TCGA-60-2695 TCGA-60-2696 TCGA-60-2698 TCGA-60-2704 
        1723         1072          642          109          311         1943 
TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2712 
        1958          661         1963         1505         1963          274 
TCGA-60-2713 TCGA-60-2715 TCGA-60-2716 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 
        1731         1075         1475           97          983          908 
TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 
         717          816          358         1957         1955         1947 
TCGA-63-7023 TCGA-66-2727 TCGA-66-2737 TCGA-66-2742 TCGA-66-2753 TCGA-66-2755 
        1952         1967           61          641           31           28 
TCGA-66-2756 TCGA-66-2758 TCGA-66-2763 TCGA-66-2767 TCGA-66-2768 TCGA-66-2770 
          30          639           30           61           61          700 
TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2782 
         578         1946           61          578         1956         1954 
TCGA-66-2783 TCGA-66-2787 TCGA-66-2788 TCGA-66-2790 TCGA-66-2794 TCGA-68-7755 
         759         1217          699          699         1645           83 
TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-A59I TCGA-77-6842 TCGA-77-6843 
         202          211          244          121         1950         1941 
TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7335 
        1942         1952         1959         1968           15         1954 
TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-8007 TCGA-77-8008 TCGA-77-8128 
        1942         1952         1954         1960         1945         1953 
TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 
        1941         1941         1947         1946         1951         1962 
TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 
         833         1943          293         1961         1684         1092 
TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 
          10         1953         1942         1955         1963         1290 
TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6561 TCGA-85-7696 TCGA-85-7697 
        1280         1939          713          395           18           10 
TCGA-85-7698 TCGA-85-7710 TCGA-85-7844 TCGA-85-8048 TCGA-85-8049 TCGA-85-8070 
          49         1965          911           26           60          960 
TCGA-85-8071 TCGA-85-8277 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8479 
         428           11           54           60           55           22 
TCGA-85-8481 TCGA-85-8580 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR 
          21          445           15         1972         1960           25 
TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 
          19         1973         1967         1972         1987           24 
TCGA-85-A53L TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7964 TCGA-90-A4ED 
          13          758          289           89          428          244 
TCGA-92-7340 TCGA-92-8063 TCGA-92-8065 TCGA-94-7033 TCGA-96-7544 TCGA-96-7545 
          82          122           70           87         1213         1344 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-8021 TCGA-98-8023 TCGA-L3-A4E7 
         189          211          183          413          308           35 
TCGA-L3-A524 TCGA-NC-A5HG TCGA-NC-A5HI 
         449         1548         1135 

  AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE 
                          1                           2 
  AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE 
                       3644                        5287 
  AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE 
                        479                         699 
[1] "1.0 - 3644.0 (479.0)" "2.0 - 5287.0 (699.0)"
[1] "hr=" "1.1"
D9V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  9(6Q12) MUTATED         0       20       42        1        17
  AMP PEAK  9(6Q12) WILD-TYPE       1       52       95        0        35
                             vv
clus                          STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK  9(6Q12) MUTATED          19         15         10        1
  AMP PEAK  9(6Q12) WILD-TYPE        52         42         10        5
D9V3, multiclass
            clus
vv           AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE
  STAGE I                            0                           1
  STAGE IA                          20                          52
  STAGE IB                          42                          95
  STAGE II                           1                           0
  STAGE IIA                         17                          35
  STAGE IIB                         19                          52
  STAGE IIIA                        15                          42
  STAGE IIIB                        10                          10
  STAGE IV                           1                           5
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2  T3  T4
  AMP PEAK  9(6Q12) MUTATED    27  78  13   8
  AMP PEAK  9(6Q12) WILD-TYPE  71 176  35  12
D9V4, multiclass
    clus
vv   AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE
  T1                        27                          71
  T2                        78                         176
  T3                        13                          35
  T4                         8                          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  9(6Q12) MUTATED    81  33   8   2
  AMP PEAK  9(6Q12) WILD-TYPE 180  80  27   3
D9V5, multiclass
    clus
vv   AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE
  N0                        81                         180
  N1                        33                          80
  N2                         8                          27
  N3                         2                           3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           M0  M1 M1A  MX
  AMP PEAK  9(6Q12) MUTATED   110   1   0  14
  AMP PEAK  9(6Q12) WILD-TYPE 248   4   1  36
D9V6, multiclass
     clus
vv    AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE
  M0                        110                         248
  M1                          1                           4
  M1A                         0                           1
  MX                         14                          36
[1] 4 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(6Q12) MUTATED    27  99
  AMP PEAK  9(6Q12) WILD-TYPE  80 214
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  9(6Q12) MUTATED     27   99
  AMP PEAK  9(6Q12) WILD-TYPE   80  214
        clus
vv       AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE
  FEMALE                        27                          80
  MALE                          99                         214
[1] 2 2
[1] FALSE
D9V8, continuous
                             vv
clus                          LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK  9(6Q12) MUTATED                                       3
  AMP PEAK  9(6Q12) WILD-TYPE                                     9
                             vv
clus                          LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK  9(6Q12) MUTATED                                        1
  AMP PEAK  9(6Q12) WILD-TYPE                                      5
                             vv
clus                          LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK  9(6Q12) MUTATED                                         1
  AMP PEAK  9(6Q12) WILD-TYPE                                       0
                             vv
clus                          LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  9(6Q12) MUTATED                                                           121
  AMP PEAK  9(6Q12) WILD-TYPE                                                         280
D9V9, multiclass
                                                             clus
vv                                                            AMP PEAK  9(6Q12) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                               3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                              1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                             1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                       121
                                                             clus
vv                                                            AMP PEAK  9(6Q12) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         280
[1] 4 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(6Q12) MUTATED     5 121
  AMP PEAK  9(6Q12) WILD-TYPE   8 286
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  9(6Q12) MUTATED      5  121
  AMP PEAK  9(6Q12) WILD-TYPE    8  286
     clus
vv    AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE
  NO                          5                           8
  YES                       121                         286
[1] 2 2
[1] FALSE
D9V11, continuous
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK  9(6Q12) MUTATED   109   2   2   4
  AMP PEAK  9(6Q12) WILD-TYPE 233   6   2  14
D9V12, multiclass
    clus
vv   AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE
  R0                       109                         233
  R1                         2                           6
  R2                         2                           2
  RX                         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                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  9(6Q12) MUTATED       1                         8    91
  AMP PEAK  9(6Q12) WILD-TYPE     8                         9   207
D9V13, multiclass
                           clus
vv                          AMP PEAK  9(6Q12) MUTATED
  ASIAN                                             1
  BLACK OR AFRICAN AMERICAN                         8
  WHITE                                            91
                           clus
vv                          AMP PEAK  9(6Q12) WILD-TYPE
  ASIAN                                               8
  BLACK OR AFRICAN AMERICAN                           9
  WHITE                                             207
[1] 3 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(6Q12) MUTATED     2  87
  AMP PEAK  9(6Q12) WILD-TYPE   6 180
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  9(6Q12) MUTATED      2   87
  AMP PEAK  9(6Q12) WILD-TYPE    6  180
                        clus
vv                       AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE
  HISPANIC OR LATINO                             2                           6
  NOT HISPANIC OR LATINO                        87                         180
[1] 2 2
[1] FALSE

Clustering(10) Variable = AMP PEAK 10(7P11.2) MUTATION ANALYSIS
D10V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 10(7P11.2) MUTATED   138  58
  AMP PEAK 10(7P11.2) WILD-TYPE 127  65
  AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE 
                          196                           192 
  AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE 
                           58                            65 
$`AMP PEAK 10(7P11.2) MUTATED`
TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
         136         2464         2417         1415          345          396 
TCGA-18-3417 TCGA-18-3421 TCGA-18-4083 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 
         758         1331          187         2754           92         3636 
TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1079 TCGA-21-1081 TCGA-21-1082 
        3016         2134         1852          965          284         3644 
TCGA-21-5784 TCGA-21-A5DI TCGA-22-0944 TCGA-22-1011 TCGA-22-1012 TCGA-22-1017 
        1268          979          223           53          429         1485 
TCGA-22-4593 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4604 TCGA-22-4605 
        1067          734           17         1161          399         1946 
TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 
         965         1964         1933         1346           24         1651 
TCGA-22-5482 TCGA-22-5491 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4538 TCGA-33-4566 
         357         1713           29         1940         2979         5287 
TCGA-33-4582 TCGA-33-4586 TCGA-33-4589 TCGA-33-6738 TCGA-34-2596 TCGA-34-2605 
        1966          428         1948          822           80          881 
TCGA-34-2609 TCGA-34-5231 TCGA-34-5234 TCGA-34-5240 TCGA-34-5928 TCGA-37-3783 
         951         1528         1715          365          552          120 
TCGA-37-3789 TCGA-37-4130 TCGA-37-4141 TCGA-37-5819 TCGA-39-5016 TCGA-39-5019 
          13          247           12          103         2253         1361 
TCGA-39-5027 TCGA-39-5031 TCGA-39-5035 TCGA-39-5037 TCGA-43-2576 TCGA-43-2581 
        1849          833          474         1086         1223         1176 
TCGA-43-3394 TCGA-43-5668 TCGA-43-5670 TCGA-43-6647 TCGA-43-6771 TCGA-43-7657 
         822          349          849          757         1936          236 
TCGA-43-A475 TCGA-43-A56V TCGA-46-6025 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 
         296          366          324           12           12          911 
TCGA-52-7809 TCGA-52-7810 TCGA-56-6545 TCGA-56-7221 TCGA-56-7223 TCGA-56-7579 
        1948          923           62           30           30           44 
TCGA-56-7582 TCGA-56-8504 TCGA-56-8624 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX 
          26          178           36           38            2           46 
TCGA-56-A5DR TCGA-58-8391 TCGA-58-8393 TCGA-58-A46L TCGA-58-A46N TCGA-60-2698 
           4         2167         1058         1723          910          311 
TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2708 TCGA-60-2709 TCGA-60-2711 
        1950         1943         1958         1963         1505         1260 
TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2719 TCGA-60-2722 TCGA-60-2723 
         274         1731         1531         1297          908         1092 
TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-66-2734 TCGA-66-2737 
         358         1973         1957         1955         1311           61 
TCGA-66-2742 TCGA-66-2744 TCGA-66-2754 TCGA-66-2755 TCGA-66-2763 TCGA-66-2767 
         641           30           61           28           30           61 
TCGA-66-2770 TCGA-66-2771 TCGA-66-2777 TCGA-66-2782 TCGA-66-2785 TCGA-66-2791 
         700          578           61         1954           60         1977 
TCGA-66-2792 TCGA-66-2793 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-8250 
         913         1952          122         1492           83          244 
TCGA-68-A59J TCGA-77-6845 TCGA-77-7138 TCGA-77-7141 TCGA-77-7338 TCGA-77-7463 
         104         1952         1959           15         1952         1954 
TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 
         479         1960         1945         1641         1953         1945 
TCGA-77-8133 TCGA-77-8136 TCGA-77-8139 TCGA-77-8144 TCGA-77-8148 TCGA-77-8150 
        1941         1947         1951          833          293         1961 
TCGA-77-8153 TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 
        1684           10         1959         1955         1963         1290 
TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 
        1280         1939          839          395           34           18 
TCGA-85-7697 TCGA-85-7844 TCGA-85-7950 TCGA-85-8049 TCGA-85-8052 TCGA-85-8276 
          10          911           60           60           16           13 
TCGA-85-8287 TCGA-85-8351 TCGA-85-8354 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4QQ 
          13           55           61            3          475         1960 
TCGA-85-A4QR TCGA-85-A50M TCGA-85-A510 TCGA-85-A513 TCGA-85-A53L TCGA-90-7769 
          25           19         1967           24           13          358 
TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 
         244          331          269          106          122          160 
TCGA-94-A4VJ TCGA-96-7545 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-8023 TCGA-L3-A4E7 
         430         1344          273          183          308           35 
TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HI 
          83         1722         1548         1135 

$`AMP PEAK 10(7P11.2) WILD-TYPE`
TCGA-18-3406 TCGA-18-3410 TCGA-18-3415 TCGA-18-3416 TCGA-18-3419 TCGA-18-4086 
         370          146         1810          862           50           85 
TCGA-18-5595 TCGA-21-1071 TCGA-21-1077 TCGA-21-1078 TCGA-21-1080 TCGA-21-1083 
         827         1426         1058          474         3724          267 
TCGA-21-5782 TCGA-21-5786 TCGA-21-5787 TCGA-22-0940 TCGA-22-1000 TCGA-22-1002 
         962         1032          329          608         1945          131 
TCGA-22-1005 TCGA-22-1016 TCGA-22-4591 TCGA-22-4594 TCGA-22-4601 TCGA-22-4607 
        1952          822          623         1470         1057          587 
TCGA-22-4613 TCGA-22-5474 TCGA-22-5480 TCGA-22-5481 TCGA-22-5483 TCGA-22-5485 
         358          445         1952         1952          573          916 
TCGA-22-5489 TCGA-22-5492 TCGA-33-4532 TCGA-33-4547 TCGA-33-4583 TCGA-33-4587 
        1912          506         2524         1311         1941         1970 
TCGA-34-2600 TCGA-34-2604 TCGA-34-2608 TCGA-34-5232 TCGA-34-5239 TCGA-34-5241 
        1874          958         1000         2062          707          428 
TCGA-34-5927 TCGA-34-8454 TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 TCGA-37-4133 
         941          166           12          200          227          238 
TCGA-37-4135 TCGA-39-5011 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 
         207         1454         1947         1996         1964           52 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5034 TCGA-39-5036 TCGA-39-5039 TCGA-39-5040 
         740           59         1107         1084          544         1964 
TCGA-43-2578 TCGA-43-3920 TCGA-43-6143 TCGA-43-6770 TCGA-43-7656 TCGA-43-7658 
         684         1007          376          310          212         1970 
TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56U TCGA-46-6026 
         407          358         1971          353          432          423 
TCGA-52-7622 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 
         541         1958         1967          881            3          555 
TCGA-56-6546 TCGA-56-7222 TCGA-56-7580 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 
          26           13           40            6         1961            1 
TCGA-56-8503 TCGA-56-8622 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 
          41           55           63           17           16           34 
TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 
          30           25            4            8          378          911 
TCGA-58-A46J TCGA-58-A46M TCGA-60-2695 TCGA-60-2696 TCGA-60-2707 TCGA-60-2710 
        2589         1072          642          109          661         1963 
TCGA-60-2715 TCGA-60-2716 TCGA-60-2720 TCGA-60-2721 TCGA-60-2724 TCGA-60-2725 
        1075         1475           97          983          717          816 
TCGA-63-7022 TCGA-63-7023 TCGA-66-2727 TCGA-66-2753 TCGA-66-2756 TCGA-66-2757 
        1947         1952         1967           31           30           30 
TCGA-66-2758 TCGA-66-2759 TCGA-66-2765 TCGA-66-2766 TCGA-66-2768 TCGA-66-2769 
         639          762           61           31           61         1947 
TCGA-66-2773 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2783 TCGA-66-2786 
        1946          578         1956          121          759          790 
TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2794 TCGA-68-7756 
        1217          699         1955          699         1645          202 
TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 
         211           96          121         1950         1941         1942 
TCGA-77-7139 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-8131 TCGA-77-8138 
        1968         1286         1954         1942         1941         1946 
TCGA-77-8140 TCGA-77-8145 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5GH 
        1962         1943         1092         1953         1942          713 
TCGA-85-6560 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-8048 
         364           49            1         1965           35           26 
TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8277 TCGA-85-8288 TCGA-85-8350 
         960          428          513           11           54           60 
TCGA-85-8352 TCGA-85-8353 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 
          67           54           61           22           21          445 
TCGA-85-8582 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A50Z TCGA-85-A511 TCGA-85-A512 
         424           15         1972         1973         1972         1987 
TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7964 TCGA-92-7340 
         111          758          289           89          428           82 
TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 
          70           87          356         1213          189          211 
TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-J1-A4AH TCGA-L3-A524 TCGA-LA-A446 
         256          413          224          222          449           36 

  AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE 
                            2                             1 
  AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE 
                         5287                          3724 
  AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE 
                        822.0                         575.5 
[1] "2.0 - 5287.0 (822.0)" "1.0 - 3724.0 (575.5)"
[1] "hr=" "1.3"
D10V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 10(7P11.2) MUTATED         1       23       76        0        25
  AMP PEAK 10(7P11.2) WILD-TYPE       0       49       61        1        27
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 10(7P11.2) MUTATED          47         30          8        4
  AMP PEAK 10(7P11.2) WILD-TYPE        24         27         12        2
D10V3, multiclass
            clus
vv           AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE
  STAGE I                              1                             0
  STAGE IA                            23                            49
  STAGE IB                            76                            61
  STAGE II                             0                             1
  STAGE IIA                           25                            27
  STAGE IIB                           47                            24
  STAGE IIIA                          30                            27
  STAGE IIIB                           8                            12
  STAGE IV                             4                             2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK 10(7P11.2) MUTATED    35 145  29   7
  AMP PEAK 10(7P11.2) WILD-TYPE  63 109  19  13
D10V4, multiclass
    clus
vv   AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE
  T1                          35                            63
  T2                         145                           109
  T3                          29                            19
  T4                           7                            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(7P11.2) MUTATED   124  67  19   2
  AMP PEAK 10(7P11.2) WILD-TYPE 137  46  16   3
D10V5, multiclass
    clus
vv   AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE
  N0                         124                           137
  N1                          67                            46
  N2                          19                            16
  N3                           2                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A  MX
  AMP PEAK 10(7P11.2) MUTATED   184   4   0  23
  AMP PEAK 10(7P11.2) WILD-TYPE 174   1   1  27
D10V6, multiclass
     clus
vv    AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE
  M0                          184                           174
  M1                            4                             1
  M1A                           0                             1
  MX                           23                            27
[1] 4 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(7P11.2) MUTATED    50 166
  AMP PEAK 10(7P11.2) WILD-TYPE  57 147
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7P11.2) MUTATED     50  166
  AMP PEAK 10(7P11.2) WILD-TYPE   57  147
        clus
vv       AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE
  FEMALE                          50                            57
  MALE                           166                           147
[1] 2 2
[1] FALSE
D10V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK 10(7P11.2) MUTATED                                       8
  AMP PEAK 10(7P11.2) WILD-TYPE                                     4
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK 10(7P11.2) MUTATED                                        1
  AMP PEAK 10(7P11.2) WILD-TYPE                                      5
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 10(7P11.2) MUTATED                                         0
  AMP PEAK 10(7P11.2) WILD-TYPE                                       1
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 10(7P11.2) MUTATED                                                           207
  AMP PEAK 10(7P11.2) WILD-TYPE                                                         194
D10V9, multiclass
                                                             clus
vv                                                            AMP PEAK 10(7P11.2) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         207
                                                             clus
vv                                                            AMP PEAK 10(7P11.2) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           194
[1] 4 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(7P11.2) MUTATED     6 210
  AMP PEAK 10(7P11.2) WILD-TYPE   7 197
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7P11.2) MUTATED      6  210
  AMP PEAK 10(7P11.2) WILD-TYPE    7  197
     clus
vv    AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE
  NO                            6                             7
  YES                         210                           197
[1] 2 2
[1] FALSE
D10V11, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 10(7P11.2) MUTATED   179   4   1   9
  AMP PEAK 10(7P11.2) WILD-TYPE 163   4   3   9
D10V12, multiclass
    clus
vv   AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE
  R0                         179                           163
  R1                           4                             4
  R2                           1                             3
  RX                           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                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 10(7P11.2) MUTATED       8                        11   143
  AMP PEAK 10(7P11.2) WILD-TYPE     1                         6   155
D10V13, multiclass
                           clus
vv                          AMP PEAK 10(7P11.2) MUTATED
  ASIAN                                               8
  BLACK OR AFRICAN AMERICAN                          11
  WHITE                                             143
                           clus
vv                          AMP PEAK 10(7P11.2) WILD-TYPE
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                               155
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V14, binary
                               cls
clus                              0   1
  AMP PEAK 10(7P11.2) MUTATED     2 133
  AMP PEAK 10(7P11.2) WILD-TYPE   6 134
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7P11.2) MUTATED      2  133
  AMP PEAK 10(7P11.2) WILD-TYPE    6  134
                        clus
vv                       AMP PEAK 10(7P11.2) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                         133
                        clus
vv                       AMP PEAK 10(7P11.2) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           134
[1] 2 2
[1] FALSE

Clustering(11) Variable = AMP PEAK 11(7Q21.2) MUTATION ANALYSIS
D11V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 11(7Q21.2) MUTATED   145  64
  AMP PEAK 11(7Q21.2) WILD-TYPE 120  59
  AMP PEAK 11(7Q21.2) MUTATED AMP PEAK 11(7Q21.2) WILD-TYPE 
                          209                           179 
  AMP PEAK 11(7Q21.2) MUTATED AMP PEAK 11(7Q21.2) WILD-TYPE 
                           64                            59 
$`AMP PEAK 11(7Q21.2) MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
         370          136         2417         1415          345          396 
TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4721 
         862          758           50         1331          187         2754 
TCGA-21-1070 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1081 
        3636         3016         2134         1852         1058          284 
TCGA-21-1083 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0944 TCGA-22-1005 
         267         1032          329          979          223         1952 
TCGA-22-1011 TCGA-22-1012 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4596 
          53          429          623         1067         1470           17 
TCGA-22-4599 TCGA-22-4604 TCGA-22-4605 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 
        1161          399         1946          965         1964         1933 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5482 TCGA-22-5483 TCGA-22-5491 
        1346           24         1651          357          573         1713 
TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 
         506           29         1940         2979         1311         5287 
TCGA-33-4586 TCGA-33-4589 TCGA-33-6738 TCGA-34-2596 TCGA-34-2600 TCGA-34-2605 
         428         1948          822           80         1874          881 
TCGA-34-2609 TCGA-34-5231 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 
         951         1528          365          428          941          552 
TCGA-37-3783 TCGA-37-3789 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-39-5011 
         120           13          238          207           12         1454 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5027 TCGA-39-5029 TCGA-39-5031 TCGA-39-5035 
        2253         1361         1849          740          833          474 
TCGA-39-5036 TCGA-43-3394 TCGA-43-3920 TCGA-43-6647 TCGA-43-7657 TCGA-43-7658 
        1084          822         1007          757          236         1970 
TCGA-43-A474 TCGA-43-A475 TCGA-43-A56V TCGA-46-6025 TCGA-51-4079 TCGA-51-4081 
         353          296          366          324           12          911 
TCGA-52-7809 TCGA-52-7810 TCGA-56-1622 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 
        1948          923          881          555           62           26 
TCGA-56-7221 TCGA-56-7223 TCGA-56-7579 TCGA-56-7582 TCGA-56-8504 TCGA-56-A49D 
          30           30           44           26          178           38 
TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A5DR TCGA-58-8391 TCGA-58-8393 TCGA-58-A46M 
           2           46            4         2167         1058         1072 
TCGA-58-A46N TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2708 
         910          311         1950         1943         1958         1963 
TCGA-60-2709 TCGA-60-2711 TCGA-60-2712 TCGA-60-2714 TCGA-60-2719 TCGA-60-2722 
        1505         1260          274         1531         1297          908 
TCGA-60-2723 TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-66-2734 
        1092          358         1973         1957         1955         1311 
TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2755 TCGA-66-2758 TCGA-66-2763 
          61          641           30           28          639           30 
TCGA-66-2766 TCGA-66-2767 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2780 
          31           61         1947          700          578         1956 
TCGA-66-2781 TCGA-66-2782 TCGA-66-2785 TCGA-66-2787 TCGA-66-2791 TCGA-66-2792 
         121         1954           60         1217         1977          913 
TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-8250 
        1952         1645          122         1492           83          244 
TCGA-77-6843 TCGA-77-6845 TCGA-77-7141 TCGA-77-7142 TCGA-77-7338 TCGA-77-7463 
        1941         1952           15         1286         1952         1954 
TCGA-77-7465 TCGA-77-8007 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8133 
         479         1960         1641         1953         1945         1941 
TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5G6 
         293         1961         1684           10         1959         1955 
TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GH TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 
        1290         1280          713          395           34           18 
TCGA-85-7699 TCGA-85-7843 TCGA-85-7950 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 
           1           35           60           60           16          960 
TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8352 TCGA-85-8354 
         513           13           11           13           67           61 
TCGA-85-8666 TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A512 TCGA-85-A53L 
         475         1960           25           19         1987           13 
TCGA-85-A5B5 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q 
         111           89          358          244          331          269 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-94-A4VJ TCGA-96-7545 TCGA-96-8169 
          82          106          122          430         1344          189 
TCGA-96-A4JK TCGA-96-A4JL TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 
         273          183          308          222           35          449 
TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HI 
          36           83         1722         1548         1135 

$`AMP PEAK 11(7Q21.2) WILD-TYPE`
TCGA-18-3408 TCGA-18-3410 TCGA-18-3415 TCGA-18-4086 TCGA-18-5592 TCGA-18-5595 
        2464          146         1810           85           92          827 
TCGA-21-1071 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1082 TCGA-21-5782 
        1426          474          965         3724         3644          962 
TCGA-21-5784 TCGA-22-0940 TCGA-22-1000 TCGA-22-1002 TCGA-22-1016 TCGA-22-1017 
        1268          608         1945          131          822         1485 
TCGA-22-4595 TCGA-22-4601 TCGA-22-4607 TCGA-22-4613 TCGA-22-5474 TCGA-22-5480 
         734         1057          587          358          445         1952 
TCGA-22-5481 TCGA-22-5485 TCGA-22-5489 TCGA-33-4532 TCGA-33-4582 TCGA-33-4583 
        1952          916         1912         2524         1966         1941 
TCGA-33-4587 TCGA-34-2604 TCGA-34-2608 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 
        1970          958         1000         2062         1715          707 
TCGA-34-8454 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-5819 
         166           12          200          247          227          103 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 TCGA-39-5030 TCGA-39-5034 
        1947         1996         1964           52           59         1107 
TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 
        1086          544         1964         1223          684         1176 
TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 
         349          849          376          310         1936          212 
TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A56U TCGA-46-6026 TCGA-51-4080 
         407          358         1971          432          423           12 
TCGA-52-7622 TCGA-52-7811 TCGA-52-7812 TCGA-56-5897 TCGA-56-7222 TCGA-56-7580 
         541         1958         1967            3           13           40 
TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 TCGA-56-8622 TCGA-56-8624 
           6         1961            1           41           55           36 
TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BY TCGA-56-A4ZJ 
          63           17           16           34           30           25 
TCGA-56-A4ZK TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 TCGA-58-A46J TCGA-58-A46L 
           4            8          378          911         2589         1723 
TCGA-60-2695 TCGA-60-2696 TCGA-60-2707 TCGA-60-2710 TCGA-60-2713 TCGA-60-2715 
         642          109          661         1963         1731         1075 
TCGA-60-2716 TCGA-60-2720 TCGA-60-2721 TCGA-60-2724 TCGA-60-2725 TCGA-63-7022 
        1475           97          983          717          816         1947 
TCGA-63-7023 TCGA-66-2727 TCGA-66-2753 TCGA-66-2754 TCGA-66-2756 TCGA-66-2757 
        1952         1967           31           61           30           30 
TCGA-66-2759 TCGA-66-2765 TCGA-66-2768 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 
         762           61           61         1946           61          578 
TCGA-66-2783 TCGA-66-2786 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-68-7756 
         759          790          699         1955          699          202 
TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 TCGA-77-6844 
         211           96          121          104         1950         1942 
TCGA-77-7138 TCGA-77-7139 TCGA-77-7335 TCGA-77-7337 TCGA-77-8008 TCGA-77-8131 
        1959         1968         1954         1942         1945         1941 
TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 
        1947         1946         1951         1962          833         1943 
TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G7 TCGA-77-A5GB TCGA-77-A5GF 
        1092         1953         1942         1963         1939          839 
TCGA-85-6560 TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 TCGA-85-7844 TCGA-85-8048 
         364           10           49         1965          911           26 
TCGA-85-8071 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 TCGA-85-8355 
         428           54           60           55           54           61 
TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 TCGA-85-A4CL 
          22           21          445          424            3           15 
TCGA-85-A4PA TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 TCGA-90-6837 
        1972         1973         1967         1972           24          758 
TCGA-90-7766 TCGA-90-7964 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 
         289          428          160           70           87          356 
TCGA-96-7544 TCGA-96-8170 TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 
        1213          211          256          413          224 

  AMP PEAK 11(7Q21.2) MUTATED AMP PEAK 11(7Q21.2) WILD-TYPE 
                            1                             1 
  AMP PEAK 11(7Q21.2) MUTATED AMP PEAK 11(7Q21.2) WILD-TYPE 
                         5287                          3724 
  AMP PEAK 11(7Q21.2) MUTATED AMP PEAK 11(7Q21.2) WILD-TYPE 
                          623                           684 
[1] "1.0 - 5287.0 (623.0)" "1.0 - 3724.0 (684.0)"
[1] "hr=" "1"  
D11V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 11(7Q21.2) MUTATED         1       30       73        1        27
  AMP PEAK 11(7Q21.2) WILD-TYPE       0       42       64        0        25
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 11(7Q21.2) MUTATED          46         32         11        4
  AMP PEAK 11(7Q21.2) WILD-TYPE        25         25          9        2
D11V3, multiclass
            clus
vv           AMP PEAK 11(7Q21.2) MUTATED AMP PEAK 11(7Q21.2) WILD-TYPE
  STAGE I                              1                             0
  STAGE IA                            30                            42
  STAGE IB                            73                            64
  STAGE II                             1                             0
  STAGE IIA                           27                            25
  STAGE IIB                           46                            25
  STAGE IIIA                          32                            25
  STAGE IIIB                          11                             9
  STAGE IV                             4                             2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK 11(7Q21.2) MUTATED    43 148  26  10
  AMP PEAK 11(7Q21.2) WILD-TYPE  55 106  22  10
D11V4, multiclass
    clus
vv   AMP PEAK 11(7Q21.2) MUTATED AMP PEAK 11(7Q21.2) WILD-TYPE
  T1                          43                            55
  T2                         148                           106
  T3                          26                            22
  T4                          10                            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  AMP PEAK 11(7Q21.2) MUTATED   132  70  21   2
  AMP PEAK 11(7Q21.2) WILD-TYPE 129  43  14   3
D11V5, multiclass
    clus
vv   AMP PEAK 11(7Q21.2) MUTATED AMP PEAK 11(7Q21.2) WILD-TYPE
  N0                         132                           129
  N1                          70                            43
  N2                          21                            14
  N3                           2                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A  MX
  AMP PEAK 11(7Q21.2) MUTATED   196   4   0  24
  AMP PEAK 11(7Q21.2) WILD-TYPE 162   1   1  26
D11V6, multiclass
     clus
vv    AMP PEAK 11(7Q21.2) MUTATED AMP PEAK 11(7Q21.2) WILD-TYPE
  M0                          196                           162
  M1                            4                             1
  M1A                           0                             1
  MX                           24                            26
[1] 4 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(7Q21.2) MUTATED    48 179
  AMP PEAK 11(7Q21.2) WILD-TYPE  59 134
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7Q21.2) MUTATED     48  179
  AMP PEAK 11(7Q21.2) WILD-TYPE   59  134
        clus
vv       AMP PEAK 11(7Q21.2) MUTATED AMP PEAK 11(7Q21.2) WILD-TYPE
  FEMALE                          48                            59
  MALE                           179                           134
[1] 2 2
[1] FALSE
D11V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK 11(7Q21.2) MUTATED                                       7
  AMP PEAK 11(7Q21.2) WILD-TYPE                                     5
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK 11(7Q21.2) MUTATED                                        1
  AMP PEAK 11(7Q21.2) WILD-TYPE                                      5
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 11(7Q21.2) MUTATED                                         0
  AMP PEAK 11(7Q21.2) WILD-TYPE                                       1
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 11(7Q21.2) MUTATED                                                           219
  AMP PEAK 11(7Q21.2) WILD-TYPE                                                         182
D11V9, multiclass
                                                             clus
vv                                                            AMP PEAK 11(7Q21.2) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         219
                                                             clus
vv                                                            AMP PEAK 11(7Q21.2) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           182
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V10, binary
                               cls
clus                              0   1
  AMP PEAK 11(7Q21.2) MUTATED     5 222
  AMP PEAK 11(7Q21.2) WILD-TYPE   8 185
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7Q21.2) MUTATED      5  222
  AMP PEAK 11(7Q21.2) WILD-TYPE    8  185
     clus
vv    AMP PEAK 11(7Q21.2) MUTATED AMP PEAK 11(7Q21.2) WILD-TYPE
  NO                            5                             8
  YES                         222                           185
[1] 2 2
[1] FALSE
D11V11, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 11(7Q21.2) MUTATED   187   6   1   7
  AMP PEAK 11(7Q21.2) WILD-TYPE 155   2   3  11
D11V12, multiclass
    clus
vv   AMP PEAK 11(7Q21.2) MUTATED AMP PEAK 11(7Q21.2) WILD-TYPE
  R0                         187                           155
  R1                           6                             2
  R2                           1                             3
  RX                           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                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 11(7Q21.2) MUTATED       7                         9   156
  AMP PEAK 11(7Q21.2) WILD-TYPE     2                         8   142
D11V13, multiclass
                           clus
vv                          AMP PEAK 11(7Q21.2) MUTATED
  ASIAN                                               7
  BLACK OR AFRICAN AMERICAN                           9
  WHITE                                             156
                           clus
vv                          AMP PEAK 11(7Q21.2) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             8
  WHITE                                               142
[1] 3 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(7Q21.2) MUTATED     3 137
  AMP PEAK 11(7Q21.2) WILD-TYPE   5 130
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7Q21.2) MUTATED      3  137
  AMP PEAK 11(7Q21.2) WILD-TYPE    5  130
                        clus
vv                       AMP PEAK 11(7Q21.2) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                         137
                        clus
vv                       AMP PEAK 11(7Q21.2) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           130
[1] 2 2
[1] FALSE

Clustering(12) Variable = AMP PEAK 12(8P11.23) MUTATION ANALYSIS
D12V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 12(8P11.23) MUTATED   120  65
  AMP PEAK 12(8P11.23) WILD-TYPE 145  58
  AMP PEAK 12(8P11.23) MUTATED AMP PEAK 12(8P11.23) WILD-TYPE 
                           185                            203 
  AMP PEAK 12(8P11.23) MUTATED AMP PEAK 12(8P11.23) WILD-TYPE 
                            65                             58 
$`AMP PEAK 12(8P11.23) MUTATED`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
         136         2417          146         1415          345          396 
TCGA-18-3415 TCGA-18-3416 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4721 
        1810          862           50         1331          187         2754 
TCGA-18-5595 TCGA-21-1070 TCGA-21-1072 TCGA-21-1075 TCGA-21-1077 TCGA-21-1079 
         827         3636         3016         2134         1058          965 
TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-5784 TCGA-21-A5DI TCGA-22-1002 
        3724          284         3644         1268          979          131 
TCGA-22-1011 TCGA-22-1017 TCGA-22-4591 TCGA-22-4595 TCGA-22-4596 TCGA-22-4601 
          53         1485          623          734           17         1057 
TCGA-22-4604 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 
         399         1964         1933          445         1346         1651 
TCGA-22-5480 TCGA-22-5482 TCGA-22-5483 TCGA-22-5489 TCGA-22-5491 TCGA-22-A5C4 
        1952          357          573         1912         1713           29 
TCGA-33-4533 TCGA-33-4547 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 
        1940         1311         1966         1941          428         1970 
TCGA-33-6738 TCGA-34-2596 TCGA-34-2604 TCGA-34-2605 TCGA-34-2609 TCGA-34-5231 
         822           80          958          881          951         1528 
TCGA-34-5232 TCGA-34-5239 TCGA-34-5241 TCGA-34-5928 TCGA-34-8454 TCGA-37-3789 
        2062          707          428          552          166           13 
TCGA-37-4132 TCGA-39-5016 TCGA-39-5019 TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 
         227         2253         1361         1964           52          740 
TCGA-39-5035 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 
         474         1086          544         1964         1223          684 
TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 TCGA-43-8116 
         822         1007          849          757          310          358 
TCGA-43-8118 TCGA-43-A56V TCGA-52-7810 TCGA-52-7811 TCGA-56-1622 TCGA-56-5897 
        1971          366          923         1958          881            3 
TCGA-56-5898 TCGA-56-6546 TCGA-56-7579 TCGA-56-7730 TCGA-56-8622 TCGA-56-8628 
         555           26           44            6           55           16 
TCGA-56-A49D TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8390 TCGA-58-A46M TCGA-60-2695 
          38            4            8          911         1072          642 
TCGA-60-2706 TCGA-60-2708 TCGA-60-2709 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 
        1958         1963         1505           97          983          908 
TCGA-60-2724 TCGA-60-2725 TCGA-63-7020 TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 
         717          816         1957         1952         1967         1311 
TCGA-66-2742 TCGA-66-2753 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2759 
         641           31           28           30           30          762 
TCGA-66-2763 TCGA-66-2767 TCGA-66-2769 TCGA-66-2770 TCGA-66-2773 TCGA-66-2780 
          30           61         1947          700         1946         1956 
TCGA-66-2781 TCGA-66-2782 TCGA-66-2788 TCGA-66-2789 TCGA-66-2792 TCGA-66-2793 
         121         1954          699         1955          913         1952 
TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-77-6843 
        1492           83          202          211          244         1941 
TCGA-77-6844 TCGA-77-7139 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 
        1942         1968         1954         1942         1952         1954 
TCGA-77-8008 TCGA-77-8128 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 
        1945         1953         1947         1946         1951         1962 
TCGA-77-8148 TCGA-77-8150 TCGA-77-8154 TCGA-77-A5G3 TCGA-77-A5G7 TCGA-77-A5G8 
         293         1961         1092         1959         1963         1290 
TCGA-77-A5GA TCGA-77-A5GH TCGA-85-6560 TCGA-85-7696 TCGA-85-7699 TCGA-85-7843 
        1280          713          364           18            1           35 
TCGA-85-8048 TCGA-85-8052 TCGA-85-8070 TCGA-85-8276 TCGA-85-8580 TCGA-85-8582 
          26           16          960           13          445          424 
TCGA-85-8664 TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 
           3           25         1973         1967         1972           24 
TCGA-85-A53L TCGA-90-7767 TCGA-90-7769 TCGA-90-A4EE TCGA-92-7340 TCGA-94-7033 
          13           89          358          331           82           87 
TCGA-94-7943 TCGA-96-7544 TCGA-96-7545 TCGA-96-A4JK TCGA-98-8021 TCGA-98-8023 
         356         1213         1344          273          413          308 
TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-LA-A446 TCGA-NC-A5HG TCGA-NC-A5HI 
         222           35           36         1548         1135 

$`AMP PEAK 12(8P11.23) WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3417 TCGA-18-4086 TCGA-18-5592 TCGA-21-1071 
         370         2464          758           85           92         1426 
TCGA-21-1076 TCGA-21-1078 TCGA-21-1083 TCGA-21-5782 TCGA-21-5786 TCGA-21-5787 
        1852          474          267          962         1032          329 
TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1005 TCGA-22-1012 TCGA-22-1016 
         608          223         1945         1952          429          822 
TCGA-22-4593 TCGA-22-4594 TCGA-22-4599 TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 
        1067         1470         1161         1946          587          358 
TCGA-22-5471 TCGA-22-5478 TCGA-22-5481 TCGA-22-5485 TCGA-22-5492 TCGA-33-4532 
         965           24         1952          916          506         2524 
TCGA-33-4538 TCGA-33-4566 TCGA-33-4589 TCGA-34-2600 TCGA-34-2608 TCGA-34-5234 
        2979         5287         1948         1874         1000         1715 
TCGA-34-5240 TCGA-34-5927 TCGA-37-3783 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 
         365          941          120           12          200          247 
TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 TCGA-39-5021 
         238          207           12          103         1454         1947 
TCGA-39-5022 TCGA-39-5027 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5036 
        1996         1849           59          833         1107         1084 
TCGA-43-2581 TCGA-43-5668 TCGA-43-6143 TCGA-43-6771 TCGA-43-7656 TCGA-43-7657 
        1176          349          376         1936          212          236 
TCGA-43-7658 TCGA-43-8115 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-46-6025 
        1970          407          353          296          432          324 
TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 
         423           12           12          911          541         1948 
TCGA-52-7812 TCGA-56-6545 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7580 
        1967           62           30           13           30           40 
TCGA-56-7582 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 TCGA-56-8504 TCGA-56-8624 
          26         1961            1           41          178           36 
TCGA-56-8625 TCGA-56-8626 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY 
          63           17           34            2           46           30 
TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-58-8388 TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J 
          25            4          378         2167         1058         2589 
TCGA-58-A46L TCGA-58-A46N TCGA-60-2696 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 
        1723          910          109          311         1950         1943 
TCGA-60-2707 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 
         661         1963         1260          274         1731         1531 
TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2723 TCGA-60-2726 TCGA-63-6202 
        1075         1475         1297         1092          358         1973 
TCGA-63-7021 TCGA-63-7022 TCGA-66-2737 TCGA-66-2744 TCGA-66-2754 TCGA-66-2758 
        1955         1947           61           30           61          639 
TCGA-66-2765 TCGA-66-2766 TCGA-66-2768 TCGA-66-2771 TCGA-66-2777 TCGA-66-2778 
          61           31           61          578           61          578 
TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2790 TCGA-66-2791 
         759           60          790         1217          699         1977 
TCGA-66-2794 TCGA-66-2795 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 
        1645          122           96          121          104         1950 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7141 TCGA-77-7142 TCGA-77-7465 TCGA-77-8007 
        1952         1959           15         1286          479         1960 
TCGA-77-8009 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8144 TCGA-77-8145 
        1641         1945         1941         1941          833         1943 
TCGA-77-8153 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5GB 
        1684           10         1953         1942         1955         1939 
TCGA-77-A5GF TCGA-85-6561 TCGA-85-6798 TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 
         839          395           34           10           49         1965 
TCGA-85-7844 TCGA-85-7950 TCGA-85-8049 TCGA-85-8071 TCGA-85-8072 TCGA-85-8277 
         911           60           60          428          513           11 
TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 
          13           54           60           55           67           54 
TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8666 TCGA-85-A4CL 
          61           61           22           21          475           15 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A512 TCGA-85-A5B5 TCGA-90-6837 
        1972         1960           19         1987          111          758 
TCGA-90-7766 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A59Q TCGA-92-7341 TCGA-92-8063 
         289          428          244          269          106          122 
TCGA-92-8064 TCGA-92-8065 TCGA-94-A4VJ TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL 
         160           70          430          189          211          183 
TCGA-98-7454 TCGA-98-8022 TCGA-L3-A524 TCGA-MF-A522 TCGA-NC-A5HE 
         256          224          449           83         1722 

  AMP PEAK 12(8P11.23) MUTATED AMP PEAK 12(8P11.23) WILD-TYPE 
                             1                              1 
  AMP PEAK 12(8P11.23) MUTATED AMP PEAK 12(8P11.23) WILD-TYPE 
                          3724                           5287 
  AMP PEAK 12(8P11.23) MUTATED AMP PEAK 12(8P11.23) WILD-TYPE 
                           827                            429 
[1] "1.0 - 3724.0 (827.0)" "1.0 - 5287.0 (429.0)"
[1] "hr=" "1.1"
D12V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 12(8P11.23) MUTATED         1       33       62        1        26
  AMP PEAK 12(8P11.23) WILD-TYPE       0       39       75        0        26
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 12(8P11.23) MUTATED          31         33          9        4
  AMP PEAK 12(8P11.23) WILD-TYPE        40         24         11        2
D12V3, multiclass
            clus
vv           AMP PEAK 12(8P11.23) MUTATED AMP PEAK 12(8P11.23) WILD-TYPE
  STAGE I                               1                              0
  STAGE IA                             33                             39
  STAGE IB                             62                             75
  STAGE II                              1                              0
  STAGE IIA                            26                             26
  STAGE IIB                            31                             40
  STAGE IIIA                           33                             24
  STAGE IIIB                            9                             11
  STAGE IV                              4                              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 12(8P11.23) MUTATED    48 120  20  13
  AMP PEAK 12(8P11.23) WILD-TYPE  50 134  28   7
D12V4, multiclass
    clus
vv   AMP PEAK 12(8P11.23) MUTATED AMP PEAK 12(8P11.23) WILD-TYPE
  T1                           48                             50
  T2                          120                            134
  T3                           20                             28
  T4                           13                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK 12(8P11.23) MUTATED   124  55  18   2
  AMP PEAK 12(8P11.23) WILD-TYPE 137  58  17   3
D12V5, multiclass
    clus
vv   AMP PEAK 12(8P11.23) MUTATED AMP PEAK 12(8P11.23) WILD-TYPE
  N0                          124                            137
  N1                           55                             58
  N2                           18                             17
  N3                            2                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A  MX
  AMP PEAK 12(8P11.23) MUTATED   171   3   1  24
  AMP PEAK 12(8P11.23) WILD-TYPE 187   2   0  26
D12V6, multiclass
     clus
vv    AMP PEAK 12(8P11.23) MUTATED AMP PEAK 12(8P11.23) WILD-TYPE
  M0                           171                            187
  M1                             3                              2
  M1A                            1                              0
  MX                            24                             26
[1] 4 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(8P11.23) MUTATED    40 161
  AMP PEAK 12(8P11.23) WILD-TYPE  67 152
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8P11.23) MUTATED     40  161
  AMP PEAK 12(8P11.23) WILD-TYPE   67  152
        clus
vv       AMP PEAK 12(8P11.23) MUTATED AMP PEAK 12(8P11.23) WILD-TYPE
  FEMALE                           40                             67
  MALE                            161                            152
[1] 2 2
[1] FALSE
D12V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK 12(8P11.23) MUTATED                                       5
  AMP PEAK 12(8P11.23) WILD-TYPE                                     7
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK 12(8P11.23) MUTATED                                        1
  AMP PEAK 12(8P11.23) WILD-TYPE                                      5
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 12(8P11.23) MUTATED                                         1
  AMP PEAK 12(8P11.23) WILD-TYPE                                       0
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 12(8P11.23) MUTATED                                                           194
  AMP PEAK 12(8P11.23) WILD-TYPE                                                         207
D12V9, multiclass
                                                             clus
vv                                                            AMP PEAK 12(8P11.23) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          194
                                                             clus
vv                                                            AMP PEAK 12(8P11.23) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            207
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V10, binary
                                cls
clus                               0   1
  AMP PEAK 12(8P11.23) MUTATED     7 194
  AMP PEAK 12(8P11.23) WILD-TYPE   6 213
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8P11.23) MUTATED      7  194
  AMP PEAK 12(8P11.23) WILD-TYPE    6  213
     clus
vv    AMP PEAK 12(8P11.23) MUTATED AMP PEAK 12(8P11.23) WILD-TYPE
  NO                             7                              6
  YES                          194                            213
[1] 2 2
[1] FALSE
D12V11, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 12(8P11.23) MUTATED   170   3   0   2
  AMP PEAK 12(8P11.23) WILD-TYPE 172   5   4  16
D12V12, multiclass
    clus
vv   AMP PEAK 12(8P11.23) MUTATED AMP PEAK 12(8P11.23) WILD-TYPE
  R0                          170                            172
  R1                            3                              5
  R2                            0                              4
  RX                            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                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 12(8P11.23) MUTATED       4                        10   139
  AMP PEAK 12(8P11.23) WILD-TYPE     5                         7   159
D12V13, multiclass
                           clus
vv                          AMP PEAK 12(8P11.23) MUTATED
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                           10
  WHITE                                              139
                           clus
vv                          AMP PEAK 12(8P11.23) WILD-TYPE
  ASIAN                                                  5
  BLACK OR AFRICAN AMERICAN                              7
  WHITE                                                159
[1] 3 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(8P11.23) MUTATED     2 125
  AMP PEAK 12(8P11.23) WILD-TYPE   6 142
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8P11.23) MUTATED      2  125
  AMP PEAK 12(8P11.23) WILD-TYPE    6  142
                        clus
vv                       AMP PEAK 12(8P11.23) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          125
                        clus
vv                       AMP PEAK 12(8P11.23) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            142
[1] 2 2
[1] FALSE

Clustering(13) Variable = AMP PEAK 13(8Q24.21) MUTATION ANALYSIS
D13V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 13(8Q24.21) MUTATED   186  90
  AMP PEAK 13(8Q24.21) WILD-TYPE  79  33
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                           276                            112 
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                            90                             33 
$`AMP PEAK 13(8Q24.21) MUTATED`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
         136         2417          146         1415          345          396 
TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 
         862          758           50         1331          187           85 
TCGA-18-4721 TCGA-18-5595 TCGA-21-1070 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 
        2754          827         3636         3016         2134         1852 
TCGA-21-1077 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 
        1058          965         3724          284         3644          267 
TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-1011 
         962         1268         1032          329          979           53 
TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4594 TCGA-22-4596 
         429          822         1485          623         1470           17 
TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 
        1057          399         1946          358          965         1964 
TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5481 
        1933          445         1346           24         1651         1952 
TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-A5C4 TCGA-33-4532 
         357          573          916         1912           29         2524 
TCGA-33-4566 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-34-2604 
        5287         1941          428         1970         1948          958 
TCGA-34-2605 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5239 TCGA-34-5241 
         881          951         1528         2062          707          428 
TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-4132 TCGA-37-4133 
         552          166          120           13          227          238 
TCGA-37-4135 TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5022 
         207          103         1454         2253         1361         1996 
TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 
        1964           52          740          833         1107          474 
TCGA-39-5037 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 
        1086         1964         1223          684         1176          822 
TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 
        1007          349          849          376          757          310 
TCGA-43-7657 TCGA-43-7658 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 
         236         1970          358         1971          353          296 
TCGA-43-A56V TCGA-46-6025 TCGA-51-4080 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 
         366          324           12          541         1948          923 
TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 
        1958         1967          881            3          555           62 
TCGA-56-6546 TCGA-56-7222 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7731 
          26           13           44           40           26         1961 
TCGA-56-7822 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8626 TCGA-56-8628 
           1           41          178           55           17           16 
TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZK TCGA-56-A5DR 
          38            2           46           30            4            4 
TCGA-56-A5DS TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N 
           8         1058         2589         1723         1072          910 
TCGA-60-2695 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 
         642          311         1950         1943         1958          661 
TCGA-60-2708 TCGA-60-2710 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2719 
        1963         1963          274         1731         1531         1297 
TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 
          97          908         1092          717          816          358 
TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7023 TCGA-66-2734 TCGA-66-2737 
        1973         1957         1955         1952         1311           61 
TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 
         641           30           31           28           30           30 
TCGA-66-2758 TCGA-66-2763 TCGA-66-2766 TCGA-66-2767 TCGA-66-2769 TCGA-66-2770 
         639           30           31           61         1947          700 
TCGA-66-2773 TCGA-66-2777 TCGA-66-2780 TCGA-66-2782 TCGA-66-2785 TCGA-66-2788 
        1946           61         1956         1954           60          699 
TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 
        1955          699         1977          913         1952         1645 
TCGA-66-2800 TCGA-68-7756 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-77-6842 
        1492          202          244           96          121         1950 
TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7335 
        1942         1952         1959         1968           15         1954 
TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8009 
        1942         1952         1954          479         1960         1641 
TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 
        1953         1945         1941         1941         1947         1946 
TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 
        1951         1962          833         1943          293         1961 
TCGA-77-8153 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA 
        1684         1959         1955         1963         1290         1280 
TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7698 
         839          713          364          395           34           49 
TCGA-85-7699 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8052 TCGA-85-8276 
           1           35          911           60           16           13 
TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 
          11           13           54           60           55           67 
TCGA-85-8353 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 
          54           21          445          424            3          475 
TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L 
        1960           25         1967         1972           24           13 
TCGA-85-A5B5 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 
         111           89          358          331          269           82 
TCGA-92-7341 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 TCGA-94-A4VJ 
         106          160           70           87          356          430 
TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-98-8022 TCGA-98-8023 
        1344          189          211          273          224          308 
TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HG 
         222           35          449           36           83         1548 

$`AMP PEAK 13(8Q24.21) WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3415 TCGA-18-5592 TCGA-21-1071 TCGA-21-1078 
         370         2464         1810           92         1426          474 
TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-4593 
         608          223         1945          131         1952         1067 
TCGA-22-4595 TCGA-22-4599 TCGA-22-4607 TCGA-22-5480 TCGA-22-5491 TCGA-22-5492 
         734         1161          587         1952         1713          506 
TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4582 TCGA-33-6738 TCGA-34-2596 
        1940         2979         1311         1966          822           80 
TCGA-34-2600 TCGA-34-2608 TCGA-34-5234 TCGA-34-5240 TCGA-34-5927 TCGA-37-3792 
        1874         1000         1715          365          941           12 
TCGA-37-4129 TCGA-37-4130 TCGA-37-4141 TCGA-39-5021 TCGA-39-5027 TCGA-39-5030 
         200          247           12         1947         1849           59 
TCGA-39-5036 TCGA-39-5039 TCGA-43-6771 TCGA-43-7656 TCGA-43-8115 TCGA-43-A56U 
        1084          544         1936          212          407          432 
TCGA-46-6026 TCGA-51-4079 TCGA-51-4081 TCGA-56-7221 TCGA-56-7223 TCGA-56-7730 
         423           12          911           30           30            6 
TCGA-56-8624 TCGA-56-8625 TCGA-56-8629 TCGA-56-A4ZJ TCGA-58-8388 TCGA-58-8390 
          36           63           34           25          378          911 
TCGA-58-8391 TCGA-60-2696 TCGA-60-2709 TCGA-60-2711 TCGA-60-2715 TCGA-60-2716 
        2167          109         1505         1260         1075         1475 
TCGA-60-2721 TCGA-63-7022 TCGA-66-2727 TCGA-66-2754 TCGA-66-2759 TCGA-66-2765 
         983         1947         1967           61          762           61 
TCGA-66-2768 TCGA-66-2771 TCGA-66-2778 TCGA-66-2781 TCGA-66-2783 TCGA-66-2786 
          61          578          578          121          759          790 
TCGA-66-2787 TCGA-66-2795 TCGA-68-7755 TCGA-68-7757 TCGA-68-A59J TCGA-77-6843 
        1217          122           83          211          104         1941 
TCGA-77-7142 TCGA-77-8008 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 
        1286         1945         1092           10         1953         1942 
TCGA-77-A5GB TCGA-85-7696 TCGA-85-7697 TCGA-85-7710 TCGA-85-8048 TCGA-85-8049 
        1939           18           10         1965           26           60 
TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 
         960          428          513           61           61           22 
TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A50M TCGA-85-A50Z TCGA-85-A512 TCGA-90-6837 
          15         1972           19         1973         1987          758 
TCGA-90-7766 TCGA-90-7964 TCGA-90-A4ED TCGA-92-8063 TCGA-96-7544 TCGA-96-A4JL 
         289          428          244          122         1213          183 
TCGA-98-7454 TCGA-98-8021 TCGA-NC-A5HE TCGA-NC-A5HI 
         256          413         1722         1135 

  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                             1                              6 
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                          5287                           2979 
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                         691.5                          578.0 
[1] "1.0 - 5287.0 (691.5)" "6.0 - 2979.0 (578.0)"
[1] "hr=" "1.1"
D13V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 13(8Q24.21) MUTATED         1       43       96        0        36
  AMP PEAK 13(8Q24.21) WILD-TYPE       0       29       41        1        16
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 13(8Q24.21) MUTATED          57         45         16        6
  AMP PEAK 13(8Q24.21) WILD-TYPE        14         12          4        0
D13V3, multiclass
            clus
vv           AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE
  STAGE I                               1                              0
  STAGE IA                             43                             29
  STAGE IB                             96                             41
  STAGE II                              0                              1
  STAGE IIA                            36                             16
  STAGE IIB                            57                             14
  STAGE IIIA                           45                             12
  STAGE IIIB                           16                              4
  STAGE IV                              6                              0
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 13(8Q24.21) MUTATED    61 184  39  18
  AMP PEAK 13(8Q24.21) WILD-TYPE  37  70   9   2
D13V4, multiclass
    clus
vv   AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE
  T1                           61                             37
  T2                          184                             70
  T3                           39                              9
  T4                           18                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK 13(8Q24.21) MUTATED   177  92  25   3
  AMP PEAK 13(8Q24.21) WILD-TYPE  84  21  10   2
D13V5, multiclass
    clus
vv   AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE
  N0                          177                             84
  N1                           92                             21
  N2                           25                             10
  N3                            3                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A  MX
  AMP PEAK 13(8Q24.21) MUTATED   262   5   1  31
  AMP PEAK 13(8Q24.21) WILD-TYPE  96   0   0  19
D13V6, multiclass
     clus
vv    AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE
  M0                           262                             96
  M1                             5                              0
  M1A                            1                              0
  MX                            31                             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"
D13V7, binary
                                cls
clus                               0   1
  AMP PEAK 13(8Q24.21) MUTATED    73 229
  AMP PEAK 13(8Q24.21) WILD-TYPE  34  84
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(8Q24.21) MUTATED     73  229
  AMP PEAK 13(8Q24.21) WILD-TYPE   34   84
        clus
vv       AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE
  FEMALE                           73                             34
  MALE                            229                             84
[1] 2 2
[1] FALSE
D13V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK 13(8Q24.21) MUTATED                                      10
  AMP PEAK 13(8Q24.21) WILD-TYPE                                     2
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK 13(8Q24.21) MUTATED                                        3
  AMP PEAK 13(8Q24.21) WILD-TYPE                                      3
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 13(8Q24.21) MUTATED                                         1
  AMP PEAK 13(8Q24.21) WILD-TYPE                                       0
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 13(8Q24.21) MUTATED                                                           288
  AMP PEAK 13(8Q24.21) WILD-TYPE                                                         113
D13V9, multiclass
                                                             clus
vv                                                            AMP PEAK 13(8Q24.21) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 10
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          288
                                                             clus
vv                                                            AMP PEAK 13(8Q24.21) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            113
[1] 4 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(8Q24.21) MUTATED    10 292
  AMP PEAK 13(8Q24.21) WILD-TYPE   3 115
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(8Q24.21) MUTATED     10  292
  AMP PEAK 13(8Q24.21) WILD-TYPE    3  115
     clus
vv    AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE
  NO                            10                              3
  YES                          292                            115
[1] 2 2
[1] FALSE
D13V11, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 13(8Q24.21) MUTATED   249   8   1  11
  AMP PEAK 13(8Q24.21) WILD-TYPE  93   0   3   7
D13V12, multiclass
    clus
vv   AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE
  R0                          249                             93
  R1                            8                              0
  R2                            1                              3
  RX                           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                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 13(8Q24.21) MUTATED       6                        13   211
  AMP PEAK 13(8Q24.21) WILD-TYPE     3                         4    87
D13V13, multiclass
                           clus
vv                          AMP PEAK 13(8Q24.21) MUTATED
  ASIAN                                                6
  BLACK OR AFRICAN AMERICAN                           13
  WHITE                                              211
                           clus
vv                          AMP PEAK 13(8Q24.21) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              4
  WHITE                                                 87
[1] 3 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(8Q24.21) MUTATED     7 190
  AMP PEAK 13(8Q24.21) WILD-TYPE   1  77
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(8Q24.21) MUTATED      7  190
  AMP PEAK 13(8Q24.21) WILD-TYPE    1   77
                        clus
vv                       AMP PEAK 13(8Q24.21) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                          190
                        clus
vv                       AMP PEAK 13(8Q24.21) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                             77
[1] 2 2
[1] FALSE

Clustering(14) Variable = AMP PEAK 14(9P13.3) MUTATION ANALYSIS
D14V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 14(9P13.3) MUTATED    73  30
  AMP PEAK 14(9P13.3) WILD-TYPE 192  93
  AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE 
                          103                           285 
  AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE 
                           30                            93 
$`AMP PEAK 14(9P13.3) MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3417 TCGA-18-4083 TCGA-18-4721 TCGA-21-1070 
         370          136          758          187         2754         3636 
TCGA-21-1075 TCGA-22-0944 TCGA-22-4591 TCGA-22-4595 TCGA-22-4604 TCGA-22-4613 
        2134          223          623          734          399          358 
TCGA-22-5474 TCGA-22-5479 TCGA-22-5481 TCGA-22-5482 TCGA-22-5489 TCGA-33-4532 
         445         1651         1952          357         1912         2524 
TCGA-33-4533 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 
        1940         5287         1966         1941          428         1970 
TCGA-33-4589 TCGA-34-2600 TCGA-34-5239 TCGA-34-5240 TCGA-37-3792 TCGA-37-4133 
        1948         1874          707          365           12          238 
TCGA-39-5011 TCGA-39-5021 TCGA-39-5024 TCGA-39-5031 TCGA-43-6143 TCGA-43-7658 
        1454         1947         1964          833          376         1970 
TCGA-43-A475 TCGA-43-A56V TCGA-46-6025 TCGA-51-4079 TCGA-52-7622 TCGA-52-7809 
         296          366          324           12          541         1948 
TCGA-52-7810 TCGA-56-7221 TCGA-56-8504 TCGA-56-8626 TCGA-56-A49D TCGA-58-A46J 
         923           30          178           17           38         2589 
TCGA-58-A46L TCGA-58-A46M TCGA-60-2695 TCGA-60-2704 TCGA-60-2712 TCGA-60-2714 
        1723         1072          642         1943          274         1531 
TCGA-60-2719 TCGA-63-6202 TCGA-66-2744 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 
        1297         1973           30           30           30          639 
TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2794 TCGA-66-2800 TCGA-68-7755 
         762           30           61         1645         1492           83 
TCGA-68-8250 TCGA-68-A59J TCGA-77-6842 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 
         244          104         1950         1959         1968           15 
TCGA-77-8007 TCGA-77-8009 TCGA-77-8128 TCGA-77-8136 TCGA-77-8150 TCGA-77-8156 
        1960         1641         1953         1947         1961           10 
TCGA-77-A5G3 TCGA-77-A5GA TCGA-77-A5GF TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 
        1959         1280          839          395           34           18 
TCGA-85-7698 TCGA-85-7699 TCGA-85-7843 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 
          49            1           35          513           13           11 
TCGA-85-8352 TCGA-85-8353 TCGA-85-A4CL TCGA-85-A511 TCGA-90-7767 TCGA-92-8064 
          67           54           15         1972           89          160 
TCGA-96-7544 TCGA-96-A4JK TCGA-98-8022 TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 
        1213          273          224           35          449           36 
TCGA-NC-A5HI 
        1135 

$`AMP PEAK 14(9P13.3) WILD-TYPE`
TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
        2464         2417          146         1415          345          396 
TCGA-18-3415 TCGA-18-3416 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 TCGA-18-5592 
        1810          862           50         1331           85           92 
TCGA-18-5595 TCGA-21-1071 TCGA-21-1072 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 
         827         1426         3016         1852         1058          474 
TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 
         965         3724          284         3644          267          962 
TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 TCGA-22-1000 
        1268         1032          329          979          608         1945 
TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 
         131         1952           53          429          822         1485 
TCGA-22-4593 TCGA-22-4594 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4605 
        1067         1470           17         1161         1057         1946 
TCGA-22-4607 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5477 TCGA-22-5478 
         587          965         1964         1933         1346           24 
TCGA-22-5480 TCGA-22-5483 TCGA-22-5485 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 
        1952          573          916         1713          506           29 
TCGA-33-4538 TCGA-33-4547 TCGA-33-6738 TCGA-34-2596 TCGA-34-2604 TCGA-34-2605 
        2979         1311          822           80          958          881 
TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5241 
        1000          951         1528         2062         1715          428 
TCGA-34-5927 TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 
         941          552          166          120           13          200 
TCGA-37-4130 TCGA-37-4132 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5016 
         247          227          207           12          103         2253 
TCGA-39-5019 TCGA-39-5022 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 
        1361         1996         1849           52          740           59 
TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 
        1107          474         1084         1086          544         1964 
TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 
        1223          684         1176          822         1007          349 
TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 TCGA-43-7657 
         849          757          310         1936          212          236 
TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56U TCGA-46-6026 
         407          358         1971          353          432          423 
TCGA-51-4080 TCGA-51-4081 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 
          12          911         1958         1967          881            3 
TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 
         555           62           26           13           30           44 
TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 
          40           26            6         1961            1           41 
TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW 
          55           36           63           16           34            2 
TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS 
          46           30           25            4            4            8 
TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8393 TCGA-58-A46N TCGA-60-2696 
         378          911         2167         1058          910          109 
TCGA-60-2698 TCGA-60-2703 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 
         311         1950         1958          661         1963         1505 
TCGA-60-2710 TCGA-60-2711 TCGA-60-2713 TCGA-60-2715 TCGA-60-2716 TCGA-60-2720 
        1963         1260         1731         1075         1475           97 
TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 
         983          908         1092          717          816          358 
TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 
        1957         1955         1947         1952         1967         1311 
TCGA-66-2737 TCGA-66-2742 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2766 
          61          641           31           61           28           31 
TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 
          61           61         1947          700          578         1946 
TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 
          61          578         1956          121         1954          759 
TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 
          60          790         1217          699         1955          699 
TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2795 TCGA-68-7756 TCGA-68-7757 
        1977          913         1952          122          202          211 
TCGA-68-8251 TCGA-68-A59I TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7142 
          96          121         1941         1942         1952         1286 
TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8008 
        1954         1942         1952         1954          479         1945 
TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 
        1945         1941         1941         1946         1951         1962 
TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8153 TCGA-77-8154 TCGA-77-A5FZ 
         833         1943          293         1684         1092         1953 
TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GB TCGA-77-A5GH 
        1942         1955         1963         1290         1939          713 
TCGA-85-6560 TCGA-85-7697 TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 
         364           10         1965          911           60           26 
TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8287 TCGA-85-8288 
          60           16          960          428           13           54 
TCGA-85-8350 TCGA-85-8351 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 
          60           55           61           61           22           21 
TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4PA TCGA-85-A4QQ 
         445          424            3          475         1972         1960 
TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A512 TCGA-85-A513 
          25           19         1973         1967         1987           24 
TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7769 TCGA-90-7964 
          13          111          758          289          358          428 
TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 
         244          331          269           82          106          122 
TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7545 TCGA-96-8169 
          70           87          356          430         1344          189 
TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8023 TCGA-J1-A4AH 
         211          183          256          413          308          222 
TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HG 
          83         1722         1548 

  AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE 
                            1                             1 
  AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE 
                         5287                          3724 
  AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE 
                          541                           699 
[1] "1.0 - 5287.0 (541.0)" "1.0 - 3724.0 (699.0)"
[1] "hr=" "1.3"
D14V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 14(9P13.3) MUTATED         0       20       31        1         8
  AMP PEAK 14(9P13.3) WILD-TYPE       1       52      106        0        44
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 14(9P13.3) MUTATED          27         16          6        2
  AMP PEAK 14(9P13.3) WILD-TYPE        44         41         14        4
D14V3, multiclass
            clus
vv           AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE
  STAGE I                              0                             1
  STAGE IA                            20                            52
  STAGE IB                            31                           106
  STAGE II                             1                             0
  STAGE IIA                            8                            44
  STAGE IIB                           27                            44
  STAGE IIIA                          16                            41
  STAGE IIIB                           6                            14
  STAGE IV                             2                             4
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK 14(9P13.3) MUTATED    25  66  14   7
  AMP PEAK 14(9P13.3) WILD-TYPE  73 188  34  13
D14V4, multiclass
    clus
vv   AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE
  T1                          25                            73
  T2                          66                           188
  T3                          14                            34
  T4                           7                            13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  AMP PEAK 14(9P13.3) MUTATED    65  35  10   0
  AMP PEAK 14(9P13.3) WILD-TYPE 196  78  25   5
D14V5, multiclass
    clus
vv   AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE
  N0                          65                           196
  N1                          35                            78
  N2                          10                            25
  N3                           0                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A  MX
  AMP PEAK 14(9P13.3) MUTATED    97   2   0  10
  AMP PEAK 14(9P13.3) WILD-TYPE 261   3   1  40
D14V6, multiclass
     clus
vv    AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE
  M0                           97                           261
  M1                            2                             3
  M1A                           0                             1
  MX                           10                            40
[1] 4 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(9P13.3) MUTATED    28  84
  AMP PEAK 14(9P13.3) WILD-TYPE  79 229
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(9P13.3) MUTATED     28   84
  AMP PEAK 14(9P13.3) WILD-TYPE   79  229
        clus
vv       AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE
  FEMALE                          28                            79
  MALE                            84                           229
[1] 2 2
[1] FALSE
D14V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK 14(9P13.3) MUTATED                                       5
  AMP PEAK 14(9P13.3) WILD-TYPE                                     7
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK 14(9P13.3) MUTATED                                        0
  AMP PEAK 14(9P13.3) WILD-TYPE                                      6
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 14(9P13.3) MUTATED                                         1
  AMP PEAK 14(9P13.3) WILD-TYPE                                       0
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 14(9P13.3) MUTATED                                                           106
  AMP PEAK 14(9P13.3) WILD-TYPE                                                         295
D14V9, multiclass
                                                             clus
vv                                                            AMP PEAK 14(9P13.3) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         106
                                                             clus
vv                                                            AMP PEAK 14(9P13.3) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           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"
D14V10, binary
                               cls
clus                              0   1
  AMP PEAK 14(9P13.3) MUTATED     3 109
  AMP PEAK 14(9P13.3) WILD-TYPE  10 298
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(9P13.3) MUTATED      3  109
  AMP PEAK 14(9P13.3) WILD-TYPE   10  298
     clus
vv    AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE
  NO                            3                            10
  YES                         109                           298
[1] 2 2
[1] FALSE
D14V11, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 14(9P13.3) MUTATED    96   2   0   2
  AMP PEAK 14(9P13.3) WILD-TYPE 246   6   4  16
D14V12, multiclass
    clus
vv   AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE
  R0                          96                           246
  R1                           2                             6
  R2                           0                             4
  RX                           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                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 14(9P13.3) MUTATED       1                         5    82
  AMP PEAK 14(9P13.3) WILD-TYPE     8                        12   216
D14V13, multiclass
                           clus
vv                          AMP PEAK 14(9P13.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           5
  WHITE                                              82
                           clus
vv                          AMP PEAK 14(9P13.3) WILD-TYPE
  ASIAN                                                 8
  BLACK OR AFRICAN AMERICAN                            12
  WHITE                                               216
[1] 3 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(9P13.3) MUTATED     2  69
  AMP PEAK 14(9P13.3) WILD-TYPE   6 198
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(9P13.3) MUTATED      2   69
  AMP PEAK 14(9P13.3) WILD-TYPE    6  198
                        clus
vv                       AMP PEAK 14(9P13.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          69
                        clus
vv                       AMP PEAK 14(9P13.3) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           198
[1] 2 2
[1] FALSE

Clustering(15) Variable = AMP PEAK 15(11Q13.3) MUTATION ANALYSIS
D15V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 15(11Q13.3) MUTATED   105  42
  AMP PEAK 15(11Q13.3) WILD-TYPE 160  81
  AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE 
                           147                            241 
  AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE 
                            42                             81 
$`AMP PEAK 15(11Q13.3) MUTATED`
TCGA-18-3410 TCGA-18-3412 TCGA-18-3416 TCGA-21-1070 TCGA-21-1072 TCGA-21-1079 
         146          345          862         3636         3016          965 
TCGA-21-1083 TCGA-21-5782 TCGA-21-5786 TCGA-22-1002 TCGA-22-1011 TCGA-22-1012 
         267          962         1032          131           53          429 
TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-5471 
        1485          623         1067         1470          734          965 
TCGA-22-5491 TCGA-22-A5C4 TCGA-33-4582 TCGA-33-4583 TCGA-33-4589 TCGA-34-5231 
        1713           29         1966         1941         1948         1528 
TCGA-34-5232 TCGA-34-5239 TCGA-37-3789 TCGA-37-4132 TCGA-37-4135 TCGA-37-4141 
        2062          707           13          227          207           12 
TCGA-37-5819 TCGA-39-5011 TCGA-39-5029 TCGA-39-5031 TCGA-39-5034 TCGA-39-5036 
         103         1454          740          833         1107         1084 
TCGA-39-5037 TCGA-43-2578 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-6771 
        1086          684          349          849          376         1936 
TCGA-43-7657 TCGA-43-7658 TCGA-43-8116 TCGA-46-6025 TCGA-52-7809 TCGA-52-7810 
         236         1970          358          324         1948          923 
TCGA-52-7812 TCGA-56-1622 TCGA-56-5898 TCGA-56-6545 TCGA-56-7221 TCGA-56-7579 
        1967          881          555           62           30           44 
TCGA-56-7582 TCGA-56-7822 TCGA-56-8503 TCGA-56-8504 TCGA-56-A49D TCGA-56-A4BX 
          26            1           41          178           38           46 
TCGA-56-A5DR TCGA-58-8390 TCGA-58-8391 TCGA-60-2698 TCGA-60-2714 TCGA-60-2715 
           4          911         2167          311         1531         1075 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 TCGA-60-2725 TCGA-60-2726 TCGA-63-7020 
        1297           97          908          816          358         1957 
TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2759 TCGA-66-2763 
        1311           61          641           30          762           30 
TCGA-66-2765 TCGA-66-2767 TCGA-66-2768 TCGA-66-2777 TCGA-66-2781 TCGA-66-2786 
          61           61           61           61          121          790 
TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2793 TCGA-68-7755 TCGA-68-A59J 
        1955          699         1977         1952           83          104 
TCGA-77-6842 TCGA-77-6845 TCGA-77-7138 TCGA-77-7141 TCGA-77-7142 TCGA-77-7337 
        1950         1952         1959           15         1286         1942 
TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8009 TCGA-77-8133 TCGA-77-8139 
        1954          479         1960         1641         1941         1951 
TCGA-77-8144 TCGA-77-8148 TCGA-77-8153 TCGA-77-8154 TCGA-77-A5G1 TCGA-77-A5G3 
         833          293         1684         1092         1942         1959 
TCGA-77-A5G7 TCGA-77-A5GB TCGA-85-7697 TCGA-85-7699 TCGA-85-7843 TCGA-85-7950 
        1963         1939           10            1           35           60 
TCGA-85-8048 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 
          26          428          513           13           11           13 
TCGA-85-8352 TCGA-85-8354 TCGA-85-8582 TCGA-85-8664 TCGA-85-A4QQ TCGA-85-A4QR 
          67           61          424            3         1960           25 
TCGA-85-A50M TCGA-85-A510 TCGA-85-A511 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7766 
          19         1967         1972           13          111          289 
TCGA-90-7767 TCGA-90-7964 TCGA-90-A4EE TCGA-92-7341 TCGA-92-8064 TCGA-94-7033 
          89          428          331          106          160           87 
TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-A4JK 
         356          430         1213         1344          189          273 
TCGA-98-8022 TCGA-MF-A522 TCGA-NC-A5HG 
         224           83         1548 

$`AMP PEAK 15(11Q13.3) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3411 TCGA-18-3414 
         370          136         2464         2417         1415          396 
TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 
        1810          758           50         1331          187           85 
TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1071 TCGA-21-1075 TCGA-21-1076 
        2754           92          827         1426         2134         1852 
TCGA-21-1077 TCGA-21-1078 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-5784 
        1058          474         3724          284         3644         1268 
TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1005 
         329          979          608          223         1945         1952 
TCGA-22-1016 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 
         822           17         1161         1057          399         1946 
TCGA-22-4607 TCGA-22-4613 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 
         587          358         1964         1933          445         1346 
TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 
          24         1651         1952         1952          357          573 
TCGA-22-5485 TCGA-22-5489 TCGA-22-5492 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 
         916         1912          506         2524         1940         2979 
TCGA-33-4547 TCGA-33-4566 TCGA-33-4586 TCGA-33-4587 TCGA-33-6738 TCGA-34-2596 
        1311         5287          428         1970          822           80 
TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5234 
        1874          958          881         1000          951         1715 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 
         365          428          941          552          166          120 
TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4133 TCGA-39-5016 TCGA-39-5019 
          12          200          247          238         2253         1361 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 
        1947         1996         1964         1849           52           59 
TCGA-39-5035 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 
         474          544         1964         1223         1176          822 
TCGA-43-3920 TCGA-43-6647 TCGA-43-6770 TCGA-43-7656 TCGA-43-8115 TCGA-43-8118 
        1007          757          310          212          407         1971 
TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-6026 TCGA-51-4079 
         353          296          432          366          423           12 
TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7811 TCGA-56-5897 TCGA-56-6546 
          12          911          541         1958            3           26 
TCGA-56-7222 TCGA-56-7223 TCGA-56-7580 TCGA-56-7730 TCGA-56-7731 TCGA-56-8622 
          13           30           40            6         1961           55 
TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW 
          36           63           17           16           34            2 
TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DS TCGA-58-8388 TCGA-58-8393 
          30           25            4            8          378         1058 
TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2696 
        2589         1723         1072          910          642          109 
TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 
        1950         1943         1958          661         1963         1505 
TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2716 TCGA-60-2721 
        1963         1260          274         1731         1475          983 
TCGA-60-2723 TCGA-60-2724 TCGA-63-6202 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 
        1092          717         1973         1955         1947         1952 
TCGA-66-2727 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 
        1967           31           61           28           30           30 
TCGA-66-2758 TCGA-66-2766 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 
         639           31         1947          700          578         1946 
TCGA-66-2778 TCGA-66-2780 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2787 
         578         1956         1954          759           60         1217 
TCGA-66-2788 TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7756 
         699          913         1645          122         1492          202 
TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-77-6843 TCGA-77-6844 
         211          244           96          121         1941         1942 
TCGA-77-7139 TCGA-77-7335 TCGA-77-7338 TCGA-77-8008 TCGA-77-8128 TCGA-77-8130 
        1968         1954         1952         1945         1953         1945 
TCGA-77-8131 TCGA-77-8136 TCGA-77-8138 TCGA-77-8140 TCGA-77-8145 TCGA-77-8150 
        1941         1947         1946         1962         1943         1961 
TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G6 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GF 
          10         1953         1955         1290         1280          839 
TCGA-77-A5GH TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7698 
         713          364          395           34           18           49 
TCGA-85-7710 TCGA-85-7844 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8288 
        1965          911           60           16          960           54 
TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 
          60           55           54           61           22           21 
TCGA-85-8580 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A50Z TCGA-85-A512 
         445          475           15         1972         1973         1987 
TCGA-85-A513 TCGA-90-6837 TCGA-90-7769 TCGA-90-A4ED TCGA-90-A59Q TCGA-92-7340 
          24          758          358          244          269           82 
TCGA-92-8063 TCGA-92-8065 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 
         122           70          211          183          256          413 
TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-NC-A5HE 
         308          222           35          449           36         1722 
TCGA-NC-A5HI 
        1135 

  AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE 
                             1                              2 
  AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE 
                          3636                           5287 
  AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE 
                           513                            700 
[1] "1.0 - 3636.0 (513.0)" "2.0 - 5287.0 (700.0)"
[1] "hr=" "1"  
D15V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 15(11Q13.3) MUTATED         0       34       41        0        22
  AMP PEAK 15(11Q13.3) WILD-TYPE       1       38       96        1        30
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 15(11Q13.3) MUTATED          29         21          6        4
  AMP PEAK 15(11Q13.3) WILD-TYPE        42         36         14        2
D15V3, multiclass
            clus
vv           AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  STAGE I                               0                              1
  STAGE IA                             34                             38
  STAGE IB                             41                             96
  STAGE II                              0                              1
  STAGE IIA                            22                             30
  STAGE IIB                            29                             42
  STAGE IIIA                           21                             36
  STAGE IIIB                            6                             14
  STAGE IV                              4                              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 15(11Q13.3) MUTATED    43  90  20   5
  AMP PEAK 15(11Q13.3) WILD-TYPE  55 164  28  15
D15V4, multiclass
    clus
vv   AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  T1                           43                             55
  T2                           90                            164
  T3                           20                             28
  T4                            5                             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 15(11Q13.3) MUTATED    98  41  13   3
  AMP PEAK 15(11Q13.3) WILD-TYPE 163  72  22   2
D15V5, multiclass
    clus
vv   AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  N0                           98                            163
  N1                           41                             72
  N2                           13                             22
  N3                            3                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A  MX
  AMP PEAK 15(11Q13.3) MUTATED   133   3   1  18
  AMP PEAK 15(11Q13.3) WILD-TYPE 225   2   0  32
D15V6, multiclass
     clus
vv    AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  M0                           133                            225
  M1                             3                              2
  M1A                            1                              0
  MX                            18                             32
[1] 4 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(11Q13.3) MUTATED    35 123
  AMP PEAK 15(11Q13.3) WILD-TYPE  72 190
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(11Q13.3) MUTATED     35  123
  AMP PEAK 15(11Q13.3) WILD-TYPE   72  190
        clus
vv       AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  FEMALE                           35                             72
  MALE                            123                            190
[1] 2 2
[1] FALSE
D15V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK 15(11Q13.3) MUTATED                                       3
  AMP PEAK 15(11Q13.3) WILD-TYPE                                     9
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK 15(11Q13.3) MUTATED                                        1
  AMP PEAK 15(11Q13.3) WILD-TYPE                                      5
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 15(11Q13.3) MUTATED                                         0
  AMP PEAK 15(11Q13.3) WILD-TYPE                                       1
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 15(11Q13.3) MUTATED                                                           154
  AMP PEAK 15(11Q13.3) WILD-TYPE                                                         247
D15V9, multiclass
                                                             clus
vv                                                            AMP PEAK 15(11Q13.3) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          154
                                                             clus
vv                                                            AMP PEAK 15(11Q13.3) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            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"
D15V10, binary
                                cls
clus                               0   1
  AMP PEAK 15(11Q13.3) MUTATED     2 156
  AMP PEAK 15(11Q13.3) WILD-TYPE  11 251
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(11Q13.3) MUTATED      2  156
  AMP PEAK 15(11Q13.3) WILD-TYPE   11  251
     clus
vv    AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  NO                             2                             11
  YES                          156                            251
[1] 2 2
[1] FALSE
D15V11, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 15(11Q13.3) MUTATED   129   2   1   7
  AMP PEAK 15(11Q13.3) WILD-TYPE 213   6   3  11
D15V12, multiclass
    clus
vv   AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  R0                          129                            213
  R1                            2                              6
  R2                            1                              3
  RX                            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                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 15(11Q13.3) MUTATED       3                         4   115
  AMP PEAK 15(11Q13.3) WILD-TYPE     6                        13   183
D15V13, multiclass
                           clus
vv                          AMP PEAK 15(11Q13.3) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            4
  WHITE                                              115
                           clus
vv                          AMP PEAK 15(11Q13.3) WILD-TYPE
  ASIAN                                                  6
  BLACK OR AFRICAN AMERICAN                             13
  WHITE                                                183
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V14, binary
                                cls
clus                               0   1
  AMP PEAK 15(11Q13.3) MUTATED     3  97
  AMP PEAK 15(11Q13.3) WILD-TYPE   5 170
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(11Q13.3) MUTATED      3   97
  AMP PEAK 15(11Q13.3) WILD-TYPE    5  170
                        clus
vv                       AMP PEAK 15(11Q13.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           97
                        clus
vv                       AMP PEAK 15(11Q13.3) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            170
[1] 2 2
[1] FALSE

Clustering(16) Variable = AMP PEAK 16(12P13.33) MUTATION ANALYSIS
D16V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 16(12P13.33) MUTATED   132  65
  AMP PEAK 16(12P13.33) WILD-TYPE 133  58
  AMP PEAK 16(12P13.33) MUTATED AMP PEAK 16(12P13.33) WILD-TYPE 
                            197                             191 
  AMP PEAK 16(12P13.33) MUTATED AMP PEAK 16(12P13.33) WILD-TYPE 
                             65                              58 
$`AMP PEAK 16(12P13.33) MUTATED`
TCGA-18-3410 TCGA-18-3412 TCGA-18-3416 TCGA-18-3417 TCGA-18-3421 TCGA-18-4721 
         146          345          862          758         1331         2754 
TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1077 TCGA-21-1079 
          92         3636         1426         3016         1058          965 
TCGA-21-1083 TCGA-21-5782 TCGA-21-5786 TCGA-21-A5DI TCGA-22-1012 TCGA-22-1016 
         267          962         1032          979          429          822 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 
         623         1067          734         1161         1057          399 
TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 TCGA-22-5480 
         358         1933          445         1346         1651         1952 
TCGA-22-5482 TCGA-22-5489 TCGA-22-5491 TCGA-33-4532 TCGA-33-4538 TCGA-33-4566 
         357         1912         1713         2524         2979         5287 
TCGA-33-4582 TCGA-33-4586 TCGA-33-4587 TCGA-33-6738 TCGA-34-2596 TCGA-34-2605 
        1966          428         1970          822           80          881 
TCGA-34-2609 TCGA-34-5231 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5928 
         951         1528          707          365          428          552 
TCGA-37-3792 TCGA-37-5819 TCGA-39-5019 TCGA-39-5021 TCGA-39-5034 TCGA-39-5035 
          12          103         1361         1947         1107          474 
TCGA-39-5036 TCGA-39-5037 TCGA-39-5040 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 
        1084         1086         1964         1176          822         1007 
TCGA-43-5668 TCGA-43-5670 TCGA-43-6770 TCGA-43-6771 TCGA-43-7658 TCGA-43-8115 
         349          849          310         1936         1970          407 
TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56V TCGA-46-6025 
         358         1971          353          296          366          324 
TCGA-46-6026 TCGA-51-4079 TCGA-51-4081 TCGA-52-7809 TCGA-52-7811 TCGA-52-7812 
         423           12          911         1948         1958         1967 
TCGA-56-1622 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7222 TCGA-56-7223 
         881          555           62           26           13           30 
TCGA-56-7582 TCGA-56-7730 TCGA-56-7822 TCGA-56-8504 TCGA-56-8622 TCGA-56-8625 
          26            6            1          178           55           63 
TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A5DR TCGA-58-8391 
          34           38            2           46            4         2167 
TCGA-58-A46N TCGA-60-2695 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 
         910          642          311         1950         1943         1958 
TCGA-60-2708 TCGA-60-2711 TCGA-60-2712 TCGA-60-2719 TCGA-60-2723 TCGA-60-2725 
        1963         1260          274         1297         1092          816 
TCGA-60-2726 TCGA-63-7020 TCGA-63-7022 TCGA-66-2727 TCGA-66-2737 TCGA-66-2744 
         358         1957         1947         1967           61           30 
TCGA-66-2756 TCGA-66-2758 TCGA-66-2767 TCGA-66-2773 TCGA-66-2777 TCGA-66-2781 
          30          639           61         1946           61          121 
TCGA-66-2785 TCGA-66-2787 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-68-7755 
          60         1217          913         1952         1645           83 
TCGA-68-7756 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 
         202          244           96          121          104         1950 
TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 
        1968           15         1286         1954         1942         1952 
TCGA-77-7463 TCGA-77-7465 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8133 
        1954          479         1641         1953         1945         1941 
TCGA-77-8138 TCGA-77-8148 TCGA-77-8156 TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 
        1946          293           10         1942         1959         1955 
TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 
        1963         1290         1280          839          713          364 
TCGA-85-7696 TCGA-85-7697 TCGA-85-7699 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 
          18           10            1          911           60           26 
TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8277 TCGA-85-8287 TCGA-85-8350 
          60           16          960           11           13           60 
TCGA-85-8352 TCGA-85-8354 TCGA-85-8481 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4QR 
          67           61           21            3          475           25 
TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A53L TCGA-90-7767 TCGA-90-7769 
        1967         1972         1987           13           89          358 
TCGA-90-7964 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8064 
         428          331          269           82          106          160 
TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-7545 TCGA-96-A4JK TCGA-98-8023 
         356          430         1213         1344          273          308 
TCGA-J1-A4AH TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HG 
         222          449           36           83         1548 

$`AMP PEAK 16(12P13.33) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3411 TCGA-18-3414 
         370          136         2464         2417         1415          396 
TCGA-18-3415 TCGA-18-3419 TCGA-18-4083 TCGA-18-4086 TCGA-18-5595 TCGA-21-1075 
        1810           50          187           85          827         2134 
TCGA-21-1076 TCGA-21-1078 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-5784 
        1852          474         3724          284         3644         1268 
TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 
         329          608          223         1945          131         1952 
TCGA-22-1011 TCGA-22-1017 TCGA-22-4594 TCGA-22-4596 TCGA-22-4605 TCGA-22-4607 
          53         1485         1470           17         1946          587 
TCGA-22-5471 TCGA-22-5472 TCGA-22-5478 TCGA-22-5481 TCGA-22-5483 TCGA-22-5485 
         965         1964           24         1952          573          916 
TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4547 TCGA-33-4583 TCGA-33-4589 
         506           29         1940         1311         1941         1948 
TCGA-34-2600 TCGA-34-2604 TCGA-34-2608 TCGA-34-5232 TCGA-34-5234 TCGA-34-5927 
        1874          958         1000         2062         1715          941 
TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 
         166          120           13          200          247          227 
TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-39-5011 TCGA-39-5016 TCGA-39-5022 
         238          207           12         1454         2253         1996 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 
        1964         1849           52          740           59          833 
TCGA-39-5039 TCGA-43-2576 TCGA-43-2578 TCGA-43-6143 TCGA-43-6647 TCGA-43-7656 
         544         1223          684          376          757          212 
TCGA-43-7657 TCGA-43-A56U TCGA-51-4080 TCGA-52-7622 TCGA-52-7810 TCGA-56-5897 
         236          432           12          541          923            3 
TCGA-56-7221 TCGA-56-7579 TCGA-56-7580 TCGA-56-7731 TCGA-56-8503 TCGA-56-8624 
          30           44           40         1961           41           36 
TCGA-56-8626 TCGA-56-8628 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DS 
          17           16           30           25            4            8 
TCGA-58-8388 TCGA-58-8390 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M 
         378          911         1058         2589         1723         1072 
TCGA-60-2696 TCGA-60-2707 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 
         109          661         1505         1963         1731         1531 
TCGA-60-2715 TCGA-60-2716 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2724 
        1075         1475           97          983          908          717 
TCGA-63-6202 TCGA-63-7021 TCGA-63-7023 TCGA-66-2734 TCGA-66-2742 TCGA-66-2753 
        1973         1955         1952         1311          641           31 
TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 
          61           28           30          762           30           61 
TCGA-66-2766 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2778 
          31           61         1947          700          578          578 
TCGA-66-2780 TCGA-66-2782 TCGA-66-2783 TCGA-66-2786 TCGA-66-2788 TCGA-66-2789 
        1956         1954          759          790          699         1955 
TCGA-66-2790 TCGA-66-2791 TCGA-66-2795 TCGA-66-2800 TCGA-68-7757 TCGA-77-6843 
         699         1977          122         1492          211         1941 
TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-8007 TCGA-77-8008 TCGA-77-8131 
        1942         1952         1959         1960         1945         1941 
TCGA-77-8136 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 TCGA-77-8150 
        1947         1951         1962          833         1943         1961 
TCGA-77-8153 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5GB TCGA-85-6561 TCGA-85-6798 
        1684         1092         1953         1939          395           34 
TCGA-85-7698 TCGA-85-7710 TCGA-85-7843 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 
          49         1965           35          428          513           13 
TCGA-85-8288 TCGA-85-8351 TCGA-85-8353 TCGA-85-8355 TCGA-85-8479 TCGA-85-8580 
          54           55           54           61           22          445 
TCGA-85-8582 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A50Z 
         424           15         1972         1960           19         1973 
TCGA-85-A513 TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-A4ED TCGA-92-8063 
          24          111          758          289          244          122 
TCGA-92-8065 TCGA-94-7033 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 
          70           87          189          211          183          256 
TCGA-98-8021 TCGA-98-8022 TCGA-L3-A4E7 TCGA-NC-A5HE TCGA-NC-A5HI 
         413          224           35         1722         1135 

  AMP PEAK 16(12P13.33) MUTATED AMP PEAK 16(12P13.33) WILD-TYPE 
                              1                               3 
  AMP PEAK 16(12P13.33) MUTATED AMP PEAK 16(12P13.33) WILD-TYPE 
                           5287                            3724 
  AMP PEAK 16(12P13.33) MUTATED AMP PEAK 16(12P13.33) WILD-TYPE 
                            639                             661 
[1] "1.0 - 5287.0 (639.0)" "3.0 - 3724.0 (661.0)"
[1] "hr=" "1.1"
D16V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 16(12P13.33) MUTATED         1       31       69        1        29
  AMP PEAK 16(12P13.33) WILD-TYPE       0       41       68        0        23
                                 vv
clus                              STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 16(12P13.33) MUTATED          41         34          7        2
  AMP PEAK 16(12P13.33) WILD-TYPE        30         23         13        4
D16V3, multiclass
            clus
vv           AMP PEAK 16(12P13.33) MUTATED AMP PEAK 16(12P13.33) WILD-TYPE
  STAGE I                                1                               0
  STAGE IA                              31                              41
  STAGE IB                              69                              68
  STAGE II                               1                               0
  STAGE IIA                             29                              23
  STAGE IIB                             41                              30
  STAGE IIIA                            34                              23
  STAGE IIIB                             7                              13
  STAGE IV                               2                               4
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  AMP PEAK 16(12P13.33) MUTATED    41 138  26  11
  AMP PEAK 16(12P13.33) WILD-TYPE  57 116  22   9
D16V4, multiclass
    clus
vv   AMP PEAK 16(12P13.33) MUTATED AMP PEAK 16(12P13.33) WILD-TYPE
  T1                            41                              57
  T2                           138                             116
  T3                            26                              22
  T4                            11                               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2  N3
  AMP PEAK 16(12P13.33) MUTATED   130  65  19   1
  AMP PEAK 16(12P13.33) WILD-TYPE 131  48  16   4
D16V5, multiclass
    clus
vv   AMP PEAK 16(12P13.33) MUTATED AMP PEAK 16(12P13.33) WILD-TYPE
  N0                           130                             131
  N1                            65                              48
  N2                            19                              16
  N3                             1                               4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               M0  M1 M1A  MX
  AMP PEAK 16(12P13.33) MUTATED   181   1   1  30
  AMP PEAK 16(12P13.33) WILD-TYPE 177   4   0  20
D16V6, multiclass
     clus
vv    AMP PEAK 16(12P13.33) MUTATED AMP PEAK 16(12P13.33) WILD-TYPE
  M0                            181                             177
  M1                              1                               4
  M1A                             1                               0
  MX                             30                              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V7, binary
                                 cls
clus                                0   1
  AMP PEAK 16(12P13.33) MUTATED    44 172
  AMP PEAK 16(12P13.33) WILD-TYPE  63 141
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 16(12P13.33) MUTATED     44  172
  AMP PEAK 16(12P13.33) WILD-TYPE   63  141
        clus
vv       AMP PEAK 16(12P13.33) MUTATED AMP PEAK 16(12P13.33) WILD-TYPE
  FEMALE                            44                              63
  MALE                             172                             141
[1] 2 2
[1] FALSE
D16V8, continuous
                                 vv
clus                              LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK 16(12P13.33) MUTATED                                       6
  AMP PEAK 16(12P13.33) WILD-TYPE                                     6
                                 vv
clus                              LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK 16(12P13.33) MUTATED                                        2
  AMP PEAK 16(12P13.33) WILD-TYPE                                      4
                                 vv
clus                              LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 16(12P13.33) MUTATED                                         1
  AMP PEAK 16(12P13.33) WILD-TYPE                                       0
                                 vv
clus                              LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 16(12P13.33) MUTATED                                                           207
  AMP PEAK 16(12P13.33) WILD-TYPE                                                         194
D16V9, multiclass
                                                             clus
vv                                                            AMP PEAK 16(12P13.33) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           207
                                                             clus
vv                                                            AMP PEAK 16(12P13.33) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                     6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                    4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             194
[1] 4 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(12P13.33) MUTATED     5 211
  AMP PEAK 16(12P13.33) WILD-TYPE   8 196
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 16(12P13.33) MUTATED      5  211
  AMP PEAK 16(12P13.33) WILD-TYPE    8  196
     clus
vv    AMP PEAK 16(12P13.33) MUTATED AMP PEAK 16(12P13.33) WILD-TYPE
  NO                              5                               8
  YES                           211                             196
[1] 2 2
[1] FALSE
D16V11, continuous
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 16(12P13.33) MUTATED   173   4   1   8
  AMP PEAK 16(12P13.33) WILD-TYPE 169   4   3  10
D16V12, multiclass
    clus
vv   AMP PEAK 16(12P13.33) MUTATED AMP PEAK 16(12P13.33) WILD-TYPE
  R0                           173                             169
  R1                             4                               4
  R2                             1                               3
  RX                             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                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 16(12P13.33) MUTATED       2                        10   165
  AMP PEAK 16(12P13.33) WILD-TYPE     7                         7   133
D16V13, multiclass
                           clus
vv                          AMP PEAK 16(12P13.33) MUTATED
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                            10
  WHITE                                               165
                           clus
vv                          AMP PEAK 16(12P13.33) WILD-TYPE
  ASIAN                                                   7
  BLACK OR AFRICAN AMERICAN                               7
  WHITE                                                 133
[1] 3 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(12P13.33) MUTATED     4 141
  AMP PEAK 16(12P13.33) WILD-TYPE   4 126
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 16(12P13.33) MUTATED      4  141
  AMP PEAK 16(12P13.33) WILD-TYPE    4  126
                        clus
vv                       AMP PEAK 16(12P13.33) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           141
                        clus
vv                       AMP PEAK 16(12P13.33) WILD-TYPE
  HISPANIC OR LATINO                                   4
  NOT HISPANIC OR LATINO                             126
[1] 2 2
[1] FALSE

Clustering(17) Variable = AMP PEAK 17(12Q15) MUTATION ANALYSIS
D17V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 17(12Q15) MUTATED    93  48
  AMP PEAK 17(12Q15) WILD-TYPE 172  75
  AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE 
                         141                          247 
  AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE 
                          48                           75 
$`AMP PEAK 17(12Q15) MUTATED`
TCGA-18-3410 TCGA-18-3412 TCGA-18-3417 TCGA-18-3421 TCGA-18-4721 TCGA-21-1070 
         146          345          758         1331         2754         3636 
TCGA-21-1071 TCGA-21-1072 TCGA-21-1077 TCGA-21-1082 TCGA-21-1083 TCGA-21-5786 
        1426         3016         1058         3644          267         1032 
TCGA-21-5787 TCGA-21-A5DI TCGA-22-1016 TCGA-22-1017 TCGA-22-4593 TCGA-22-4594 
         329          979          822         1485         1067         1470 
TCGA-22-4601 TCGA-22-4604 TCGA-22-5471 TCGA-22-5473 TCGA-22-5477 TCGA-22-5479 
        1057          399          965         1933         1346         1651 
TCGA-22-5480 TCGA-22-5491 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4538 TCGA-33-4582 
        1952         1713           29         2524         2979         1966 
TCGA-33-4583 TCGA-33-4586 TCGA-34-2596 TCGA-34-2605 TCGA-34-2609 TCGA-34-5231 
        1941          428           80          881          951         1528 
TCGA-34-5239 TCGA-34-5241 TCGA-37-3792 TCGA-37-4130 TCGA-37-4133 TCGA-37-5819 
         707          428           12          247          238          103 
TCGA-39-5011 TCGA-39-5019 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-43-3394 
        1454         1361         1107          474         1084          822 
TCGA-43-5668 TCGA-43-6770 TCGA-43-6771 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 
         349          310         1936          407          358         1971 
TCGA-43-A475 TCGA-46-6025 TCGA-51-4079 TCGA-52-7809 TCGA-52-7811 TCGA-52-7812 
         296          324           12         1948         1958         1967 
TCGA-56-1622 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7223 TCGA-56-7582 
         881          555           62           26           30           26 
TCGA-56-7730 TCGA-56-A49D TCGA-56-A4BX TCGA-56-A5DR TCGA-60-2695 TCGA-60-2698 
           6           38           46            4          642          311 
TCGA-60-2704 TCGA-60-2706 TCGA-60-2708 TCGA-60-2711 TCGA-60-2712 TCGA-60-2715 
        1943         1958         1963         1260          274         1075 
TCGA-60-2719 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-66-2744 
        1297         1092          717          816          358           30 
TCGA-66-2754 TCGA-66-2756 TCGA-66-2758 TCGA-66-2766 TCGA-66-2767 TCGA-66-2773 
          61           30          639           31           61         1946 
TCGA-66-2781 TCGA-66-2793 TCGA-66-2794 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 
         121         1952         1645         1492           83          202 
TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-77-6842 TCGA-77-7142 TCGA-77-7463 
         244           96          121         1950         1286         1954 
TCGA-77-7465 TCGA-77-8009 TCGA-77-8128 TCGA-77-8133 TCGA-77-8144 TCGA-77-8148 
         479         1641         1953         1941          833          293 
TCGA-77-8150 TCGA-77-8154 TCGA-77-A5G3 TCGA-77-A5G7 TCGA-77-A5GA TCGA-77-A5GF 
        1961         1092         1959         1963         1280          839 
TCGA-85-7950 TCGA-85-8048 TCGA-85-8052 TCGA-85-8070 TCGA-85-8276 TCGA-85-8277 
          60           26           16          960           13           11 
TCGA-85-8350 TCGA-85-8353 TCGA-85-8354 TCGA-85-8479 TCGA-85-8664 TCGA-85-A4QR 
          60           54           61           22            3           25 
TCGA-85-A510 TCGA-85-A513 TCGA-85-A5B5 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4EE 
        1967           24          111           89          358          331 
TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-94-7943 TCGA-98-8023 TCGA-J1-A4AH 
         269           82          106          356          308          222 
TCGA-L3-A524 TCGA-LA-A446 TCGA-NC-A5HG 
         449           36         1548 

$`AMP PEAK 17(12Q15) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3411 TCGA-18-3414 
         370          136         2464         2417         1415          396 
TCGA-18-3415 TCGA-18-3416 TCGA-18-3419 TCGA-18-4083 TCGA-18-4086 TCGA-18-5592 
        1810          862           50          187           85           92 
TCGA-18-5595 TCGA-21-1075 TCGA-21-1076 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 
         827         2134         1852          474          965         3724 
TCGA-21-1081 TCGA-21-5782 TCGA-21-5784 TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 
         284          962         1268          608          223         1945 
TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-4591 TCGA-22-4595 
         131         1952           53          429          623          734 
TCGA-22-4596 TCGA-22-4599 TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 TCGA-22-5472 
          17         1161         1946          587          358         1964 
TCGA-22-5474 TCGA-22-5478 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 
         445           24         1952          357          573          916 
TCGA-22-5489 TCGA-22-5492 TCGA-33-4533 TCGA-33-4547 TCGA-33-4566 TCGA-33-4587 
        1912          506         1940         1311         5287         1970 
TCGA-33-4589 TCGA-33-6738 TCGA-34-2600 TCGA-34-2604 TCGA-34-2608 TCGA-34-5232 
        1948          822         1874          958         1000         2062 
TCGA-34-5234 TCGA-34-5240 TCGA-34-5927 TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 
        1715          365          941          552          166          120 
TCGA-37-3789 TCGA-37-4129 TCGA-37-4132 TCGA-37-4135 TCGA-37-4141 TCGA-39-5016 
          13          200          227          207           12         2253 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 
        1947         1996         1964         1849           52          740 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 
          59          833         1086          544         1964         1223 
TCGA-43-2578 TCGA-43-2581 TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 
         684         1176         1007          849          376          757 
TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-A474 TCGA-43-A56U TCGA-43-A56V 
         212          236         1970          353          432          366 
TCGA-46-6026 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7810 TCGA-56-5897 
         423           12          911          541          923            3 
TCGA-56-7221 TCGA-56-7222 TCGA-56-7579 TCGA-56-7580 TCGA-56-7731 TCGA-56-7822 
          30           13           44           40         1961            1 
TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 
          41          178           55           36           63           17 
TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK 
          16           34            2           30           25            4 
TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J 
           8          378          911         2167         1058         2589 
TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2696 TCGA-60-2703 TCGA-60-2707 
        1723         1072          910          109         1950          661 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 TCGA-60-2720 
        1505         1963         1731         1531         1475           97 
TCGA-60-2721 TCGA-60-2722 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 
         983          908         1973         1957         1955         1947 
TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2753 
        1952         1967         1311           61          641           31 
TCGA-66-2755 TCGA-66-2757 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2768 
          28           30          762           30           61           61 
TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 
        1947          700          578           61          578         1956 
TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 
        1954          759           60          790         1217          699 
TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2795 TCGA-68-7757 
        1955          699         1977          913          122          211 
TCGA-68-A59J TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 
         104         1941         1942         1952         1959         1968 
TCGA-77-7141 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-8007 TCGA-77-8008 
          15         1954         1942         1952         1960         1945 
TCGA-77-8130 TCGA-77-8131 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 
        1945         1941         1947         1946         1951         1962 
TCGA-77-8145 TCGA-77-8153 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 
        1943         1684           10         1953         1942         1955 
TCGA-77-A5G8 TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 
        1290         1939          713          364          395           34 
TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 
          18           10           49            1         1965           35 
TCGA-85-7844 TCGA-85-8049 TCGA-85-8071 TCGA-85-8072 TCGA-85-8287 TCGA-85-8288 
         911           60          428          513           13           54 
TCGA-85-8351 TCGA-85-8352 TCGA-85-8355 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 
          55           67           61           21          445          424 
TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A50Z 
         475           15         1972         1960           19         1973 
TCGA-85-A511 TCGA-85-A512 TCGA-85-A53L TCGA-90-6837 TCGA-90-7766 TCGA-90-7964 
        1972         1987           13          758          289          428 
TCGA-90-A4ED TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-A4VJ 
         244          122          160           70           87          430 
TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL 
        1213         1344          189          211          273          183 
TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-L3-A4E7 TCGA-MF-A522 TCGA-NC-A5HE 
         256          413          224           35           83         1722 
TCGA-NC-A5HI 
        1135 

  AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE 
                           3                            1 
  AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE 
                        3644                         5287 
  AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE 
                         639                          661 
[1] "3.0 - 3644.0 (639.0)" "1.0 - 5287.0 (661.0)"
[1] "hr=" "1.3"
D17V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 17(12Q15) MUTATED         1       27       44        1        22
  AMP PEAK 17(12Q15) WILD-TYPE       0       45       93        0        30
                              vv
clus                           STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 17(12Q15) MUTATED          22         28          8        2
  AMP PEAK 17(12Q15) WILD-TYPE        49         29         12        4
D17V3, multiclass
            clus
vv           AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE
  STAGE I                             1                            0
  STAGE IA                           27                           45
  STAGE IB                           44                           93
  STAGE II                            1                            0
  STAGE IIA                          22                           30
  STAGE IIB                          22                           49
  STAGE IIIA                         28                           29
  STAGE IIIB                          8                           12
  STAGE IV                            2                            4
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            T1  T2  T3  T4
  AMP PEAK 17(12Q15) MUTATED    34  92  19  10
  AMP PEAK 17(12Q15) WILD-TYPE  64 162  29  10
D17V4, multiclass
    clus
vv   AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE
  T1                         34                           64
  T2                         92                          162
  T3                         19                           29
  T4                         10                           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 17(12Q15) MUTATED    92  44  16   1
  AMP PEAK 17(12Q15) WILD-TYPE 169  69  19   4
D17V5, multiclass
    clus
vv   AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE
  N0                         92                          169
  N1                         44                           69
  N2                         16                           19
  N3                          1                            4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            M0  M1 M1A  MX
  AMP PEAK 17(12Q15) MUTATED   133   1   1  19
  AMP PEAK 17(12Q15) WILD-TYPE 225   4   0  31
D17V6, multiclass
     clus
vv    AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE
  M0                         133                          225
  M1                           1                            4
  M1A                          1                            0
  MX                          19                           31
[1] 4 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(12Q15) MUTATED    31 124
  AMP PEAK 17(12Q15) WILD-TYPE  76 189
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 17(12Q15) MUTATED     31  124
  AMP PEAK 17(12Q15) WILD-TYPE   76  189
        clus
vv       AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE
  FEMALE                         31                           76
  MALE                          124                          189
[1] 2 2
[1] FALSE
D17V8, continuous
                              vv
clus                           LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK 17(12Q15) MUTATED                                       4
  AMP PEAK 17(12Q15) WILD-TYPE                                     8
                              vv
clus                           LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK 17(12Q15) MUTATED                                        3
  AMP PEAK 17(12Q15) WILD-TYPE                                      3
                              vv
clus                           LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 17(12Q15) MUTATED                                         0
  AMP PEAK 17(12Q15) WILD-TYPE                                       1
                              vv
clus                           LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 17(12Q15) MUTATED                                                           148
  AMP PEAK 17(12Q15) WILD-TYPE                                                         253
D17V9, multiclass
                                                             clus
vv                                                            AMP PEAK 17(12Q15) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                               3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                              0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                        148
                                                             clus
vv                                                            AMP PEAK 17(12Q15) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          253
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V10, binary
                              cls
clus                             0   1
  AMP PEAK 17(12Q15) MUTATED     3 152
  AMP PEAK 17(12Q15) WILD-TYPE  10 255
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 17(12Q15) MUTATED      3  152
  AMP PEAK 17(12Q15) WILD-TYPE   10  255
     clus
vv    AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE
  NO                           3                           10
  YES                        152                          255
[1] 2 2
[1] FALSE
D17V11, continuous
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 17(12Q15) MUTATED   126   2   1   7
  AMP PEAK 17(12Q15) WILD-TYPE 216   6   3  11
D17V12, multiclass
    clus
vv   AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE
  R0                        126                          216
  R1                          2                            6
  R2                          1                            3
  RX                          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                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 17(12Q15) MUTATED       2                        10   116
  AMP PEAK 17(12Q15) WILD-TYPE     7                         7   182
D17V13, multiclass
                           clus
vv                          AMP PEAK 17(12Q15) MUTATED
  ASIAN                                              2
  BLACK OR AFRICAN AMERICAN                         10
  WHITE                                            116
                           clus
vv                          AMP PEAK 17(12Q15) WILD-TYPE
  ASIAN                                                7
  BLACK OR AFRICAN AMERICAN                            7
  WHITE                                              182
[1] 3 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(12Q15) MUTATED     4 106
  AMP PEAK 17(12Q15) WILD-TYPE   4 161
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 17(12Q15) MUTATED      4  106
  AMP PEAK 17(12Q15) WILD-TYPE    4  161
                        clus
vv                       AMP PEAK 17(12Q15) MUTATED
  HISPANIC OR LATINO                              4
  NOT HISPANIC OR LATINO                        106
                        clus
vv                       AMP PEAK 17(12Q15) WILD-TYPE
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          161
[1] 2 2
[1] FALSE

Clustering(18) Variable = AMP PEAK 18(13Q34) MUTATION ANALYSIS
D18V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 18(13Q34) MUTATED    49  22
  AMP PEAK 18(13Q34) WILD-TYPE 216 101
  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE 
                          71                          317 
  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE 
                          22                          101 
$`AMP PEAK 18(13Q34) MUTATED`
TCGA-18-3407 TCGA-18-3411 TCGA-21-1070 TCGA-21-1079 TCGA-21-1081 TCGA-21-1082 
         136         1415         3636          965          284         3644 
TCGA-21-5782 TCGA-21-5786 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4599 
         962         1032         1067         1470          734         1161 
TCGA-22-5479 TCGA-33-4538 TCGA-33-4587 TCGA-37-4130 TCGA-37-5819 TCGA-39-5011 
        1651         2979         1970          247          103         1454 
TCGA-39-5021 TCGA-39-5024 TCGA-39-5034 TCGA-39-5035 TCGA-39-5037 TCGA-43-2576 
        1947         1964         1107          474         1086         1223 
TCGA-43-6143 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8118 TCGA-43-A56V 
         376          236         1970          407         1971          366 
TCGA-51-4081 TCGA-52-7809 TCGA-52-7810 TCGA-56-5897 TCGA-56-5898 TCGA-56-7223 
         911         1948          923            3          555           30 
TCGA-56-7822 TCGA-56-8626 TCGA-56-A4BX TCGA-56-A4ZK TCGA-58-A46N TCGA-60-2695 
           1           17           46            4          910          642 
TCGA-60-2698 TCGA-60-2704 TCGA-60-2706 TCGA-60-2708 TCGA-60-2714 TCGA-66-2737 
         311         1943         1958         1963         1531           61 
TCGA-66-2763 TCGA-66-2766 TCGA-66-2791 TCGA-77-6845 TCGA-77-7138 TCGA-77-7337 
          30           31         1977         1952         1959         1942 
TCGA-77-8133 TCGA-77-8156 TCGA-77-A5G1 TCGA-77-A5GH TCGA-85-6798 TCGA-85-7696 
        1941           10         1942          713           34           18 
TCGA-85-7843 TCGA-85-7950 TCGA-85-8072 TCGA-85-8277 TCGA-85-8353 TCGA-85-8479 
          35           60          513           11           54           22 
TCGA-90-A59Q TCGA-92-8065 TCGA-94-7943 TCGA-L3-A4E7 TCGA-MF-A522 
         269           70          356           35           83 

$`AMP PEAK 18(13Q34) WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3412 TCGA-18-3414 
         370         2464         2417          146          345          396 
TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 
        1810          862          758           50         1331          187 
TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1071 TCGA-21-1072 
          85         2754           92          827         1426         3016 
TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1080 TCGA-21-1083 
        2134         1852         1058          474         3724          267 
TCGA-21-5784 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 
        1268          329          979          608          223         1945 
TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 
         131         1952           53          429          822         1485 
TCGA-22-4591 TCGA-22-4596 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 
         623           17         1057          399         1946          587 
TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 
         358          965         1964         1933          445         1346 
TCGA-22-5478 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 
          24         1952         1952          357          573          916 
TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 
        1912         1713          506           29         2524         1940 
TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4589 
        1311         5287         1966         1941          428         1948 
TCGA-33-6738 TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 
         822           80         1874          958          881         1000 
TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 
         951         1528         2062         1715          707          365 
TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 
         428          941          552          166          120           13 
TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 
          12          200          227          238          207           12 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5022 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 
        2253         1361         1996         1849           52          740 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5036 TCGA-39-5039 TCGA-39-5040 TCGA-43-2578 
          59          833         1084          544         1964          684 
TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6647 
        1176          822         1007          349          849          757 
TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 TCGA-43-8116 TCGA-43-A474 TCGA-43-A475 
         310         1936          212          358          353          296 
TCGA-43-A56U TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-52-7622 
         432          324          423           12           12          541 
TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 
        1958         1967          881           62           26           30 
TCGA-56-7222 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 
          13           44           40           26            6         1961 
TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8628 
          41          178           55           36           63           16 
TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR 
          34           38            2           30           25            4 
TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J 
           8          378          911         2167         1058         2589 
TCGA-58-A46L TCGA-58-A46M TCGA-60-2696 TCGA-60-2703 TCGA-60-2707 TCGA-60-2709 
        1723         1072          109         1950          661         1505 
TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2715 TCGA-60-2716 
        1963         1260          274         1731         1075         1475 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 
        1297           97          983          908         1092          717 
TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 
         816          358         1973         1957         1955         1947 
TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 
        1952         1967         1311          641           30           31 
TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 
          61           28           30           30          639          762 
TCGA-66-2765 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 
          61           61           61         1947          700          578 
TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 
        1946           61          578         1956          121         1954 
TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 
         759           60          790         1217          699         1955 
TCGA-66-2790 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 
         699          913         1952         1645          122         1492 
TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I 
          83          202          211          244           96          121 
TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-7139 TCGA-77-7141 
         104         1950         1941         1942         1968           15 
TCGA-77-7142 TCGA-77-7335 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 
        1286         1954         1952         1954          479         1960 
TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8136 
        1945         1641         1953         1945         1941         1947 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 
        1946         1951         1962          833         1943          293 
TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G3 TCGA-77-A5G6 
        1961         1684         1092         1953         1959         1955 
TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-85-6560 
        1963         1290         1280         1939          839          364 
TCGA-85-6561 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7844 
         395           10           49            1         1965          911 
TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8276 
          26           60           16          960          428           13 
TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8354 
          13           54           60           55           67           61 
TCGA-85-8355 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 
          61           21          445          424            3          475 
TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z 
          15         1972         1960           25           19         1973 
TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 
        1967         1972         1987           24           13          111 
TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED 
         758          289           89          358          428          244 
TCGA-90-A4EE TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-94-7033 
         331           82          106          122          160           87 
TCGA-94-A4VJ TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK 
         430         1213         1344          189          211          273 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-J1-A4AH 
         183          256          413          224          308          222 
TCGA-L3-A524 TCGA-LA-A446 TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HI 
         449           36         1722         1548         1135 

  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE 
                           1                            1 
  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE 
                        3644                         5287 
  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE 
                         713                          639 
[1] "1.0 - 3644.0 (713.0)" "1.0 - 5287.0 (639.0)"
[1] "hr=" "1.1"
D18V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 18(13Q34) MUTATED         0       12       22        0         9
  AMP PEAK 18(13Q34) WILD-TYPE       1       60      115        1        43
                              vv
clus                           STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 18(13Q34) MUTATED          13         16          2        1
  AMP PEAK 18(13Q34) WILD-TYPE        58         41         18        5
D18V3, multiclass
            clus
vv           AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE
  STAGE I                             0                            1
  STAGE IA                           12                           60
  STAGE IB                           22                          115
  STAGE II                            0                            1
  STAGE IIA                           9                           43
  STAGE IIB                          13                           58
  STAGE IIIA                         16                           41
  STAGE IIIB                          2                           18
  STAGE IV                            1                            5
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            T1  T2  T3  T4
  AMP PEAK 18(13Q34) MUTATED    16  44  14   1
  AMP PEAK 18(13Q34) WILD-TYPE  82 210  34  19
D18V4, multiclass
    clus
vv   AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE
  T1                         16                           82
  T2                         44                          210
  T3                         14                           34
  T4                          1                           19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            N0  N1  N2  N3
  AMP PEAK 18(13Q34) MUTATED    44  19  10   1
  AMP PEAK 18(13Q34) WILD-TYPE 217  94  25   4
D18V5, multiclass
    clus
vv   AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE
  N0                         44                          217
  N1                         19                           94
  N2                         10                           25
  N3                          1                            4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            M0  M1 M1A  MX
  AMP PEAK 18(13Q34) MUTATED    62   0   1  11
  AMP PEAK 18(13Q34) WILD-TYPE 296   5   0  39
D18V6, multiclass
     clus
vv    AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE
  M0                          62                          296
  M1                           0                            5
  M1A                          1                            0
  MX                          11                           39
[1] 4 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(13Q34) MUTATED    24  51
  AMP PEAK 18(13Q34) WILD-TYPE  83 262
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(13Q34) MUTATED     24   51
  AMP PEAK 18(13Q34) WILD-TYPE   83  262
        clus
vv       AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE
  FEMALE                         24                           83
  MALE                           51                          262
[1] 2 2
[1] FALSE
D18V8, continuous
                              vv
clus                           LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK 18(13Q34) MUTATED                                       4
  AMP PEAK 18(13Q34) WILD-TYPE                                     8
                              vv
clus                           LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK 18(13Q34) MUTATED                                        2
  AMP PEAK 18(13Q34) WILD-TYPE                                      4
                              vv
clus                           LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 18(13Q34) MUTATED                                         1
  AMP PEAK 18(13Q34) WILD-TYPE                                       0
                              vv
clus                           LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 18(13Q34) MUTATED                                                            68
  AMP PEAK 18(13Q34) WILD-TYPE                                                         333
D18V9, multiclass
                                                             clus
vv                                                            AMP PEAK 18(13Q34) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                               2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                              1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         68
                                                             clus
vv                                                            AMP PEAK 18(13Q34) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          333
[1] 4 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(13Q34) MUTATED     2  73
  AMP PEAK 18(13Q34) WILD-TYPE  11 334
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(13Q34) MUTATED      2   73
  AMP PEAK 18(13Q34) WILD-TYPE   11  334
     clus
vv    AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE
  NO                           2                           11
  YES                         73                          334
[1] 2 2
[1] FALSE
D18V11, continuous
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 18(13Q34) MUTATED    59   2   0   6
  AMP PEAK 18(13Q34) WILD-TYPE 283   6   4  12
D18V12, multiclass
    clus
vv   AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE
  R0                         59                          283
  R1                          2                            6
  R2                          0                            4
  RX                          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                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 18(13Q34) MUTATED       2                         4    57
  AMP PEAK 18(13Q34) WILD-TYPE     7                        13   241
D18V13, multiclass
                           clus
vv                          AMP PEAK 18(13Q34) MUTATED
  ASIAN                                              2
  BLACK OR AFRICAN AMERICAN                          4
  WHITE                                             57
                           clus
vv                          AMP PEAK 18(13Q34) WILD-TYPE
  ASIAN                                                7
  BLACK OR AFRICAN AMERICAN                           13
  WHITE                                              241
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V14, binary
                              cls
clus                             0   1
  AMP PEAK 18(13Q34) MUTATED     1  54
  AMP PEAK 18(13Q34) WILD-TYPE   7 213
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(13Q34) MUTATED      1   54
  AMP PEAK 18(13Q34) WILD-TYPE    7  213
                        clus
vv                       AMP PEAK 18(13Q34) MUTATED
  HISPANIC OR LATINO                              1
  NOT HISPANIC OR LATINO                         54
                        clus
vv                       AMP PEAK 18(13Q34) WILD-TYPE
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                          213
[1] 2 2
[1] FALSE

Clustering(19) Variable = AMP PEAK 19(14Q13.3) MUTATION ANALYSIS
D19V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 19(14Q13.3) MUTATED    85  35
  AMP PEAK 19(14Q13.3) WILD-TYPE 180  88
  AMP PEAK 19(14Q13.3) MUTATED AMP PEAK 19(14Q13.3) WILD-TYPE 
                           120                            268 
  AMP PEAK 19(14Q13.3) MUTATED AMP PEAK 19(14Q13.3) WILD-TYPE 
                            35                             88 
$`AMP PEAK 19(14Q13.3) MUTATED`
TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 TCGA-18-3421 TCGA-18-5592 
        2464         1415          345         1810         1331           92 
TCGA-21-1076 TCGA-21-1079 TCGA-21-1082 TCGA-21-5782 TCGA-21-5786 TCGA-22-1011 
        1852          965         3644          962         1032           53 
TCGA-22-1017 TCGA-22-4591 TCGA-22-4594 TCGA-22-4595 TCGA-22-4604 TCGA-22-4613 
        1485          623         1470          734          399          358 
TCGA-22-5471 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4566 
         965           29         2524         1940         2979         5287 
TCGA-33-4582 TCGA-33-4586 TCGA-33-4589 TCGA-33-6738 TCGA-37-3783 TCGA-37-3792 
        1966          428         1948          822          120           12 
TCGA-37-5819 TCGA-39-5011 TCGA-39-5019 TCGA-39-5029 TCGA-39-5031 TCGA-39-5037 
         103         1454         1361          740          833         1086 
TCGA-39-5039 TCGA-43-2578 TCGA-43-6143 TCGA-43-6771 TCGA-43-8118 TCGA-43-A56V 
         544          684          376         1936         1971          366 
TCGA-46-6025 TCGA-51-4081 TCGA-52-7622 TCGA-52-7811 TCGA-56-1622 TCGA-56-5898 
         324          911          541         1958          881          555 
TCGA-56-6545 TCGA-56-6546 TCGA-56-7580 TCGA-56-7730 TCGA-56-8504 TCGA-56-8624 
          62           26           40            6          178           36 
TCGA-56-8629 TCGA-56-A49D TCGA-58-8393 TCGA-58-A46J TCGA-58-A46N TCGA-60-2698 
          34           38         1058         2589          910          311 
TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2714 TCGA-60-2719 TCGA-60-2722 
        1958          661         1963         1531         1297          908 
TCGA-60-2724 TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7022 TCGA-66-2744 
         717          358         1973         1957         1947           30 
TCGA-66-2756 TCGA-66-2763 TCGA-66-2765 TCGA-66-2771 TCGA-66-2782 TCGA-66-2788 
          30           30           61          578         1954          699 
TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 
        1977          913         1952          122         1492           83 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7141 TCGA-77-7142 TCGA-77-7337 TCGA-77-7463 
        1952         1959           15         1286         1942         1954 
TCGA-77-8007 TCGA-77-8130 TCGA-77-8136 TCGA-77-8139 TCGA-77-8148 TCGA-77-8150 
        1960         1945         1947         1951          293         1961 
TCGA-77-8153 TCGA-77-A5G3 TCGA-77-A5G8 TCGA-85-6560 TCGA-85-6561 TCGA-85-7698 
        1684         1959         1290          364          395           49 
TCGA-85-7843 TCGA-85-8276 TCGA-85-8353 TCGA-85-8355 TCGA-85-A4QQ TCGA-85-A50M 
          35           13           54           61         1960           19 
TCGA-85-A510 TCGA-85-A5B5 TCGA-90-7766 TCGA-92-7340 TCGA-92-7341 TCGA-92-8064 
        1967          111          289           82          106          160 
TCGA-94-A4VJ TCGA-96-A4JK TCGA-L3-A4E7 TCGA-MF-A522 TCGA-NC-A5HG TCGA-NC-A5HI 
         430          273           35           83         1548         1135 

$`AMP PEAK 19(14Q13.3) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3414 TCGA-18-3416 
         370          136         2417          146          396          862 
TCGA-18-3417 TCGA-18-3419 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5595 
         758           50          187           85         2754          827 
TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1077 TCGA-21-1078 
        3636         1426         3016         2134         1058          474 
TCGA-21-1080 TCGA-21-1081 TCGA-21-1083 TCGA-21-5784 TCGA-21-5787 TCGA-21-A5DI 
        3724          284          267         1268          329          979 
TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1012 
         608          223         1945          131         1952          429 
TCGA-22-1016 TCGA-22-4593 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4605 
         822         1067           17         1161         1057         1946 
TCGA-22-4607 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 
         587         1964         1933          445         1346           24 
TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 
        1651         1952         1952          357          573          916 
TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4547 TCGA-33-4583 TCGA-33-4587 
        1912         1713          506         1311         1941         1970 
TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 
          80         1874          958          881         1000          951 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 
        1528         2062         1715          707          365          428 
TCGA-34-5927 TCGA-34-5928 TCGA-34-8454 TCGA-37-3789 TCGA-37-4129 TCGA-37-4130 
         941          552          166           13          200          247 
TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-39-5016 TCGA-39-5021 
         227          238          207           12         2253         1947 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 TCGA-39-5034 
        1996         1964         1849           52           59         1107 
TCGA-39-5035 TCGA-39-5036 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 
         474         1084         1964         1223         1176          822 
TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 TCGA-43-7656 
        1007          349          849          757          310          212 
TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-A474 TCGA-43-A475 
         236         1970          407          358          353          296 
TCGA-43-A56U TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-52-7809 TCGA-52-7810 
         432          423           12           12         1948          923 
TCGA-52-7812 TCGA-56-5897 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 
        1967            3           30           13           30           44 
TCGA-56-7582 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 TCGA-56-8622 TCGA-56-8625 
          26         1961            1           41           55           63 
TCGA-56-8626 TCGA-56-8628 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ 
          17           16            2           46           30           25 
TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 
           4            4            8          378          911         2167 
TCGA-58-A46L TCGA-58-A46M TCGA-60-2695 TCGA-60-2696 TCGA-60-2703 TCGA-60-2704 
        1723         1072          642          109         1950         1943 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2715 
        1505         1963         1260          274         1731         1075 
TCGA-60-2716 TCGA-60-2720 TCGA-60-2721 TCGA-60-2723 TCGA-60-2725 TCGA-63-7021 
        1475           97          983         1092          816         1955 
TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2753 
        1952         1967         1311           61          641           31 
TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2766 
          61           28           30          639          762           31 
TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2773 TCGA-66-2777 
          61           61         1947          700         1946           61 
TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 
         578         1956          121          759           60          790 
TCGA-66-2787 TCGA-66-2789 TCGA-66-2790 TCGA-66-2794 TCGA-68-7756 TCGA-68-7757 
        1217         1955          699         1645          202          211 
TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 
         244           96          121          104         1950         1941 
TCGA-77-6844 TCGA-77-7139 TCGA-77-7335 TCGA-77-7338 TCGA-77-7465 TCGA-77-8008 
        1942         1968         1954         1952          479         1945 
TCGA-77-8009 TCGA-77-8128 TCGA-77-8131 TCGA-77-8133 TCGA-77-8138 TCGA-77-8140 
        1641         1953         1941         1941         1946         1962 
TCGA-77-8144 TCGA-77-8145 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 
         833         1943         1092           10         1953         1942 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH 
        1955         1963         1280         1939          839          713 
TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7699 TCGA-85-7710 TCGA-85-7844 
          34           18           10            1         1965          911 
TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 
          60           26           60           16          960          428 
TCGA-85-8072 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 
         513           11           13           54           60           55 
TCGA-85-8352 TCGA-85-8354 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 
          67           61           22           21          445          424 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QR TCGA-85-A50Z 
           3          475           15         1972           25         1973 
TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 TCGA-90-7767 
        1972         1987           24           13          758           89 
TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-8063 
         358          428          244          331          269          122 
TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 
          70           87          356         1213         1344          189 
TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 
         211          183          256          413          224          308 
TCGA-J1-A4AH TCGA-L3-A524 TCGA-LA-A446 TCGA-NC-A5HE 
         222          449           36         1722 

  AMP PEAK 19(14Q13.3) MUTATED AMP PEAK 19(14Q13.3) WILD-TYPE 
                             6                              1 
  AMP PEAK 19(14Q13.3) MUTATED AMP PEAK 19(14Q13.3) WILD-TYPE 
                          5287                           3724 
  AMP PEAK 19(14Q13.3) MUTATED AMP PEAK 19(14Q13.3) WILD-TYPE 
                         827.5                          532.5 
[1] "6.0 - 5287.0 (827.5)" "1.0 - 3724.0 (532.5)"
[1] "hr=" "1.4"
D19V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 19(14Q13.3) MUTATED         0       16       42        0        18
  AMP PEAK 19(14Q13.3) WILD-TYPE       1       56       95        1        34
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 19(14Q13.3) MUTATED          26         22          5        1
  AMP PEAK 19(14Q13.3) WILD-TYPE        45         35         15        5
D19V3, multiclass
            clus
vv           AMP PEAK 19(14Q13.3) MUTATED AMP PEAK 19(14Q13.3) WILD-TYPE
  STAGE I                               0                              1
  STAGE IA                             16                             56
  STAGE IB                             42                             95
  STAGE II                              0                              1
  STAGE IIA                            18                             34
  STAGE IIB                            26                             45
  STAGE IIIA                           22                             35
  STAGE IIIB                            5                             15
  STAGE IV                              1                              5
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 19(14Q13.3) MUTATED    24  81  19   6
  AMP PEAK 19(14Q13.3) WILD-TYPE  74 173  29  14
D19V4, multiclass
    clus
vv   AMP PEAK 19(14Q13.3) MUTATED AMP PEAK 19(14Q13.3) WILD-TYPE
  T1                           24                             74
  T2                           81                            173
  T3                           19                             29
  T4                            6                             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 19(14Q13.3) MUTATED    79  33  16   1
  AMP PEAK 19(14Q13.3) WILD-TYPE 182  80  19   4
D19V5, multiclass
    clus
vv   AMP PEAK 19(14Q13.3) MUTATED AMP PEAK 19(14Q13.3) WILD-TYPE
  N0                           79                            182
  N1                           33                             80
  N2                           16                             19
  N3                            1                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A  MX
  AMP PEAK 19(14Q13.3) MUTATED   116   0   1  12
  AMP PEAK 19(14Q13.3) WILD-TYPE 242   5   0  38
D19V6, multiclass
     clus
vv    AMP PEAK 19(14Q13.3) MUTATED AMP PEAK 19(14Q13.3) WILD-TYPE
  M0                           116                            242
  M1                             0                              5
  M1A                            1                              0
  MX                            12                             38
[1] 4 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(14Q13.3) MUTATED    31  99
  AMP PEAK 19(14Q13.3) WILD-TYPE  76 214
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(14Q13.3) MUTATED     31   99
  AMP PEAK 19(14Q13.3) WILD-TYPE   76  214
        clus
vv       AMP PEAK 19(14Q13.3) MUTATED AMP PEAK 19(14Q13.3) WILD-TYPE
  FEMALE                           31                             76
  MALE                             99                            214
[1] 2 2
[1] FALSE
D19V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK 19(14Q13.3) MUTATED                                       3
  AMP PEAK 19(14Q13.3) WILD-TYPE                                     9
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK 19(14Q13.3) MUTATED                                        1
  AMP PEAK 19(14Q13.3) WILD-TYPE                                      5
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 19(14Q13.3) MUTATED                                         0
  AMP PEAK 19(14Q13.3) WILD-TYPE                                       1
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 19(14Q13.3) MUTATED                                                           126
  AMP PEAK 19(14Q13.3) WILD-TYPE                                                         275
D19V9, multiclass
                                                             clus
vv                                                            AMP PEAK 19(14Q13.3) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          126
                                                             clus
vv                                                            AMP PEAK 19(14Q13.3) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            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"
D19V10, binary
                                cls
clus                               0   1
  AMP PEAK 19(14Q13.3) MUTATED     3 127
  AMP PEAK 19(14Q13.3) WILD-TYPE  10 280
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(14Q13.3) MUTATED      3  127
  AMP PEAK 19(14Q13.3) WILD-TYPE   10  280
     clus
vv    AMP PEAK 19(14Q13.3) MUTATED AMP PEAK 19(14Q13.3) WILD-TYPE
  NO                             3                             10
  YES                          127                            280
[1] 2 2
[1] FALSE
D19V11, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 19(14Q13.3) MUTATED   106   3   1   8
  AMP PEAK 19(14Q13.3) WILD-TYPE 236   5   3  10
D19V12, multiclass
    clus
vv   AMP PEAK 19(14Q13.3) MUTATED AMP PEAK 19(14Q13.3) WILD-TYPE
  R0                          106                            236
  R1                            3                              5
  R2                            1                              3
  RX                            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                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 19(14Q13.3) MUTATED       3                         3    91
  AMP PEAK 19(14Q13.3) WILD-TYPE     6                        14   207
D19V13, multiclass
                           clus
vv                          AMP PEAK 19(14Q13.3) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               91
                           clus
vv                          AMP PEAK 19(14Q13.3) WILD-TYPE
  ASIAN                                                  6
  BLACK OR AFRICAN AMERICAN                             14
  WHITE                                                207
[1] 3 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(14Q13.3) MUTATED     6  73
  AMP PEAK 19(14Q13.3) WILD-TYPE   2 194
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(14Q13.3) MUTATED      6   73
  AMP PEAK 19(14Q13.3) WILD-TYPE    2  194
                        clus
vv                       AMP PEAK 19(14Q13.3) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                           73
                        clus
vv                       AMP PEAK 19(14Q13.3) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            194
[1] 2 2
[1] FALSE

Clustering(20) Variable = AMP PEAK 20(14Q32.33) MUTATION ANALYSIS
D20V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 20(14Q32.33) MUTATED    87  33
  AMP PEAK 20(14Q32.33) WILD-TYPE 178  90
  AMP PEAK 20(14Q32.33) MUTATED AMP PEAK 20(14Q32.33) WILD-TYPE 
                            120                             268 
  AMP PEAK 20(14Q32.33) MUTATED AMP PEAK 20(14Q32.33) WILD-TYPE 
                             33                              90 
$`AMP PEAK 20(14Q32.33) MUTATED`
TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 TCGA-18-3419 TCGA-18-3421 
        2464         1415          345         1810           50         1331 
TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1076 
         187           85         2754           92         3636         1852 
TCGA-21-1079 TCGA-21-1081 TCGA-21-1082 TCGA-21-5786 TCGA-22-1016 TCGA-22-4591 
         965          284         3644         1032          822          623 
TCGA-22-4595 TCGA-22-5471 TCGA-22-5473 TCGA-22-5482 TCGA-22-5483 TCGA-22-A5C4 
         734          965         1933          357          573           29 
TCGA-33-4532 TCGA-33-4533 TCGA-33-4566 TCGA-33-4582 TCGA-33-4589 TCGA-34-5240 
        2524         1940         5287         1966         1948          365 
TCGA-34-5241 TCGA-37-3789 TCGA-37-3792 TCGA-37-4133 TCGA-37-5819 TCGA-39-5011 
         428           13           12          238          103         1454 
TCGA-39-5029 TCGA-39-5031 TCGA-39-5036 TCGA-39-5037 TCGA-43-2578 TCGA-43-6143 
         740          833         1084         1086          684          376 
TCGA-43-6771 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56V TCGA-46-6025 
        1936         1971          353          296          366          324 
TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7811 TCGA-56-5898 TCGA-56-6546 
         911          541         1948         1958          555           26 
TCGA-56-7580 TCGA-56-7730 TCGA-56-8504 TCGA-56-8624 TCGA-56-A49D TCGA-56-A4ZK 
          40            6          178           36           38            4 
TCGA-58-8391 TCGA-58-A46N TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2722 
        2167          910         1958          661         1963          908 
TCGA-60-2724 TCGA-63-7020 TCGA-63-7022 TCGA-66-2744 TCGA-66-2756 TCGA-66-2763 
         717         1957         1947           30           30           30 
TCGA-66-2771 TCGA-66-2781 TCGA-66-2782 TCGA-66-2788 TCGA-66-2789 TCGA-66-2792 
         578          121         1954          699         1955          913 
TCGA-66-2793 TCGA-66-2800 TCGA-68-7755 TCGA-68-7757 TCGA-68-A59I TCGA-68-A59J 
        1952         1492           83          211          121          104 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7337 TCGA-77-7463 TCGA-77-8007 TCGA-77-8130 
        1952         1959         1942         1954         1960         1945 
TCGA-77-8136 TCGA-77-8139 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 
        1947         1951          293         1961         1684         1092 
TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G8 TCGA-77-A5GF TCGA-85-6561 TCGA-85-6798 
        1959         1955         1290          839          395           34 
TCGA-85-7698 TCGA-85-7843 TCGA-85-8071 TCGA-85-8353 TCGA-85-8355 TCGA-85-8582 
          49           35          428           54           61          424 
TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A5B5 TCGA-90-7769 TCGA-92-7340 TCGA-92-7341 
        1960           19          111          358           82          106 
TCGA-94-7033 TCGA-96-A4JK TCGA-L3-A4E7 TCGA-L3-A524 TCGA-NC-A5HG TCGA-NC-A5HI 
          87          273           35          449         1548         1135 

$`AMP PEAK 20(14Q32.33) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3414 TCGA-18-3416 
         370          136         2417          146          396          862 
TCGA-18-3417 TCGA-18-5595 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1077 
         758          827         1426         3016         2134         1058 
TCGA-21-1078 TCGA-21-1080 TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 TCGA-21-5787 
         474         3724          267          962         1268          329 
TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 
         979          608          223         1945          131         1952 
TCGA-22-1011 TCGA-22-1012 TCGA-22-1017 TCGA-22-4593 TCGA-22-4594 TCGA-22-4596 
          53          429         1485         1067         1470           17 
TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 
        1161         1057          399         1946          587          358 
TCGA-22-5472 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 
        1964          445         1346           24         1651         1952 
TCGA-22-5481 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4538 
        1952          916         1912         1713          506         2979 
TCGA-33-4547 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-6738 TCGA-34-2596 
        1311         1941          428         1970          822           80 
TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 
        1874          958          881         1000          951         1528 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5927 TCGA-34-5928 TCGA-34-8454 
        2062         1715          707          941          552          166 
TCGA-37-3783 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4135 TCGA-37-4141 
         120          200          247          227          207           12 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 
        2253         1361         1947         1996         1964         1849 
TCGA-39-5028 TCGA-39-5030 TCGA-39-5034 TCGA-39-5035 TCGA-39-5039 TCGA-39-5040 
          52           59         1107          474          544         1964 
TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 
        1223         1176          822         1007          349          849 
TCGA-43-6647 TCGA-43-6770 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 
         757          310          212          236         1970          407 
TCGA-43-8116 TCGA-43-A56U TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-52-7810 
         358          432          423           12           12          923 
TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-6545 TCGA-56-7221 TCGA-56-7222 
        1967          881            3           62           30           13 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7582 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 
          30           44           26         1961            1           41 
TCGA-56-8622 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW 
          55           63           17           16           34            2 
TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8388 
          46           30           25            4            8          378 
TCGA-58-8390 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-60-2695 
         911         1058         2589         1723         1072          642 
TCGA-60-2696 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2709 TCGA-60-2710 
         109          311         1950         1943         1505         1963 
TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 
        1260          274         1731         1531         1075         1475 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2723 TCGA-60-2725 TCGA-60-2726 
        1297           97          983         1092          816          358 
TCGA-63-6202 TCGA-63-7021 TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 
        1973         1955         1952         1967         1311           61 
TCGA-66-2742 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 TCGA-66-2758 
         641           31           61           28           30          639 
TCGA-66-2759 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 
         762           61           31           61           61         1947 
TCGA-66-2770 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2783 
         700         1946           61          578         1956          759 
TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2790 TCGA-66-2791 TCGA-66-2794 
          60          790         1217          699         1977         1645 
TCGA-66-2795 TCGA-68-7756 TCGA-68-8250 TCGA-68-8251 TCGA-77-6842 TCGA-77-6843 
         122          202          244           96         1950         1941 
TCGA-77-6844 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7338 
        1942         1968           15         1286         1954         1952 
TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8131 TCGA-77-8133 
         479         1945         1641         1953         1941         1941 
TCGA-77-8138 TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 TCGA-77-8156 TCGA-77-A5FZ 
        1946         1962          833         1943           10         1953 
TCGA-77-A5G1 TCGA-77-A5G7 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6560 
        1942         1963         1280         1939          713          364 
TCGA-85-7696 TCGA-85-7697 TCGA-85-7699 TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 
          18           10            1         1965          911           60 
TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8072 TCGA-85-8276 
          26           60           16          960          513           13 
TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 
          11           13           54           60           55           67 
TCGA-85-8354 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8664 TCGA-85-8666 
          61           22           21          445            3          475 
TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 
          15         1972           25         1973         1967         1972 
TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 
        1987           24           13          758          289           89 
TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-8063 TCGA-92-8064 
         428          244          331          269          122          160 
TCGA-92-8065 TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 
          70          356          430         1213         1344          189 
TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 
         211          183          256          413          224          308 
TCGA-J1-A4AH TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE 
         222           36           83         1722 

  AMP PEAK 20(14Q32.33) MUTATED AMP PEAK 20(14Q32.33) WILD-TYPE 
                              4                               1 
  AMP PEAK 20(14Q32.33) MUTATED AMP PEAK 20(14Q32.33) WILD-TYPE 
                           5287                            3724 
  AMP PEAK 20(14Q32.33) MUTATED AMP PEAK 20(14Q32.33) WILD-TYPE 
                          708.0                           597.5 
[1] "4.0 - 5287.0 (708.0)" "1.0 - 3724.0 (597.5)"
[1] "hr=" "1.5"
D20V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 20(14Q32.33) MUTATED         0       17       44        0        13
  AMP PEAK 20(14Q32.33) WILD-TYPE       1       55       93        1        39
                                 vv
clus                              STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 20(14Q32.33) MUTATED          29         20          6        2
  AMP PEAK 20(14Q32.33) WILD-TYPE        42         37         14        4
D20V3, multiclass
            clus
vv           AMP PEAK 20(14Q32.33) MUTATED AMP PEAK 20(14Q32.33) WILD-TYPE
  STAGE I                                0                               1
  STAGE IA                              17                              55
  STAGE IB                              44                              93
  STAGE II                               0                               1
  STAGE IIA                             13                              39
  STAGE IIB                             29                              42
  STAGE IIIA                            20                              37
  STAGE IIIB                             6                              14
  STAGE IV                               2                               4
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  AMP PEAK 20(14Q32.33) MUTATED    23  79  24   5
  AMP PEAK 20(14Q32.33) WILD-TYPE  75 175  24  15
D20V4, multiclass
    clus
vv   AMP PEAK 20(14Q32.33) MUTATED AMP PEAK 20(14Q32.33) WILD-TYPE
  T1                            23                              75
  T2                            79                             175
  T3                            24                              24
  T4                             5                              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 20(14Q32.33) MUTATED    81  35  12   1
  AMP PEAK 20(14Q32.33) WILD-TYPE 180  78  23   4
D20V5, multiclass
    clus
vv   AMP PEAK 20(14Q32.33) MUTATED AMP PEAK 20(14Q32.33) WILD-TYPE
  N0                            81                             180
  N1                            35                              78
  N2                            12                              23
  N3                             1                               4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               M0  M1 M1A  MX
  AMP PEAK 20(14Q32.33) MUTATED   116   1   1  11
  AMP PEAK 20(14Q32.33) WILD-TYPE 242   4   0  39
D20V6, multiclass
     clus
vv    AMP PEAK 20(14Q32.33) MUTATED AMP PEAK 20(14Q32.33) WILD-TYPE
  M0                            116                             242
  M1                              1                               4
  M1A                             1                               0
  MX                             11                              39
[1] 4 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(14Q32.33) MUTATED    29 102
  AMP PEAK 20(14Q32.33) WILD-TYPE  78 211
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(14Q32.33) MUTATED     29  102
  AMP PEAK 20(14Q32.33) WILD-TYPE   78  211
        clus
vv       AMP PEAK 20(14Q32.33) MUTATED AMP PEAK 20(14Q32.33) WILD-TYPE
  FEMALE                            29                              78
  MALE                             102                             211
[1] 2 2
[1] FALSE
D20V8, continuous
                                 vv
clus                              LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK 20(14Q32.33) MUTATED                                       5
  AMP PEAK 20(14Q32.33) WILD-TYPE                                     7
                                 vv
clus                              LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK 20(14Q32.33) MUTATED                                        1
  AMP PEAK 20(14Q32.33) WILD-TYPE                                      5
                                 vv
clus                              LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 20(14Q32.33) MUTATED                                         0
  AMP PEAK 20(14Q32.33) WILD-TYPE                                       1
                                 vv
clus                              LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 20(14Q32.33) MUTATED                                                           125
  AMP PEAK 20(14Q32.33) WILD-TYPE                                                         276
D20V9, multiclass
                                                             clus
vv                                                            AMP PEAK 20(14Q32.33) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           125
                                                             clus
vv                                                            AMP PEAK 20(14Q32.33) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                     7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                    5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             276
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V10, binary
                                 cls
clus                                0   1
  AMP PEAK 20(14Q32.33) MUTATED     3 128
  AMP PEAK 20(14Q32.33) WILD-TYPE  10 279
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(14Q32.33) MUTATED      3  128
  AMP PEAK 20(14Q32.33) WILD-TYPE   10  279
     clus
vv    AMP PEAK 20(14Q32.33) MUTATED AMP PEAK 20(14Q32.33) WILD-TYPE
  NO                              3                              10
  YES                           128                             279
[1] 2 2
[1] FALSE
D20V11, continuous
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 20(14Q32.33) MUTATED   112   3   1   4
  AMP PEAK 20(14Q32.33) WILD-TYPE 230   5   3  14
D20V12, multiclass
    clus
vv   AMP PEAK 20(14Q32.33) MUTATED AMP PEAK 20(14Q32.33) WILD-TYPE
  R0                           112                             230
  R1                             3                               5
  R2                             1                               3
  RX                             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                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 20(14Q32.33) MUTATED       2                         5    87
  AMP PEAK 20(14Q32.33) WILD-TYPE     7                        12   211
D20V13, multiclass
                           clus
vv                          AMP PEAK 20(14Q32.33) MUTATED
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             5
  WHITE                                                87
                           clus
vv                          AMP PEAK 20(14Q32.33) WILD-TYPE
  ASIAN                                                   7
  BLACK OR AFRICAN AMERICAN                              12
  WHITE                                                 211
[1] 3 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(14Q32.33) MUTATED     5  76
  AMP PEAK 20(14Q32.33) WILD-TYPE   3 191
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(14Q32.33) MUTATED      5   76
  AMP PEAK 20(14Q32.33) WILD-TYPE    3  191
                        clus
vv                       AMP PEAK 20(14Q32.33) MUTATED
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                            76
                        clus
vv                       AMP PEAK 20(14Q32.33) WILD-TYPE
  HISPANIC OR LATINO                                   3
  NOT HISPANIC OR LATINO                             191
[1] 2 2
[1] FALSE

Clustering(21) Variable = AMP PEAK 21(15Q26.3) MUTATION ANALYSIS
D21V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 21(15Q26.3) MUTATED    91  40
  AMP PEAK 21(15Q26.3) WILD-TYPE 174  83
  AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE 
                           131                            257 
  AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE 
                            40                             83 
$`AMP PEAK 21(15Q26.3) MUTATED`
TCGA-18-3410 TCGA-18-3411 TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 
         146         1415          396         1810          862          758 
TCGA-18-4083 TCGA-18-4086 TCGA-21-1072 TCGA-21-1077 TCGA-21-1079 TCGA-21-1082 
         187           85         3016         1058          965         3644 
TCGA-21-5786 TCGA-22-0944 TCGA-22-4591 TCGA-22-4593 TCGA-22-4604 TCGA-22-4605 
        1032          223          623         1067          399         1946 
TCGA-22-4613 TCGA-22-5472 TCGA-22-5474 TCGA-22-5482 TCGA-22-5483 TCGA-33-4532 
         358         1964          445          357          573         2524 
TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4583 TCGA-33-4589 TCGA-34-2596 
        2979         1311         5287         1941         1948           80 
TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2609 TCGA-34-5231 TCGA-34-5234 
        1874          958          881          951         1528         1715 
TCGA-34-5240 TCGA-37-3789 TCGA-37-3792 TCGA-39-5031 TCGA-39-5037 TCGA-43-2578 
         365           13           12          833         1086          684 
TCGA-43-3394 TCGA-43-5670 TCGA-43-6143 TCGA-43-6770 TCGA-43-A475 TCGA-46-6025 
         822          849          376          310          296          324 
TCGA-46-6026 TCGA-52-7809 TCGA-56-5898 TCGA-56-7222 TCGA-56-7582 TCGA-56-7730 
         423         1948          555           13           26            6 
TCGA-56-8504 TCGA-56-8626 TCGA-56-A4BW TCGA-56-A4ZK TCGA-56-A5DR TCGA-58-8390 
         178           17            2            4            4          911 
TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J TCGA-60-2695 TCGA-60-2696 TCGA-60-2706 
        2167         1058         2589          642          109         1958 
TCGA-60-2710 TCGA-60-2711 TCGA-60-2722 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 
        1963         1260          908          717          816          358 
TCGA-63-7020 TCGA-63-7022 TCGA-66-2734 TCGA-66-2754 TCGA-66-2765 TCGA-66-2766 
        1957         1947         1311           61           61           31 
TCGA-66-2767 TCGA-66-2769 TCGA-66-2770 TCGA-66-2773 TCGA-66-2781 TCGA-66-2787 
          61         1947          700         1946          121         1217 
TCGA-66-2789 TCGA-66-2791 TCGA-66-2795 TCGA-68-7755 TCGA-68-A59I TCGA-68-A59J 
        1955         1977          122           83          121          104 
TCGA-77-7141 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8009 TCGA-77-8133 
          15         1952         1954          479         1641         1941 
TCGA-77-8136 TCGA-77-8150 TCGA-77-8153 TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5GF 
        1947         1961         1684         1942         1959          839 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7844 TCGA-85-7950 TCGA-85-8049 
         395           34           18          911           60           60 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8276 TCGA-85-8277 TCGA-85-8351 TCGA-85-8352 
          16          960           13           11           55           67 
TCGA-85-8354 TCGA-85-8481 TCGA-85-8664 TCGA-85-A4CL TCGA-85-A50Z TCGA-85-A510 
          61           21            3           15         1973         1967 
TCGA-90-7766 TCGA-90-A59Q TCGA-92-7341 TCGA-92-8063 TCGA-94-7943 TCGA-96-7544 
         289          269          106          122          356         1213 
TCGA-96-7545 TCGA-L3-A524 TCGA-LA-A446 TCGA-NC-A5HE TCGA-NC-A5HG 
        1344          449           36         1722         1548 

$`AMP PEAK 21(15Q26.3) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3412 TCGA-18-3419 
         370          136         2464         2417          345           50 
TCGA-18-3421 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 
        1331         2754           92          827         3636         1426 
TCGA-21-1075 TCGA-21-1076 TCGA-21-1078 TCGA-21-1080 TCGA-21-1081 TCGA-21-1083 
        2134         1852          474         3724          284          267 
TCGA-21-5782 TCGA-21-5784 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 TCGA-22-1000 
         962         1268          329          979          608         1945 
TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 
         131         1952           53          429          822         1485 
TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4607 
        1470          734           17         1161         1057          587 
TCGA-22-5471 TCGA-22-5473 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 
         965         1933         1346           24         1651         1952 
TCGA-22-5481 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 
        1952          916         1912         1713          506           29 
TCGA-33-4533 TCGA-33-4582 TCGA-33-4586 TCGA-33-4587 TCGA-33-6738 TCGA-34-2608 
        1940         1966          428         1970          822         1000 
TCGA-34-5232 TCGA-34-5239 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-8454 
        2062          707          428          941          552          166 
TCGA-37-3783 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 
         120          200          247          227          238          207 
TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 
          12          103         1454         2253         1361         1947 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 
        1996         1964         1849           52          740           59 
TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 
        1107          474         1084          544         1964         1223 
TCGA-43-2581 TCGA-43-3920 TCGA-43-5668 TCGA-43-6647 TCGA-43-6771 TCGA-43-7656 
        1176         1007          349          757         1936          212 
TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 
         236         1970          407          358         1971          353 
TCGA-43-A56U TCGA-43-A56V TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 
         432          366           12           12          911          541 
TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-6545 
         923         1958         1967          881            3           62 
TCGA-56-6546 TCGA-56-7221 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7731 
          26           30           30           44           40         1961 
TCGA-56-7822 TCGA-56-8503 TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8628 
           1           41           55           36           63           16 
TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DS 
          34           38           46           30           25            8 
TCGA-58-8388 TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2698 TCGA-60-2703 
         378         1723         1072          910          311         1950 
TCGA-60-2704 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2712 TCGA-60-2713 
        1943          661         1963         1505          274         1731 
TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 
        1531         1075         1475         1297           97          983 
TCGA-60-2723 TCGA-63-6202 TCGA-63-7021 TCGA-63-7023 TCGA-66-2727 TCGA-66-2737 
        1092         1973         1955         1952         1967           61 
TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 
         641           30           31           28           30           30 
TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2768 TCGA-66-2771 TCGA-66-2777 
         639          762           30           61          578           61 
TCGA-66-2778 TCGA-66-2780 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 
         578         1956         1954          759           60          790 
TCGA-66-2788 TCGA-66-2790 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2800 
         699          699          913         1952         1645         1492 
TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-77-6842 TCGA-77-6843 
         202          211          244           96         1950         1941 
TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7142 TCGA-77-7335 
        1942         1952         1959         1968         1286         1954 
TCGA-77-7337 TCGA-77-8007 TCGA-77-8008 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 
        1942         1960         1945         1953         1945         1941 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 
        1946         1951         1962          833         1943          293 
TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 
        1092           10         1953         1955         1963         1290 
TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6560 TCGA-85-7697 TCGA-85-7698 
        1280         1939          713          364           10           49 
TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-8048 TCGA-85-8071 TCGA-85-8072 
           1         1965           35           26          428          513 
TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8353 TCGA-85-8355 TCGA-85-8479 
          13           54           60           54           61           22 
TCGA-85-8580 TCGA-85-8582 TCGA-85-8666 TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR 
         445          424          475         1972         1960           25 
TCGA-85-A50M TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 
          19         1972         1987           24           13          111 
TCGA-90-6837 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE 
         758           89          358          428          244          331 
TCGA-92-7340 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-A4VJ TCGA-96-8169 
          82          160           70           87          430          189 
TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 
         211          273          183          256          413          224 
TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-MF-A522 TCGA-NC-A5HI 
         308          222           35           83         1135 

  AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE 
                             2                              1 
  AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE 
                          5287                           3724 
  AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE 
                           700                            608 
[1] "2.0 - 5287.0 (700.0)" "1.0 - 3724.0 (608.0)"
[1] "hr=" "1.1"
D21V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 21(15Q26.3) MUTATED         0       22       48        0        21
  AMP PEAK 21(15Q26.3) WILD-TYPE       1       50       89        1        31
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 21(15Q26.3) MUTATED          23         22          7        3
  AMP PEAK 21(15Q26.3) WILD-TYPE        48         35         13        3
D21V3, multiclass
            clus
vv           AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE
  STAGE I                               0                              1
  STAGE IA                             22                             50
  STAGE IB                             48                             89
  STAGE II                              0                              1
  STAGE IIA                            21                             31
  STAGE IIB                            23                             48
  STAGE IIIA                           22                             35
  STAGE IIIB                            7                             13
  STAGE IV                              3                              3
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 21(15Q26.3) MUTATED    30  97  15   5
  AMP PEAK 21(15Q26.3) WILD-TYPE  68 157  33  15
D21V4, multiclass
    clus
vv   AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE
  T1                           30                             68
  T2                           97                            157
  T3                           15                             33
  T4                            5                             15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK 21(15Q26.3) MUTATED    84  46  12   3
  AMP PEAK 21(15Q26.3) WILD-TYPE 177  67  23   2
D21V5, multiclass
    clus
vv   AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE
  N0                           84                            177
  N1                           46                             67
  N2                           12                             23
  N3                            3                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A  MX
  AMP PEAK 21(15Q26.3) MUTATED   129   2   1  13
  AMP PEAK 21(15Q26.3) WILD-TYPE 229   3   0  37
D21V6, multiclass
     clus
vv    AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE
  M0                           129                            229
  M1                             2                              3
  M1A                            1                              0
  MX                            13                             37
[1] 4 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(15Q26.3) MUTATED    35 112
  AMP PEAK 21(15Q26.3) WILD-TYPE  72 201
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(15Q26.3) MUTATED     35  112
  AMP PEAK 21(15Q26.3) WILD-TYPE   72  201
        clus
vv       AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE
  FEMALE                           35                             72
  MALE                            112                            201
[1] 2 2
[1] FALSE
D21V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK 21(15Q26.3) MUTATED                                       6
  AMP PEAK 21(15Q26.3) WILD-TYPE                                     6
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK 21(15Q26.3) MUTATED                                        2
  AMP PEAK 21(15Q26.3) WILD-TYPE                                      4
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 21(15Q26.3) MUTATED                                         0
  AMP PEAK 21(15Q26.3) WILD-TYPE                                       1
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 21(15Q26.3) MUTATED                                                           139
  AMP PEAK 21(15Q26.3) WILD-TYPE                                                         262
D21V9, multiclass
                                                             clus
vv                                                            AMP PEAK 21(15Q26.3) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          139
                                                             clus
vv                                                            AMP PEAK 21(15Q26.3) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            262
[1] 4 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(15Q26.3) MUTATED     4 143
  AMP PEAK 21(15Q26.3) WILD-TYPE   9 264
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(15Q26.3) MUTATED      4  143
  AMP PEAK 21(15Q26.3) WILD-TYPE    9  264
     clus
vv    AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE
  NO                             4                              9
  YES                          143                            264
[1] 2 2
[1] FALSE
D21V11, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 21(15Q26.3) MUTATED   120   5   1   6
  AMP PEAK 21(15Q26.3) WILD-TYPE 222   3   3  12
D21V12, multiclass
    clus
vv   AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE
  R0                          120                            222
  R1                            5                              3
  R2                            1                              3
  RX                            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                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 21(15Q26.3) MUTATED       1                         7   103
  AMP PEAK 21(15Q26.3) WILD-TYPE     8                        10   195
D21V13, multiclass
                           clus
vv                          AMP PEAK 21(15Q26.3) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            7
  WHITE                                              103
                           clus
vv                          AMP PEAK 21(15Q26.3) WILD-TYPE
  ASIAN                                                  8
  BLACK OR AFRICAN AMERICAN                             10
  WHITE                                                195
[1] 3 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(15Q26.3) MUTATED     2  95
  AMP PEAK 21(15Q26.3) WILD-TYPE   6 172
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(15Q26.3) MUTATED      2   95
  AMP PEAK 21(15Q26.3) WILD-TYPE    6  172
                        clus
vv                       AMP PEAK 21(15Q26.3) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           95
                        clus
vv                       AMP PEAK 21(15Q26.3) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            172
[1] 2 2
[1] FALSE

Clustering(22) Variable = AMP PEAK 22(17Q25.1) MUTATION ANALYSIS
D22V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 22(17Q25.1) MUTATED   133  55
  AMP PEAK 22(17Q25.1) WILD-TYPE 132  68
  AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE 
                           188                            200 
  AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE 
                            55                             68 
$`AMP PEAK 22(17Q25.1) MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 
         370          136          146         1415          345         1810 
TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-21-1071 
         862          758           50         1331          187         1426 
TCGA-21-1072 TCGA-21-1075 TCGA-21-1077 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 
        3016         2134         1058          284         3644          267 
TCGA-21-5786 TCGA-21-5787 TCGA-22-1012 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 
        1032          329          429          623         1067         1470 
TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4607 TCGA-22-4613 
         734         1161         1057          399          587          358 
TCGA-22-5471 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5483 
         965          445         1346           24         1651          573 
TCGA-22-5491 TCGA-33-4532 TCGA-33-4582 TCGA-33-4586 TCGA-33-6738 TCGA-34-2596 
        1713         2524         1966          428          822           80 
TCGA-34-2604 TCGA-34-2609 TCGA-34-5231 TCGA-34-5240 TCGA-37-3783 TCGA-37-3792 
         958          951         1528          365          120           12 
TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5016 
         227          238          207           12          103         2253 
TCGA-39-5019 TCGA-39-5022 TCGA-39-5027 TCGA-39-5035 TCGA-39-5037 TCGA-39-5040 
        1361         1996         1849          474         1086         1964 
TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 
        1223          684         1176          822         1007          349 
TCGA-43-5670 TCGA-43-6770 TCGA-43-7657 TCGA-43-8115 TCGA-43-A475 TCGA-43-A56V 
         849          310          236          407          296          366 
TCGA-46-6025 TCGA-46-6026 TCGA-51-4080 TCGA-52-7812 TCGA-56-1622 TCGA-56-7222 
         324          423           12         1967          881           13 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7582 TCGA-56-7730 TCGA-56-8504 TCGA-56-8629 
          30           44           26            6          178           34 
TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-58-8390 TCGA-58-8391 TCGA-58-A46J 
          46           30           25          911         2167         2589 
TCGA-58-A46M TCGA-58-A46N TCGA-60-2703 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 
        1072          910         1950         1958          661         1963 
TCGA-60-2711 TCGA-60-2715 TCGA-60-2722 TCGA-60-2723 TCGA-60-2725 TCGA-60-2726 
        1260         1075          908         1092          816          358 
TCGA-63-6202 TCGA-63-7021 TCGA-63-7022 TCGA-66-2742 TCGA-66-2754 TCGA-66-2756 
        1973         1955         1947          641           61           30 
TCGA-66-2757 TCGA-66-2758 TCGA-66-2763 TCGA-66-2767 TCGA-66-2770 TCGA-66-2771 
          30          639           30           61          700          578 
TCGA-66-2777 TCGA-66-2781 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 
          61          121         1217          699         1955          699 
TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2795 TCGA-68-7755 TCGA-68-7756 
        1977          913         1952          122           83          202 
TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 TCGA-77-6845 
         244           96          121          104         1950         1952 
TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7465 TCGA-77-8007 
        1959         1968           15         1286          479         1960 
TCGA-77-8009 TCGA-77-8128 TCGA-77-8133 TCGA-77-8136 TCGA-77-8139 TCGA-77-8144 
        1641         1953         1941         1947         1951          833 
TCGA-77-8153 TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5GA 
        1684           10         1959         1955         1963         1280 
TCGA-77-A5GF TCGA-85-6560 TCGA-85-7696 TCGA-85-7843 TCGA-85-7844 TCGA-85-8070 
         839          364           18           35          911          960 
TCGA-85-8072 TCGA-85-8277 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 
         513           11           60           55           67           54 
TCGA-85-8354 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4QR TCGA-85-A50Z 
          61            3          475           15           25         1973 
TCGA-85-A510 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4ED 
        1967           13          111           89          358          244 
TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-94-7033 TCGA-94-A4VJ 
         331          269           82          106           87          430 
TCGA-96-7544 TCGA-96-7545 TCGA-96-A4JK TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A524 
        1213         1344          273          308          222          449 
TCGA-MF-A522 TCGA-NC-A5HG 
          83         1548 

$`AMP PEAK 22(17Q25.1) WILD-TYPE`
TCGA-18-3408 TCGA-18-3409 TCGA-18-3414 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 
        2464         2417          396           85         2754           92 
TCGA-18-5595 TCGA-21-1070 TCGA-21-1076 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 
         827         3636         1852          474          965         3724 
TCGA-21-5782 TCGA-21-5784 TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 
         962         1268          979          608          223         1945 
TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1016 TCGA-22-1017 TCGA-22-4596 
         131         1952           53          822         1485           17 
TCGA-22-4605 TCGA-22-5472 TCGA-22-5473 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 
        1946         1964         1933         1952         1952          357 
TCGA-22-5485 TCGA-22-5489 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4538 
         916         1912          506           29         1940         2979 
TCGA-33-4547 TCGA-33-4566 TCGA-33-4583 TCGA-33-4587 TCGA-33-4589 TCGA-34-2600 
        1311         5287         1941         1970         1948         1874 
TCGA-34-2605 TCGA-34-2608 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5241 
         881         1000         2062         1715          707          428 
TCGA-34-5927 TCGA-34-5928 TCGA-34-8454 TCGA-37-3789 TCGA-37-4129 TCGA-37-4130 
         941          552          166           13          200          247 
TCGA-39-5011 TCGA-39-5021 TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 
        1454         1947         1964           52          740           59 
TCGA-39-5031 TCGA-39-5034 TCGA-39-5036 TCGA-39-5039 TCGA-43-6143 TCGA-43-6647 
         833         1107         1084          544          376          757 
TCGA-43-6771 TCGA-43-7656 TCGA-43-7658 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 
        1936          212         1970          358         1971          353 
TCGA-43-A56U TCGA-51-4079 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 
         432           12          911          541         1948          923 
TCGA-52-7811 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 
        1958            3          555           62           26           30 
TCGA-56-7580 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 TCGA-56-8622 TCGA-56-8624 
          40         1961            1           41           55           36 
TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4ZK 
          63           17           16           38            2            4 
TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8388 TCGA-58-8393 TCGA-58-A46L TCGA-60-2695 
           4            8          378         1058         1723          642 
TCGA-60-2696 TCGA-60-2698 TCGA-60-2704 TCGA-60-2709 TCGA-60-2710 TCGA-60-2712 
         109          311         1943         1505         1963          274 
TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 
        1731         1531         1475         1297           97          983 
TCGA-60-2724 TCGA-63-7020 TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 
         717         1957         1952         1967         1311           61 
TCGA-66-2744 TCGA-66-2753 TCGA-66-2755 TCGA-66-2759 TCGA-66-2765 TCGA-66-2766 
          30           31           28          762           61           31 
TCGA-66-2768 TCGA-66-2769 TCGA-66-2773 TCGA-66-2778 TCGA-66-2780 TCGA-66-2782 
          61         1947         1946          578         1956         1954 
TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2794 TCGA-66-2800 TCGA-68-7757 
         759           60          790         1645         1492          211 
TCGA-77-6843 TCGA-77-6844 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 
        1941         1942         1954         1942         1952         1954 
TCGA-77-8008 TCGA-77-8130 TCGA-77-8131 TCGA-77-8138 TCGA-77-8140 TCGA-77-8145 
        1945         1945         1941         1946         1962         1943 
TCGA-77-8148 TCGA-77-8150 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G8 
         293         1961         1092         1953         1942         1290 
TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6561 TCGA-85-6798 TCGA-85-7697 TCGA-85-7698 
        1939          713          395           34           10           49 
TCGA-85-7699 TCGA-85-7710 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 
           1         1965           60           26           60           16 
TCGA-85-8071 TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 TCGA-85-8355 TCGA-85-8479 
         428           13           13           54           61           22 
TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M 
          21          445          424         1972         1960           19 
TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-90-6837 TCGA-90-7766 TCGA-90-7964 
        1972         1987           24          758          289          428 
TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7943 TCGA-96-8169 TCGA-96-8170 
         122          160           70          356          189          211 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-L3-A4E7 TCGA-LA-A446 
         183          256          413          224           35           36 
TCGA-NC-A5HE TCGA-NC-A5HI 
        1722         1135 

  AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE 
                             3                              1 
  AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE 
                          3644                           5287 
  AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE 
                         582.5                          728.5 
[1] "3.0 - 3644.0 (582.5)" "1.0 - 5287.0 (728.5)"
[1] "hr=" "1"  
D22V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 22(17Q25.1) MUTATED         0       27       58        0        32
  AMP PEAK 22(17Q25.1) WILD-TYPE       1       45       79        1        20
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 22(17Q25.1) MUTATED          39         30          9        5
  AMP PEAK 22(17Q25.1) WILD-TYPE        32         27         11        1
D22V3, multiclass
            clus
vv           AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE
  STAGE I                               0                              1
  STAGE IA                             27                             45
  STAGE IB                             58                             79
  STAGE II                              0                              1
  STAGE IIA                            32                             20
  STAGE IIB                            39                             32
  STAGE IIIA                           30                             27
  STAGE IIIB                            9                             11
  STAGE IV                              5                              1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 22(17Q25.1) MUTATED    36 135  22   8
  AMP PEAK 22(17Q25.1) WILD-TYPE  62 119  26  12
D22V4, multiclass
    clus
vv   AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE
  T1                           36                             62
  T2                          135                            119
  T3                           22                             26
  T4                            8                             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 22(17Q25.1) MUTATED   112  66  19   3
  AMP PEAK 22(17Q25.1) WILD-TYPE 149  47  16   2
D22V5, multiclass
    clus
vv   AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE
  N0                          112                            149
  N1                           66                             47
  N2                           19                             16
  N3                            3                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A  MX
  AMP PEAK 22(17Q25.1) MUTATED   169   4   1  24
  AMP PEAK 22(17Q25.1) WILD-TYPE 189   1   0  26
D22V6, multiclass
     clus
vv    AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE
  M0                           169                            189
  M1                             4                              1
  M1A                            1                              0
  MX                            24                             26
[1] 4 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(17Q25.1) MUTATED    40 161
  AMP PEAK 22(17Q25.1) WILD-TYPE  67 152
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(17Q25.1) MUTATED     40  161
  AMP PEAK 22(17Q25.1) WILD-TYPE   67  152
        clus
vv       AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE
  FEMALE                           40                             67
  MALE                            161                            152
[1] 2 2
[1] FALSE
D22V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK 22(17Q25.1) MUTATED                                       6
  AMP PEAK 22(17Q25.1) WILD-TYPE                                     6
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK 22(17Q25.1) MUTATED                                        1
  AMP PEAK 22(17Q25.1) WILD-TYPE                                      5
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 22(17Q25.1) MUTATED                                         0
  AMP PEAK 22(17Q25.1) WILD-TYPE                                       1
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 22(17Q25.1) MUTATED                                                           194
  AMP PEAK 22(17Q25.1) WILD-TYPE                                                         207
D22V9, multiclass
                                                             clus
vv                                                            AMP PEAK 22(17Q25.1) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          194
                                                             clus
vv                                                            AMP PEAK 22(17Q25.1) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            207
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V10, binary
                                cls
clus                               0   1
  AMP PEAK 22(17Q25.1) MUTATED     8 193
  AMP PEAK 22(17Q25.1) WILD-TYPE   5 214
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(17Q25.1) MUTATED      8  193
  AMP PEAK 22(17Q25.1) WILD-TYPE    5  214
     clus
vv    AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE
  NO                             8                              5
  YES                          193                            214
[1] 2 2
[1] FALSE
D22V11, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 22(17Q25.1) MUTATED   168   3   2   5
  AMP PEAK 22(17Q25.1) WILD-TYPE 174   5   2  13
D22V12, multiclass
    clus
vv   AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE
  R0                          168                            174
  R1                            3                              5
  R2                            2                              2
  RX                            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                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 22(17Q25.1) MUTATED       3                         8   142
  AMP PEAK 22(17Q25.1) WILD-TYPE     6                         9   156
D22V13, multiclass
                           clus
vv                          AMP PEAK 22(17Q25.1) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            8
  WHITE                                              142
                           clus
vv                          AMP PEAK 22(17Q25.1) WILD-TYPE
  ASIAN                                                  6
  BLACK OR AFRICAN AMERICAN                              9
  WHITE                                                156
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V14, binary
                                cls
clus                               0   1
  AMP PEAK 22(17Q25.1) MUTATED     3 125
  AMP PEAK 22(17Q25.1) WILD-TYPE   5 142
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(17Q25.1) MUTATED      3  125
  AMP PEAK 22(17Q25.1) WILD-TYPE    5  142
                        clus
vv                       AMP PEAK 22(17Q25.1) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          125
                        clus
vv                       AMP PEAK 22(17Q25.1) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            142
[1] 2 2
[1] FALSE

Clustering(23) Variable = AMP PEAK 23(18P11.32) MUTATION ANALYSIS
D23V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 23(18P11.32) MUTATED   100  40
  AMP PEAK 23(18P11.32) WILD-TYPE 165  83
  AMP PEAK 23(18P11.32) MUTATED AMP PEAK 23(18P11.32) WILD-TYPE 
                            140                             248 
  AMP PEAK 23(18P11.32) MUTATED AMP PEAK 23(18P11.32) WILD-TYPE 
                             40                              83 
$`AMP PEAK 23(18P11.32) MUTATED`
TCGA-18-3407 TCGA-18-3411 TCGA-18-3412 TCGA-18-3416 TCGA-18-4083 TCGA-21-1075 
         136         1415          345          862          187         2134 
TCGA-21-1079 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 
         965         3644          267          962         1268         1032 
TCGA-22-0944 TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 TCGA-22-4604 TCGA-22-5471 
         223          623         1067          734          399          965 
TCGA-22-5480 TCGA-22-5483 TCGA-22-5489 TCGA-22-5491 TCGA-33-4532 TCGA-33-4566 
        1952          573         1912         1713         2524         5287 
TCGA-34-2596 TCGA-34-2604 TCGA-34-5231 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 
          80          958         1528          707          365          428 
TCGA-37-3789 TCGA-37-3792 TCGA-37-4130 TCGA-37-4135 TCGA-37-4141 TCGA-39-5016 
          13           12          247          207           12         2253 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5027 TCGA-39-5029 TCGA-39-5031 TCGA-39-5037 
        1361         1947         1849          740          833         1086 
TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 
        1964         1223          684          349          849          376 
TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56V 
         236         1970         1971          353          296          366 
TCGA-46-6026 TCGA-51-4081 TCGA-52-7809 TCGA-52-7811 TCGA-56-5898 TCGA-56-7222 
         423          911         1948         1958          555           13 
TCGA-56-7223 TCGA-56-7580 TCGA-56-7730 TCGA-56-A49D TCGA-56-A4BY TCGA-56-A5DR 
          30           40            6           38           30            4 
TCGA-56-A5DS TCGA-58-8391 TCGA-60-2698 TCGA-60-2711 TCGA-60-2722 TCGA-60-2723 
           8         2167          311         1260          908         1092 
TCGA-60-2725 TCGA-60-2726 TCGA-63-7020 TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 
         816          358         1957         1952         1967         1311 
TCGA-66-2742 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2767 TCGA-66-2769 
         641          639          762           30           61         1947 
TCGA-66-2770 TCGA-66-2777 TCGA-66-2781 TCGA-66-2783 TCGA-66-2787 TCGA-66-2789 
         700           61          121          759         1217         1955 
TCGA-66-2794 TCGA-66-2800 TCGA-68-8250 TCGA-68-A59J TCGA-77-7141 TCGA-77-7335 
        1645         1492          244          104           15         1954 
TCGA-77-7463 TCGA-77-7465 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8140 
        1954          479         1641         1953         1945         1962 
TCGA-77-8150 TCGA-77-8153 TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5GF TCGA-85-6561 
        1961         1684           10         1959          839          395 
TCGA-85-6798 TCGA-85-7843 TCGA-85-7844 TCGA-85-8049 TCGA-85-8070 TCGA-85-8071 
          34           35          911           60          960          428 
TCGA-85-8276 TCGA-85-8277 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8580 
          13           11           67           54           61          445 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A50M TCGA-85-A510 TCGA-85-A5B5 TCGA-90-7766 
           3          475           19         1967          111          289 
TCGA-90-7769 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-8064 TCGA-94-A4VJ TCGA-96-7545 
         358          331          269          160          430         1344 
TCGA-96-8169 TCGA-96-A4JK TCGA-98-8021 TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 
         189          273          413          222           35          449 
TCGA-MF-A522 TCGA-NC-A5HI 
          83         1135 

$`AMP PEAK 23(18P11.32) WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3414 TCGA-18-3415 
         370         2464         2417          146          396         1810 
TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 
         758           50         1331           85         2754           92 
TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1076 TCGA-21-1077 
         827         3636         1426         3016         1852         1058 
TCGA-21-1078 TCGA-21-1080 TCGA-21-1081 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 
         474         3724          284          329          979          608 
TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 
        1945          131         1952           53          429          822 
TCGA-22-1017 TCGA-22-4594 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4605 
        1485         1470           17         1161         1057         1946 
TCGA-22-4607 TCGA-22-4613 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 
         587          358         1964         1933          445         1346 
TCGA-22-5478 TCGA-22-5479 TCGA-22-5481 TCGA-22-5482 TCGA-22-5485 TCGA-22-5492 
          24         1651         1952          357          916          506 
TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4582 TCGA-33-4583 
          29         1940         2979         1311         1966         1941 
TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-33-6738 TCGA-34-2600 TCGA-34-2605 
         428         1970         1948          822         1874          881 
TCGA-34-2608 TCGA-34-2609 TCGA-34-5232 TCGA-34-5234 TCGA-34-5927 TCGA-34-5928 
        1000          951         2062         1715          941          552 
TCGA-34-8454 TCGA-37-3783 TCGA-37-4129 TCGA-37-4132 TCGA-37-4133 TCGA-37-5819 
         166          120          200          227          238          103 
TCGA-39-5011 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 TCGA-39-5030 TCGA-39-5034 
        1454         1996         1964           52           59         1107 
TCGA-39-5035 TCGA-39-5036 TCGA-39-5039 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 
         474         1084          544         1176          822         1007 
TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 
         757          310         1936          212          407          358 
TCGA-43-A56U TCGA-46-6025 TCGA-51-4079 TCGA-51-4080 TCGA-52-7622 TCGA-52-7810 
         432          324           12           12          541          923 
TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 
        1967          881            3           62           26           30 
TCGA-56-7579 TCGA-56-7582 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 TCGA-56-8504 
          44           26         1961            1           41          178 
TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 
          55           36           63           17           16           34 
TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-58-8388 TCGA-58-8390 
           2           46           25            4          378          911 
TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 
        1058         2589         1723         1072          910          642 
TCGA-60-2696 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 
         109         1950         1943         1958          661         1963 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 
        1505         1963          274         1731         1531         1075 
TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2724 TCGA-63-6202 
        1475         1297           97          983          717         1973 
TCGA-63-7021 TCGA-63-7022 TCGA-66-2737 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 
        1955         1947           61           30           31           61 
TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2765 TCGA-66-2766 TCGA-66-2768 
          28           30           30           61           31           61 
TCGA-66-2771 TCGA-66-2773 TCGA-66-2778 TCGA-66-2780 TCGA-66-2782 TCGA-66-2785 
         578         1946          578         1956         1954           60 
TCGA-66-2786 TCGA-66-2788 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 
         790          699          699         1977          913         1952 
TCGA-66-2795 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I 
         122           83          202          211           96          121 
TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 
        1950         1941         1942         1952         1959         1968 
TCGA-77-7142 TCGA-77-7337 TCGA-77-7338 TCGA-77-8007 TCGA-77-8008 TCGA-77-8131 
        1286         1942         1952         1960         1945         1941 
TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8144 TCGA-77-8145 
        1941         1947         1946         1951          833         1943 
TCGA-77-8148 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 
         293         1092         1953         1942         1955         1963 
TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6560 TCGA-85-7696 
        1290         1280         1939          713          364           18 
TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7950 TCGA-85-8048 
          10           49            1         1965           60           26 
TCGA-85-8052 TCGA-85-8072 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 
          16          513           13           54           60           55 
TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8582 TCGA-85-A4CL TCGA-85-A4PA 
          61           22           21          424           15         1972 
TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 
        1960           25         1973         1972         1987           24 
TCGA-85-A53L TCGA-90-6837 TCGA-90-7767 TCGA-90-7964 TCGA-90-A4ED TCGA-92-7340 
          13          758           89          428          244           82 
TCGA-92-7341 TCGA-92-8063 TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 TCGA-96-7544 
         106          122           70           87          356         1213 
TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8022 TCGA-98-8023 TCGA-LA-A446 
         211          183          256          224          308           36 
TCGA-NC-A5HE TCGA-NC-A5HG 
        1722         1548 

  AMP PEAK 23(18P11.32) MUTATED AMP PEAK 23(18P11.32) WILD-TYPE 
                              3                               1 
  AMP PEAK 23(18P11.32) MUTATED AMP PEAK 23(18P11.32) WILD-TYPE 
                           5287                            3724 
  AMP PEAK 23(18P11.32) MUTATED AMP PEAK 23(18P11.32) WILD-TYPE 
                            598                             699 
[1] "3.0 - 5287.0 (598.0)" "1.0 - 3724.0 (699.0)"
[1] "hr=" "1.1"
D23V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 23(18P11.32) MUTATED         0       23       52        0        21
  AMP PEAK 23(18P11.32) WILD-TYPE       1       49       85        1        31
                                 vv
clus                              STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 23(18P11.32) MUTATED          23         21         10        2
  AMP PEAK 23(18P11.32) WILD-TYPE        48         36         10        4
D23V3, multiclass
            clus
vv           AMP PEAK 23(18P11.32) MUTATED AMP PEAK 23(18P11.32) WILD-TYPE
  STAGE I                                0                               1
  STAGE IA                              23                              49
  STAGE IB                              52                              85
  STAGE II                               0                               1
  STAGE IIA                             21                              31
  STAGE IIB                             23                              48
  STAGE IIIA                            21                              36
  STAGE IIIB                            10                              10
  STAGE IV                               2                               4
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  AMP PEAK 23(18P11.32) MUTATED    31 100  17   5
  AMP PEAK 23(18P11.32) WILD-TYPE  67 154  31  15
D23V4, multiclass
    clus
vv   AMP PEAK 23(18P11.32) MUTATED AMP PEAK 23(18P11.32) WILD-TYPE
  T1                            31                              67
  T2                           100                             154
  T3                            17                              31
  T4                             5                              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 23(18P11.32) MUTATED    90  43  15   3
  AMP PEAK 23(18P11.32) WILD-TYPE 171  70  20   2
D23V5, multiclass
    clus
vv   AMP PEAK 23(18P11.32) MUTATED AMP PEAK 23(18P11.32) WILD-TYPE
  N0                            90                             171
  N1                            43                              70
  N2                            15                              20
  N3                             3                               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               M0  M1 M1A  MX
  AMP PEAK 23(18P11.32) MUTATED   132   2   0  16
  AMP PEAK 23(18P11.32) WILD-TYPE 226   3   1  34
D23V6, multiclass
     clus
vv    AMP PEAK 23(18P11.32) MUTATED AMP PEAK 23(18P11.32) WILD-TYPE
  M0                            132                             226
  M1                              2                               3
  M1A                             0                               1
  MX                             16                              34
[1] 4 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(18P11.32) MUTATED    36 117
  AMP PEAK 23(18P11.32) WILD-TYPE  71 196
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 23(18P11.32) MUTATED     36  117
  AMP PEAK 23(18P11.32) WILD-TYPE   71  196
        clus
vv       AMP PEAK 23(18P11.32) MUTATED AMP PEAK 23(18P11.32) WILD-TYPE
  FEMALE                            36                              71
  MALE                             117                             196
[1] 2 2
[1] FALSE
D23V8, continuous
                                 vv
clus                              LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK 23(18P11.32) MUTATED                                       4
  AMP PEAK 23(18P11.32) WILD-TYPE                                     8
                                 vv
clus                              LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK 23(18P11.32) MUTATED                                        1
  AMP PEAK 23(18P11.32) WILD-TYPE                                      5
                                 vv
clus                              LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 23(18P11.32) MUTATED                                         0
  AMP PEAK 23(18P11.32) WILD-TYPE                                       1
                                 vv
clus                              LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 23(18P11.32) MUTATED                                                           148
  AMP PEAK 23(18P11.32) WILD-TYPE                                                         253
D23V9, multiclass
                                                             clus
vv                                                            AMP PEAK 23(18P11.32) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           148
                                                             clus
vv                                                            AMP PEAK 23(18P11.32) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                     8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                    5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             253
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V10, binary
                                 cls
clus                                0   1
  AMP PEAK 23(18P11.32) MUTATED     7 146
  AMP PEAK 23(18P11.32) WILD-TYPE   6 261
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 23(18P11.32) MUTATED      7  146
  AMP PEAK 23(18P11.32) WILD-TYPE    6  261
     clus
vv    AMP PEAK 23(18P11.32) MUTATED AMP PEAK 23(18P11.32) WILD-TYPE
  NO                              7                               6
  YES                           146                             261
[1] 2 2
[1] FALSE
D23V11, continuous
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 23(18P11.32) MUTATED   122   2   3   6
  AMP PEAK 23(18P11.32) WILD-TYPE 220   6   1  12
D23V12, multiclass
    clus
vv   AMP PEAK 23(18P11.32) MUTATED AMP PEAK 23(18P11.32) WILD-TYPE
  R0                           122                             220
  R1                             2                               6
  R2                             3                               1
  RX                             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                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 23(18P11.32) MUTATED       4                         2   113
  AMP PEAK 23(18P11.32) WILD-TYPE     5                        15   185
D23V13, multiclass
                           clus
vv                          AMP PEAK 23(18P11.32) MUTATED
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                               113
                           clus
vv                          AMP PEAK 23(18P11.32) WILD-TYPE
  ASIAN                                                   5
  BLACK OR AFRICAN AMERICAN                              15
  WHITE                                                 185
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V14, binary
                                 cls
clus                                0   1
  AMP PEAK 23(18P11.32) MUTATED     2  97
  AMP PEAK 23(18P11.32) WILD-TYPE   6 170
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 23(18P11.32) MUTATED      2   97
  AMP PEAK 23(18P11.32) WILD-TYPE    6  170
                        clus
vv                       AMP PEAK 23(18P11.32) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            97
                        clus
vv                       AMP PEAK 23(18P11.32) WILD-TYPE
  HISPANIC OR LATINO                                   6
  NOT HISPANIC OR LATINO                             170
[1] 2 2
[1] FALSE

Clustering(24) Variable = AMP PEAK 24(18Q11.2) MUTATION ANALYSIS
D24V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 24(18Q11.2) MUTATED    85  40
  AMP PEAK 24(18Q11.2) WILD-TYPE 180  83
  AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE 
                           125                            263 
  AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE 
                            40                             83 
$`AMP PEAK 24(18Q11.2) MUTATED`
TCGA-18-3407 TCGA-18-3411 TCGA-18-3412 TCGA-18-4083 TCGA-21-1082 TCGA-21-1083 
         136         1415          345          187         3644          267 
TCGA-21-5784 TCGA-22-1012 TCGA-22-4595 TCGA-22-4599 TCGA-22-4604 TCGA-22-4613 
        1268          429          734         1161          399          358 
TCGA-22-5471 TCGA-22-5478 TCGA-22-5480 TCGA-22-5481 TCGA-22-5483 TCGA-22-5489 
         965           24         1952         1952          573         1912 
TCGA-22-5491 TCGA-33-4532 TCGA-33-4566 TCGA-33-4586 TCGA-34-2596 TCGA-34-2609 
        1713         2524         5287          428           80          951 
TCGA-34-5231 TCGA-34-5239 TCGA-34-5240 TCGA-37-3789 TCGA-37-4130 TCGA-37-4132 
        1528          707          365           13          247          227 
TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-39-5011 TCGA-39-5019 TCGA-39-5021 
         238          207           12         1454         1361         1947 
TCGA-39-5027 TCGA-39-5029 TCGA-39-5031 TCGA-39-5037 TCGA-39-5040 TCGA-43-2578 
        1849          740          833         1086         1964          684 
TCGA-43-3920 TCGA-43-5668 TCGA-43-6647 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 
        1007          349          757          236         1970          407 
TCGA-43-8118 TCGA-43-A475 TCGA-43-A56V TCGA-46-6026 TCGA-51-4079 TCGA-51-4081 
        1971          296          366          423           12          911 
TCGA-52-7809 TCGA-52-7811 TCGA-56-5898 TCGA-56-7223 TCGA-56-7580 TCGA-56-7730 
        1948         1958          555           30           40            6 
TCGA-56-A49D TCGA-56-A4BX TCGA-58-8391 TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 
          38           46         2167         1072          910          642 
TCGA-60-2711 TCGA-60-2712 TCGA-60-2722 TCGA-60-2723 TCGA-60-2725 TCGA-60-2726 
        1260          274          908         1092          816          358 
TCGA-63-7020 TCGA-63-7023 TCGA-66-2734 TCGA-66-2758 TCGA-66-2759 TCGA-66-2768 
        1957         1952         1311          639          762           61 
TCGA-66-2769 TCGA-66-2770 TCGA-66-2777 TCGA-66-2786 TCGA-66-2787 TCGA-66-2790 
        1947          700           61          790         1217          699 
TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2800 TCGA-68-7755 TCGA-77-6842 
         913         1952         1645         1492           83         1950 
TCGA-77-7463 TCGA-77-7465 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8140 
        1954          479         1641         1953         1945         1962 
TCGA-77-8150 TCGA-77-8153 TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5GF TCGA-77-A5GH 
        1961         1684           10         1959          839          713 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8070 
         395           34           35          911           60          960 
TCGA-85-8071 TCGA-85-8276 TCGA-85-8277 TCGA-85-8350 TCGA-85-8352 TCGA-85-8664 
         428           13           11           60           67            3 
TCGA-90-7769 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-8064 TCGA-96-7545 TCGA-98-8021 
         358          331          269          160         1344          413 
TCGA-98-8022 TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-MF-A522 TCGA-NC-A5HG 
         224          222           35           83         1548 

$`AMP PEAK 24(18Q11.2) WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3414 TCGA-18-3415 
         370         2464         2417          146          396         1810 
TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 
         862          758           50         1331           85         2754 
TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 
          92          827         3636         1426         3016         2134 
TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 
        1852         1058          474          965         3724          284 
TCGA-21-5782 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 
         962         1032          329          979          608          223 
TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1016 TCGA-22-1017 
        1945          131         1952           53          822         1485 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4596 TCGA-22-4601 TCGA-22-4605 
         623         1067         1470           17         1057         1946 
TCGA-22-4607 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 
         587         1964         1933          445         1346         1651 
TCGA-22-5482 TCGA-22-5485 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4538 
         357          916          506           29         1940         2979 
TCGA-33-4547 TCGA-33-4582 TCGA-33-4583 TCGA-33-4587 TCGA-33-4589 TCGA-33-6738 
        1311         1966         1941         1970         1948          822 
TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-5232 TCGA-34-5234 
        1874          958          881         1000         2062         1715 
TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 TCGA-37-3792 
         428          941          552          166          120           12 
TCGA-37-4129 TCGA-37-5819 TCGA-39-5016 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 
         200          103         2253         1996         1964           52 
TCGA-39-5030 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5039 TCGA-43-2576 
          59         1107          474         1084          544         1223 
TCGA-43-2581 TCGA-43-3394 TCGA-43-5670 TCGA-43-6143 TCGA-43-6770 TCGA-43-6771 
        1176          822          849          376          310         1936 
TCGA-43-7656 TCGA-43-8116 TCGA-43-A474 TCGA-43-A56U TCGA-46-6025 TCGA-51-4080 
         212          358          353          432          324           12 
TCGA-52-7622 TCGA-52-7810 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-6545 
         541          923         1967          881            3           62 
TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7579 TCGA-56-7582 TCGA-56-7731 
          26           30           13           44           26         1961 
TCGA-56-7822 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 
           1           41          178           55           36           63 
TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BY TCGA-56-A4ZJ 
          17           16           34            2           30           25 
TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 TCGA-58-8393 
           4            4            8          378          911         1058 
TCGA-58-A46J TCGA-58-A46L TCGA-60-2696 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 
        2589         1723          109          311         1950         1943 
TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 
        1958          661         1963         1505         1963         1731 
TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 
        1531         1075         1475         1297           97          983 
TCGA-60-2724 TCGA-63-6202 TCGA-63-7021 TCGA-63-7022 TCGA-66-2727 TCGA-66-2737 
         717         1973         1955         1947         1967           61 
TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 
         641           30           31           61           28           30 
TCGA-66-2757 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2771 
          30           30           61           31           61          578 
TCGA-66-2773 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 
        1946          578         1956          121         1954          759 
TCGA-66-2785 TCGA-66-2788 TCGA-66-2789 TCGA-66-2791 TCGA-66-2795 TCGA-68-7756 
          60          699         1955         1977          122          202 
TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6843 
         211          244           96          121          104         1941 
TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 
        1942         1952         1959         1968           15         1286 
TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-8007 TCGA-77-8008 TCGA-77-8131 
        1954         1942         1952         1960         1945         1941 
TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8144 TCGA-77-8145 
        1941         1947         1946         1951          833         1943 
TCGA-77-8148 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 
         293         1092         1953         1942         1955         1963 
TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-85-6560 TCGA-85-7696 TCGA-85-7697 
        1290         1280         1939          364           18           10 
TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 
          49            1         1965           26           60           16 
TCGA-85-8072 TCGA-85-8287 TCGA-85-8288 TCGA-85-8351 TCGA-85-8353 TCGA-85-8354 
         513           13           54           55           54           61 
TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8666 
          61           22           21          445          424          475 
TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z 
          15         1972         1960           25           19         1973 
TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 
        1967         1972         1987           24           13          111 
TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7964 TCGA-90-A4ED TCGA-92-7340 
         758          289           89          428          244           82 
TCGA-92-7341 TCGA-92-8063 TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 TCGA-94-A4VJ 
         106          122           70           87          356          430 
TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 
        1213          189          211          273          183          256 
TCGA-98-8023 TCGA-L3-A524 TCGA-LA-A446 TCGA-NC-A5HE TCGA-NC-A5HI 
         308          449           36         1722         1135 

  AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE 
                             3                              1 
  AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE 
                          5287                           3724 
  AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE 
                           707                            578 
[1] "3.0 - 5287.0 (707.0)" "1.0 - 3724.0 (578.0)"
[1] "hr=" "1.1"
D24V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 24(18Q11.2) MUTATED         0       22       43        0        18
  AMP PEAK 24(18Q11.2) WILD-TYPE       1       50       94        1        34
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 24(18Q11.2) MUTATED          27         16          8        1
  AMP PEAK 24(18Q11.2) WILD-TYPE        44         41         12        5
D24V3, multiclass
            clus
vv           AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE
  STAGE I                               0                              1
  STAGE IA                             22                             50
  STAGE IB                             43                             94
  STAGE II                              0                              1
  STAGE IIA                            18                             34
  STAGE IIB                            27                             44
  STAGE IIIA                           16                             41
  STAGE IIIB                            8                             12
  STAGE IV                              1                              5
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 24(18Q11.2) MUTATED    30  88  10   7
  AMP PEAK 24(18Q11.2) WILD-TYPE  68 166  38  13
D24V4, multiclass
    clus
vv   AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE
  T1                           30                             68
  T2                           88                            166
  T3                           10                             38
  T4                            7                             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK 24(18Q11.2) MUTATED    77  44  13   0
  AMP PEAK 24(18Q11.2) WILD-TYPE 184  69  22   5
D24V5, multiclass
    clus
vv   AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE
  N0                           77                            184
  N1                           44                             69
  N2                           13                             22
  N3                            0                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A  MX
  AMP PEAK 24(18Q11.2) MUTATED   118   1   0  13
  AMP PEAK 24(18Q11.2) WILD-TYPE 240   4   1  37
D24V6, multiclass
     clus
vv    AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE
  M0                           118                            240
  M1                             1                              4
  M1A                            0                              1
  MX                            13                             37
[1] 4 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(18Q11.2) MUTATED    34 101
  AMP PEAK 24(18Q11.2) WILD-TYPE  73 212
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(18Q11.2) MUTATED     34  101
  AMP PEAK 24(18Q11.2) WILD-TYPE   73  212
        clus
vv       AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE
  FEMALE                           34                             73
  MALE                            101                            212
[1] 2 2
[1] FALSE
D24V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK 24(18Q11.2) MUTATED                                       5
  AMP PEAK 24(18Q11.2) WILD-TYPE                                     7
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK 24(18Q11.2) MUTATED                                        1
  AMP PEAK 24(18Q11.2) WILD-TYPE                                      5
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 24(18Q11.2) MUTATED                                         0
  AMP PEAK 24(18Q11.2) WILD-TYPE                                       1
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 24(18Q11.2) MUTATED                                                           129
  AMP PEAK 24(18Q11.2) WILD-TYPE                                                         272
D24V9, multiclass
                                                             clus
vv                                                            AMP PEAK 24(18Q11.2) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          129
                                                             clus
vv                                                            AMP PEAK 24(18Q11.2) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            272
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V10, binary
                                cls
clus                               0   1
  AMP PEAK 24(18Q11.2) MUTATED     6 129
  AMP PEAK 24(18Q11.2) WILD-TYPE   7 278
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(18Q11.2) MUTATED      6  129
  AMP PEAK 24(18Q11.2) WILD-TYPE    7  278
     clus
vv    AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE
  NO                             6                              7
  YES                          129                            278
[1] 2 2
[1] FALSE
D24V11, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 24(18Q11.2) MUTATED   111   3   2   4
  AMP PEAK 24(18Q11.2) WILD-TYPE 231   5   2  14
D24V12, multiclass
    clus
vv   AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE
  R0                          111                            231
  R1                            3                              5
  R2                            2                              2
  RX                            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                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 24(18Q11.2) MUTATED       2                         3    99
  AMP PEAK 24(18Q11.2) WILD-TYPE     7                        14   199
D24V13, multiclass
                           clus
vv                          AMP PEAK 24(18Q11.2) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               99
                           clus
vv                          AMP PEAK 24(18Q11.2) WILD-TYPE
  ASIAN                                                  7
  BLACK OR AFRICAN AMERICAN                             14
  WHITE                                                199
[1] 3 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(18Q11.2) MUTATED     2  85
  AMP PEAK 24(18Q11.2) WILD-TYPE   6 182
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(18Q11.2) MUTATED      2   85
  AMP PEAK 24(18Q11.2) WILD-TYPE    6  182
                        clus
vv                       AMP PEAK 24(18Q11.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           85
                        clus
vv                       AMP PEAK 24(18Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            182
[1] 2 2
[1] FALSE

Clustering(25) Variable = AMP PEAK 25(19Q12) MUTATION ANALYSIS
D25V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 25(19Q12) MUTATED   115  58
  AMP PEAK 25(19Q12) WILD-TYPE 150  65
  AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE 
                         173                          215 
  AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE 
                          58                           65 
$`AMP PEAK 25(19Q12) MUTATED`
TCGA-18-3407 TCGA-18-3410 TCGA-18-3411 TCGA-18-3416 TCGA-18-3417 TCGA-21-1070 
         136          146         1415          862          758         3636 
TCGA-21-1071 TCGA-21-1076 TCGA-21-1080 TCGA-21-1081 TCGA-21-5786 TCGA-21-5787 
        1426         1852         3724          284         1032          329 
TCGA-22-0940 TCGA-22-1011 TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 
         608           53         1485          623         1067          734 
TCGA-22-4599 TCGA-22-4601 TCGA-22-5471 TCGA-22-5474 TCGA-22-5477 TCGA-22-5481 
        1161         1057          965          445         1346         1952 
TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4538 
         573          916         1912           29         1940         2979 
TCGA-33-4566 TCGA-33-4582 TCGA-33-4586 TCGA-33-6738 TCGA-34-2596 TCGA-34-2600 
        5287         1966          428          822           80         1874 
TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-5231 TCGA-34-5239 TCGA-34-5240 
         958          881         1000         1528          707          365 
TCGA-34-5928 TCGA-37-3792 TCGA-37-4130 TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 
         552           12          247          103         1454         2253 
TCGA-39-5019 TCGA-39-5029 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5039 
        1361          740          833         1107          474          544 
TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 
        1964         1223          684          822         1007          349 
TCGA-43-5670 TCGA-43-6143 TCGA-43-7656 TCGA-43-7657 TCGA-43-A475 TCGA-43-A56V 
         849          376          212          236          296          366 
TCGA-46-6026 TCGA-52-7809 TCGA-56-6545 TCGA-56-6546 TCGA-56-7580 TCGA-56-7582 
         423         1948           62           26           40           26 
TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A5DR TCGA-58-8393 
          34           38           46           30            4         1058 
TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2698 TCGA-60-2704 
        1723         1072          910          642          311         1943 
TCGA-60-2706 TCGA-60-2708 TCGA-60-2712 TCGA-60-2719 TCGA-60-2722 TCGA-60-2723 
        1958         1963          274         1297          908         1092 
TCGA-63-7020 TCGA-63-7022 TCGA-66-2742 TCGA-66-2756 TCGA-66-2758 TCGA-66-2759 
        1957         1947          641           30          639          762 
TCGA-66-2763 TCGA-66-2766 TCGA-66-2770 TCGA-66-2777 TCGA-66-2781 TCGA-66-2782 
          30           31          700           61          121         1954 
TCGA-66-2785 TCGA-66-2787 TCGA-66-2788 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 
          60         1217          699         1977          913         1952 
TCGA-66-2795 TCGA-66-2800 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 
         122         1492           96          121          104         1950 
TCGA-77-6843 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 
        1941         1952         1959         1968           15         1286 
TCGA-77-7335 TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 
        1954          479         1945         1641         1953         1945 
TCGA-77-8136 TCGA-77-8138 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 
        1947         1946         1943          293         1961         1684 
TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF 
        1942         1959         1955         1963         1290          839 
TCGA-77-A5GH TCGA-85-6798 TCGA-85-7696 TCGA-85-7699 TCGA-85-7843 TCGA-85-8048 
         713           34           18            1           35           26 
TCGA-85-8070 TCGA-85-8072 TCGA-85-8277 TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 
         960          513           11           60           55           54 
TCGA-85-8354 TCGA-85-8582 TCGA-85-A4CL TCGA-85-A4QR TCGA-85-A50M TCGA-85-A510 
          61          424           15           25           19         1967 
TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7769 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 
          13          111          358          331          269           82 
TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7545 
         106          122          160          356          430         1344 
TCGA-98-8021 TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 
         413          222           35          449           36 

$`AMP PEAK 25(19Q12) WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3409 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 
         370         2464         2417          345          396         1810 
TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 
          50         1331          187           85         2754           92 
TCGA-18-5595 TCGA-21-1072 TCGA-21-1075 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 
         827         3016         2134         1058          474          965 
TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 TCGA-21-A5DI TCGA-22-0944 
        3644          267          962         1268          979          223 
TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1012 TCGA-22-1016 TCGA-22-4594 
        1945          131         1952          429          822         1470 
TCGA-22-4596 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 TCGA-22-5472 
          17          399         1946          587          358         1964 
TCGA-22-5473 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5482 TCGA-22-5491 
        1933           24         1651         1952          357         1713 
TCGA-22-5492 TCGA-33-4532 TCGA-33-4547 TCGA-33-4583 TCGA-33-4587 TCGA-33-4589 
         506         2524         1311         1941         1970         1948 
TCGA-34-2609 TCGA-34-5232 TCGA-34-5234 TCGA-34-5241 TCGA-34-5927 TCGA-34-8454 
         951         2062         1715          428          941          166 
TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 
         120           13          200          227          238          207 
TCGA-37-4141 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 
          12         1947         1996         1964         1849           52 
TCGA-39-5030 TCGA-39-5036 TCGA-39-5037 TCGA-43-2581 TCGA-43-6647 TCGA-43-6770 
          59         1084         1086         1176          757          310 
TCGA-43-6771 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 
        1936         1970          407          358         1971          353 
TCGA-43-A56U TCGA-46-6025 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 
         432          324           12           12          911          541 
TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 
         923         1958         1967          881            3          555 
TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7730 TCGA-56-7731 
          30           13           30           44            6         1961 
TCGA-56-7822 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 
           1           41          178           55           36           63 
TCGA-56-8626 TCGA-56-8628 TCGA-56-A4BW TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DS 
          17           16            2           25            4            8 
TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-A46J TCGA-60-2696 TCGA-60-2703 
         378          911         2167         2589          109         1950 
TCGA-60-2707 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2713 TCGA-60-2714 
         661         1505         1963         1260         1731         1531 
TCGA-60-2715 TCGA-60-2716 TCGA-60-2720 TCGA-60-2721 TCGA-60-2724 TCGA-60-2725 
        1075         1475           97          983          717          816 
TCGA-60-2726 TCGA-63-6202 TCGA-63-7021 TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 
         358         1973         1955         1952         1967         1311 
TCGA-66-2737 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 
          61           30           31           61           28           30 
TCGA-66-2765 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2771 TCGA-66-2773 
          61           61           61         1947          578         1946 
TCGA-66-2778 TCGA-66-2780 TCGA-66-2783 TCGA-66-2786 TCGA-66-2789 TCGA-66-2790 
         578         1956          759          790         1955          699 
TCGA-66-2794 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-77-6844 
        1645           83          202          211          244         1942 
TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-8007 TCGA-77-8131 TCGA-77-8133 
        1942         1952         1954         1960         1941         1941 
TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ 
        1951         1962          833         1092           10         1953 
TCGA-77-A5GA TCGA-77-A5GB TCGA-85-6560 TCGA-85-6561 TCGA-85-7697 TCGA-85-7698 
        1280         1939          364          395           10           49 
TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 TCGA-85-8049 TCGA-85-8052 TCGA-85-8071 
        1965          911           60           60           16          428 
TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 TCGA-85-8352 TCGA-85-8355 TCGA-85-8479 
          13           13           54           67           61           22 
TCGA-85-8481 TCGA-85-8580 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4PA TCGA-85-A4QQ 
          21          445            3          475         1972         1960 
TCGA-85-A50Z TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-90-6837 TCGA-90-7766 
        1973         1972         1987           24          758          289 
TCGA-90-7767 TCGA-90-7964 TCGA-90-A4ED TCGA-92-8065 TCGA-94-7033 TCGA-96-7544 
          89          428          244           70           87         1213 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-8022 
         189          211          273          183          256          224 
TCGA-98-8023 TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HI 
         308           83         1722         1548         1135 

  AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE 
                           1                            1 
  AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE 
                        5287                         3644 
  AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE 
                         700                          555 
[1] "1.0 - 5287.0 (700.0)" "1.0 - 3644.0 (555.0)"
[1] "hr=" "1.2"
D25V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 25(19Q12) MUTATED         0       30       53        1        24
  AMP PEAK 25(19Q12) WILD-TYPE       1       42       84        0        28
                              vv
clus                           STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 25(19Q12) MUTATED          31         34         10        3
  AMP PEAK 25(19Q12) WILD-TYPE        40         23         10        3
D25V3, multiclass
            clus
vv           AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE
  STAGE I                             0                            1
  STAGE IA                           30                           42
  STAGE IB                           53                           84
  STAGE II                            1                            0
  STAGE IIA                          24                           28
  STAGE IIB                          31                           40
  STAGE IIIA                         34                           23
  STAGE IIIB                         10                           10
  STAGE IV                            3                            3
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            T1  T2  T3  T4
  AMP PEAK 25(19Q12) MUTATED    39 115  22  10
  AMP PEAK 25(19Q12) WILD-TYPE  59 139  26  10
D25V4, multiclass
    clus
vv   AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE
  T1                         39                           59
  T2                        115                          139
  T3                         22                           26
  T4                         10                           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 25(19Q12) MUTATED   108  52  23   1
  AMP PEAK 25(19Q12) WILD-TYPE 153  61  12   4
D25V5, multiclass
    clus
vv   AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE
  N0                        108                          153
  N1                         52                           61
  N2                         23                           12
  N3                          1                            4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            M0  M1 M1A  MX
  AMP PEAK 25(19Q12) MUTATED   161   3   0  21
  AMP PEAK 25(19Q12) WILD-TYPE 197   2   1  29
D25V6, multiclass
     clus
vv    AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE
  M0                         161                          197
  M1                           3                            2
  M1A                          0                            1
  MX                          21                           29
[1] 4 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(19Q12) MUTATED    44 142
  AMP PEAK 25(19Q12) WILD-TYPE  63 171
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 25(19Q12) MUTATED     44  142
  AMP PEAK 25(19Q12) WILD-TYPE   63  171
        clus
vv       AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE
  FEMALE                         44                           63
  MALE                          142                          171
[1] 2 2
[1] FALSE
D25V8, continuous
                              vv
clus                           LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK 25(19Q12) MUTATED                                       8
  AMP PEAK 25(19Q12) WILD-TYPE                                     4
                              vv
clus                           LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK 25(19Q12) MUTATED                                        2
  AMP PEAK 25(19Q12) WILD-TYPE                                      4
                              vv
clus                           LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 25(19Q12) MUTATED                                         0
  AMP PEAK 25(19Q12) WILD-TYPE                                       1
                              vv
clus                           LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 25(19Q12) MUTATED                                                           176
  AMP PEAK 25(19Q12) WILD-TYPE                                                         225
D25V9, multiclass
                                                             clus
vv                                                            AMP PEAK 25(19Q12) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                               2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                              0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                        176
                                                             clus
vv                                                            AMP PEAK 25(19Q12) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          225
[1] 4 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(19Q12) MUTATED     8 178
  AMP PEAK 25(19Q12) WILD-TYPE   5 229
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 25(19Q12) MUTATED      8  178
  AMP PEAK 25(19Q12) WILD-TYPE    5  229
     clus
vv    AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE
  NO                           8                            5
  YES                        178                          229
[1] 2 2
[1] FALSE
D25V11, continuous
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 25(19Q12) MUTATED   152   4   2   8
  AMP PEAK 25(19Q12) WILD-TYPE 190   4   2  10
D25V12, multiclass
    clus
vv   AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE
  R0                        152                          190
  R1                          4                            4
  R2                          2                            2
  RX                          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                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 25(19Q12) MUTATED       5                         7   127
  AMP PEAK 25(19Q12) WILD-TYPE     4                        10   171
D25V13, multiclass
                           clus
vv                          AMP PEAK 25(19Q12) MUTATED
  ASIAN                                              5
  BLACK OR AFRICAN AMERICAN                          7
  WHITE                                            127
                           clus
vv                          AMP PEAK 25(19Q12) WILD-TYPE
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                           10
  WHITE                                              171
[1] 3 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(19Q12) MUTATED     3 110
  AMP PEAK 25(19Q12) WILD-TYPE   5 157
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 25(19Q12) MUTATED      3  110
  AMP PEAK 25(19Q12) WILD-TYPE    5  157
                        clus
vv                       AMP PEAK 25(19Q12) MUTATED
  HISPANIC OR LATINO                              3
  NOT HISPANIC OR LATINO                        110
                        clus
vv                       AMP PEAK 25(19Q12) WILD-TYPE
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          157
[1] 2 2
[1] FALSE

Clustering(26) Variable = AMP PEAK 26(19Q13.2) MUTATION ANALYSIS
D26V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 26(19Q13.2) MUTATED   120  62
  AMP PEAK 26(19Q13.2) WILD-TYPE 145  61
  AMP PEAK 26(19Q13.2) MUTATED AMP PEAK 26(19Q13.2) WILD-TYPE 
                           182                            206 
  AMP PEAK 26(19Q13.2) MUTATED AMP PEAK 26(19Q13.2) WILD-TYPE 
                            62                             61 
$`AMP PEAK 26(19Q13.2) MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 TCGA-18-3417 
         370          136          146         1415          345          758 
TCGA-18-3421 TCGA-21-1070 TCGA-21-1071 TCGA-21-1076 TCGA-21-1080 TCGA-21-1081 
        1331         3636         1426         1852         3724          284 
TCGA-21-5786 TCGA-21-5787 TCGA-22-0940 TCGA-22-1005 TCGA-22-1011 TCGA-22-4591 
        1032          329          608         1952           53          623 
TCGA-22-4593 TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 TCGA-22-5471 TCGA-22-5473 
        1067          734         1161         1057          965         1933 
TCGA-22-5474 TCGA-22-5477 TCGA-22-5481 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 
         445         1346         1952          573          916         1912 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4582 TCGA-33-4586 
          29         2524         1940         2979         1966          428 
TCGA-33-6738 TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 
         822           80         1874          958          881         1000 
TCGA-34-2609 TCGA-34-5231 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5928 
         951         1528          707          365          428          552 
TCGA-37-3792 TCGA-37-4130 TCGA-37-5819 TCGA-39-5016 TCGA-39-5019 TCGA-39-5029 
          12          247          103         2253         1361          740 
TCGA-39-5034 TCGA-39-5035 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 
        1107          474          544         1964         1223          684 
TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-7657 
         822         1007          349          849          376          236 
TCGA-43-A475 TCGA-46-6025 TCGA-46-6026 TCGA-52-7809 TCGA-56-1622 TCGA-56-5898 
         296          324          423         1948          881          555 
TCGA-56-6545 TCGA-56-6546 TCGA-56-7580 TCGA-56-7582 TCGA-56-8622 TCGA-56-8629 
          62           26           40           26           55           34 
TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A5DR TCGA-58-8393 TCGA-58-A46L 
          38           46           30            4         1058         1723 
TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2698 TCGA-60-2704 TCGA-60-2706 
        1072          910          642          311         1943         1958 
TCGA-60-2708 TCGA-60-2709 TCGA-60-2712 TCGA-60-2719 TCGA-60-2722 TCGA-60-2723 
        1963         1505          274         1297          908         1092 
TCGA-63-7020 TCGA-63-7022 TCGA-66-2742 TCGA-66-2756 TCGA-66-2758 TCGA-66-2759 
        1957         1947          641           30          639          762 
TCGA-66-2763 TCGA-66-2766 TCGA-66-2767 TCGA-66-2770 TCGA-66-2777 TCGA-66-2781 
          30           31           61          700           61          121 
TCGA-66-2782 TCGA-66-2785 TCGA-66-2787 TCGA-66-2788 TCGA-66-2791 TCGA-66-2792 
        1954           60         1217          699         1977          913 
TCGA-66-2793 TCGA-66-2795 TCGA-66-2800 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J 
        1952          122         1492           96          121          104 
TCGA-77-6842 TCGA-77-6843 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 
        1950         1941         1952         1959         1968           15 
TCGA-77-7142 TCGA-77-7335 TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 
        1286         1954          479         1945         1641         1953 
TCGA-77-8130 TCGA-77-8136 TCGA-77-8138 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 
        1945         1947         1946         1943          293         1961 
TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA 
        1942         1959         1955         1963         1290         1280 
TCGA-77-A5GF TCGA-77-A5GH TCGA-85-7696 TCGA-85-7699 TCGA-85-7843 TCGA-85-8048 
         839          713           18            1           35           26 
TCGA-85-8070 TCGA-85-8276 TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 TCGA-85-8354 
         960           13           60           55           54           61 
TCGA-85-8355 TCGA-85-8582 TCGA-85-8664 TCGA-85-A4CL TCGA-85-A50M TCGA-85-A510 
          61          424            3           15           19         1967 
TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4EE 
          24           13          111          358          428          331 
TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-94-7943 
         269           82          106          122          160          356 
TCGA-94-A4VJ TCGA-96-7545 TCGA-98-8021 TCGA-98-8022 TCGA-J1-A4AH TCGA-L3-A4E7 
         430         1344          413          224          222           35 
TCGA-L3-A524 TCGA-LA-A446 
         449           36 

$`AMP PEAK 26(19Q13.2) WILD-TYPE`
TCGA-18-3408 TCGA-18-3409 TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3419 
        2464         2417          396         1810          862           50 
TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1072 
         187           85         2754           92          827         3016 
TCGA-21-1075 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1082 TCGA-21-1083 
        2134         1058          474          965         3644          267 
TCGA-21-5782 TCGA-21-5784 TCGA-21-A5DI TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 
         962         1268          979          223         1945          131 
TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4594 TCGA-22-4596 TCGA-22-4604 
         429          822         1485         1470           17          399 
TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 TCGA-22-5472 TCGA-22-5478 TCGA-22-5479 
        1946          587          358         1964           24         1651 
TCGA-22-5480 TCGA-22-5482 TCGA-22-5491 TCGA-22-5492 TCGA-33-4547 TCGA-33-4566 
        1952          357         1713          506         1311         5287 
TCGA-33-4583 TCGA-33-4587 TCGA-33-4589 TCGA-34-5232 TCGA-34-5234 TCGA-34-5927 
        1941         1970         1948         2062         1715          941 
TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 TCGA-37-4132 TCGA-37-4133 
         166          120           13          200          227          238 
TCGA-37-4135 TCGA-37-4141 TCGA-39-5011 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 
         207           12         1454         1947         1996         1964 
TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 TCGA-39-5031 TCGA-39-5036 TCGA-39-5037 
        1849           52           59          833         1084         1086 
TCGA-43-2581 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 TCGA-43-7658 
        1176          757          310         1936          212         1970 
TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56U TCGA-43-A56V 
         407          358         1971          353          432          366 
TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7810 TCGA-52-7811 
          12           12          911          541          923         1958 
TCGA-52-7812 TCGA-56-5897 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 
        1967            3           30           13           30           44 
TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 TCGA-56-8504 TCGA-56-8624 
           6         1961            1           41          178           36 
TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-A4BW TCGA-56-A4ZJ TCGA-56-A4ZK 
          63           17           16            2           25            4 
TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-A46J TCGA-60-2696 
           8          378          911         2167         2589          109 
TCGA-60-2703 TCGA-60-2707 TCGA-60-2710 TCGA-60-2711 TCGA-60-2713 TCGA-60-2714 
        1950          661         1963         1260         1731         1531 
TCGA-60-2715 TCGA-60-2716 TCGA-60-2720 TCGA-60-2721 TCGA-60-2724 TCGA-60-2725 
        1075         1475           97          983          717          816 
TCGA-60-2726 TCGA-63-6202 TCGA-63-7021 TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 
         358         1973         1955         1952         1967         1311 
TCGA-66-2737 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 
          61           30           31           61           28           30 
TCGA-66-2765 TCGA-66-2768 TCGA-66-2769 TCGA-66-2771 TCGA-66-2773 TCGA-66-2778 
          61           61         1947          578         1946          578 
TCGA-66-2780 TCGA-66-2783 TCGA-66-2786 TCGA-66-2789 TCGA-66-2790 TCGA-66-2794 
        1956          759          790         1955          699         1645 
TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-77-6844 TCGA-77-7337 
          83          202          211          244         1942         1942 
TCGA-77-7338 TCGA-77-7463 TCGA-77-8007 TCGA-77-8131 TCGA-77-8133 TCGA-77-8139 
        1952         1954         1960         1941         1941         1951 
TCGA-77-8140 TCGA-77-8144 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ 
        1962          833         1684         1092           10         1953 
TCGA-77-A5GB TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7697 TCGA-85-7698 
        1939          364          395           34           10           49 
TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 TCGA-85-8049 TCGA-85-8052 TCGA-85-8071 
        1965          911           60           60           16          428 
TCGA-85-8072 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8352 TCGA-85-8479 
         513           11           13           54           67           22 
TCGA-85-8481 TCGA-85-8580 TCGA-85-8666 TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR 
          21          445          475         1972         1960           25 
TCGA-85-A50Z TCGA-85-A511 TCGA-85-A512 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 
        1973         1972         1987          758          289           89 
TCGA-90-A4ED TCGA-92-8065 TCGA-94-7033 TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 
         244           70           87         1213          189          211 
TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-8023 TCGA-MF-A522 TCGA-NC-A5HE 
         273          183          256          308           83         1722 
TCGA-NC-A5HG TCGA-NC-A5HI 
        1548         1135 

  AMP PEAK 26(19Q13.2) MUTATED AMP PEAK 26(19Q13.2) WILD-TYPE 
                             1                              1 
  AMP PEAK 26(19Q13.2) MUTATED AMP PEAK 26(19Q13.2) WILD-TYPE 
                          3724                           5287 
  AMP PEAK 26(19Q13.2) MUTATED AMP PEAK 26(19Q13.2) WILD-TYPE 
                         663.0                          582.5 
[1] "1.0 - 3724.0 (663.0)" "1.0 - 5287.0 (582.5)"
[1] "hr=" "1.4"
D26V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 26(19Q13.2) MUTATED         0       31       62        1        24
  AMP PEAK 26(19Q13.2) WILD-TYPE       1       41       75        0        28
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 26(19Q13.2) MUTATED          34         32         10        2
  AMP PEAK 26(19Q13.2) WILD-TYPE        37         25         10        4
D26V3, multiclass
            clus
vv           AMP PEAK 26(19Q13.2) MUTATED AMP PEAK 26(19Q13.2) WILD-TYPE
  STAGE I                               0                              1
  STAGE IA                             31                             41
  STAGE IB                             62                             75
  STAGE II                              1                              0
  STAGE IIA                            24                             28
  STAGE IIB                            34                             37
  STAGE IIIA                           32                             25
  STAGE IIIB                           10                             10
  STAGE IV                              2                              4
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 26(19Q13.2) MUTATED    41 125  20  10
  AMP PEAK 26(19Q13.2) WILD-TYPE  57 129  28  10
D26V4, multiclass
    clus
vv   AMP PEAK 26(19Q13.2) MUTATED AMP PEAK 26(19Q13.2) WILD-TYPE
  T1                           41                             57
  T2                          125                            129
  T3                           20                             28
  T4                           10                             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 26(19Q13.2) MUTATED   117  53  22   2
  AMP PEAK 26(19Q13.2) WILD-TYPE 144  60  13   3
D26V5, multiclass
    clus
vv   AMP PEAK 26(19Q13.2) MUTATED AMP PEAK 26(19Q13.2) WILD-TYPE
  N0                          117                            144
  N1                           53                             60
  N2                           22                             13
  N3                            2                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A  MX
  AMP PEAK 26(19Q13.2) MUTATED   171   2   0  22
  AMP PEAK 26(19Q13.2) WILD-TYPE 187   3   1  28
D26V6, multiclass
     clus
vv    AMP PEAK 26(19Q13.2) MUTATED AMP PEAK 26(19Q13.2) WILD-TYPE
  M0                           171                            187
  M1                             2                              3
  M1A                            0                              1
  MX                            22                             28
[1] 4 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(19Q13.2) MUTATED    42 154
  AMP PEAK 26(19Q13.2) WILD-TYPE  65 159
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 26(19Q13.2) MUTATED     42  154
  AMP PEAK 26(19Q13.2) WILD-TYPE   65  159
        clus
vv       AMP PEAK 26(19Q13.2) MUTATED AMP PEAK 26(19Q13.2) WILD-TYPE
  FEMALE                           42                             65
  MALE                            154                            159
[1] 2 2
[1] FALSE
D26V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK 26(19Q13.2) MUTATED                                       8
  AMP PEAK 26(19Q13.2) WILD-TYPE                                     4
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK 26(19Q13.2) MUTATED                                        1
  AMP PEAK 26(19Q13.2) WILD-TYPE                                      5
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 26(19Q13.2) MUTATED                                         0
  AMP PEAK 26(19Q13.2) WILD-TYPE                                       1
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 26(19Q13.2) MUTATED                                                           187
  AMP PEAK 26(19Q13.2) WILD-TYPE                                                         214
D26V9, multiclass
                                                             clus
vv                                                            AMP PEAK 26(19Q13.2) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          187
                                                             clus
vv                                                            AMP PEAK 26(19Q13.2) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            214
[1] 4 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(19Q13.2) MUTATED     8 188
  AMP PEAK 26(19Q13.2) WILD-TYPE   5 219
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 26(19Q13.2) MUTATED      8  188
  AMP PEAK 26(19Q13.2) WILD-TYPE    5  219
     clus
vv    AMP PEAK 26(19Q13.2) MUTATED AMP PEAK 26(19Q13.2) WILD-TYPE
  NO                             8                              5
  YES                          188                            219
[1] 2 2
[1] FALSE
D26V11, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 26(19Q13.2) MUTATED   164   4   2   7
  AMP PEAK 26(19Q13.2) WILD-TYPE 178   4   2  11
D26V12, multiclass
    clus
vv   AMP PEAK 26(19Q13.2) MUTATED AMP PEAK 26(19Q13.2) WILD-TYPE
  R0                          164                            178
  R1                            4                              4
  R2                            2                              2
  RX                            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                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 26(19Q13.2) MUTATED       5                         8   138
  AMP PEAK 26(19Q13.2) WILD-TYPE     4                         9   160
D26V13, multiclass
                           clus
vv                          AMP PEAK 26(19Q13.2) MUTATED
  ASIAN                                                5
  BLACK OR AFRICAN AMERICAN                            8
  WHITE                                              138
                           clus
vv                          AMP PEAK 26(19Q13.2) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                              9
  WHITE                                                160
[1] 3 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(19Q13.2) MUTATED     3 122
  AMP PEAK 26(19Q13.2) WILD-TYPE   5 145
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 26(19Q13.2) MUTATED      3  122
  AMP PEAK 26(19Q13.2) WILD-TYPE    5  145
                        clus
vv                       AMP PEAK 26(19Q13.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          122
                        clus
vv                       AMP PEAK 26(19Q13.2) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            145
[1] 2 2
[1] FALSE

Clustering(27) Variable = AMP PEAK 27(20P12.2) MUTATION ANALYSIS
D27V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 27(20P12.2) MUTATED   137  75
  AMP PEAK 27(20P12.2) WILD-TYPE 128  48
  AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE 
                           212                            176 
  AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE 
                            75                             48 
$`AMP PEAK 27(20P12.2) MUTATED`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
         136         2417          146         1415          345          396 
TCGA-18-3415 TCGA-18-3417 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1076 
        1810          758           92         3636         1426         1852 
TCGA-21-1077 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 
        1058         3724          284         3644          267          962 
TCGA-21-5784 TCGA-21-5786 TCGA-21-A5DI TCGA-22-1011 TCGA-22-1016 TCGA-22-4591 
        1268         1032          979           53          822          623 
TCGA-22-4593 TCGA-22-4594 TCGA-22-4599 TCGA-22-4604 TCGA-22-4605 TCGA-22-5471 
        1067         1470         1161          399         1946          965 
TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5480 
        1964         1933          445         1346           24         1952 
TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5491 TCGA-22-A5C4 TCGA-33-4532 
         357          573          916         1713           29         2524 
TCGA-33-4538 TCGA-33-4582 TCGA-33-4587 TCGA-33-4589 TCGA-33-6738 TCGA-34-2596 
        2979         1966         1970         1948          822           80 
TCGA-34-2600 TCGA-34-2605 TCGA-34-2608 TCGA-34-5231 TCGA-34-5239 TCGA-34-5240 
        1874          881         1000         1528          707          365 
TCGA-34-5928 TCGA-37-3783 TCGA-37-4130 TCGA-37-4141 TCGA-37-5819 TCGA-39-5016 
         552          120          247           12          103         2253 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5028 TCGA-39-5029 TCGA-39-5031 TCGA-39-5036 
        1361         1947           52          740          833         1084 
TCGA-39-5037 TCGA-39-5039 TCGA-43-2576 TCGA-43-2578 TCGA-43-3920 TCGA-43-5670 
        1086          544         1223          684         1007          849 
TCGA-43-6143 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 TCGA-43-A474 
         376          212          236         1970         1971          353 
TCGA-43-A56V TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4081 TCGA-52-7622 
         366          324          423           12          911          541 
TCGA-52-7809 TCGA-52-7811 TCGA-56-1622 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 
        1948         1958          881          555           62           26 
TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 
          13           30           44           40           26            6 
TCGA-56-7822 TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 TCGA-56-A49D TCGA-56-A4BW 
           1          178           55           36           38            2 
TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-58-8391 TCGA-58-8393 TCGA-58-A46M 
          25            4            4         2167         1058         1072 
TCGA-60-2695 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2707 TCGA-60-2708 
         642          311         1950         1943          661         1963 
TCGA-60-2711 TCGA-60-2715 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 
        1260         1075         1297           97          983          908 
TCGA-60-2723 TCGA-60-2726 TCGA-63-7020 TCGA-66-2727 TCGA-66-2737 TCGA-66-2742 
        1092          358         1957         1967           61          641 
TCGA-66-2756 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2769 TCGA-66-2770 
          30          639          762           30         1947          700 
TCGA-66-2773 TCGA-66-2777 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 
        1946           61         1956          121         1954          759 
TCGA-66-2787 TCGA-66-2788 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2800 
        1217          699         1977          913         1952         1492 
TCGA-68-7756 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-77-6842 TCGA-77-6844 
         202          244           96          121         1950         1942 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7338 
        1952         1959         1968           15         1286         1952 
TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 
        1960         1945         1641         1945         1941         1947 
TCGA-77-8140 TCGA-77-8145 TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 
        1962         1943           10         1959         1955         1963 
TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6798 
        1290         1280         1939          839          713           34 
TCGA-85-7696 TCGA-85-7698 TCGA-85-7843 TCGA-85-7950 TCGA-85-8049 TCGA-85-8052 
          18           49           35           60           60           16 
TCGA-85-8070 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8350 TCGA-85-8353 
         960           13           11           13           60           54 
TCGA-85-8354 TCGA-85-8481 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4QQ TCGA-85-A50M 
          61           21            3          475         1960           19 
TCGA-85-A510 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4ED 
        1967           13          111           89          358          244 
TCGA-90-A4EE TCGA-92-7341 TCGA-92-8064 TCGA-94-7943 TCGA-96-7545 TCGA-96-A4JK 
         331          106          160          356         1344          273 
TCGA-98-8021 TCGA-98-8022 TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 
         413          224          222           35          449           36 
TCGA-MF-A522 TCGA-NC-A5HI 
          83         1135 

$`AMP PEAK 27(20P12.2) WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3416 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 
         370         2464          862           50         1331          187 
TCGA-18-4086 TCGA-18-4721 TCGA-18-5595 TCGA-21-1072 TCGA-21-1075 TCGA-21-1078 
          85         2754          827         3016         2134          474 
TCGA-21-1079 TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 
         965          329          608          223         1945          131 
TCGA-22-1005 TCGA-22-1012 TCGA-22-1017 TCGA-22-4595 TCGA-22-4596 TCGA-22-4601 
        1952          429         1485          734           17         1057 
TCGA-22-4607 TCGA-22-4613 TCGA-22-5479 TCGA-22-5481 TCGA-22-5489 TCGA-22-5492 
         587          358         1651         1952         1912          506 
TCGA-33-4533 TCGA-33-4547 TCGA-33-4566 TCGA-33-4583 TCGA-33-4586 TCGA-34-2604 
        1940         1311         5287         1941          428          958 
TCGA-34-2609 TCGA-34-5232 TCGA-34-5234 TCGA-34-5241 TCGA-34-5927 TCGA-34-8454 
         951         2062         1715          428          941          166 
TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 
          13           12          200          227          238          207 
TCGA-39-5011 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5030 TCGA-39-5034 
        1454         1996         1964         1849           59         1107 
TCGA-39-5035 TCGA-39-5040 TCGA-43-2581 TCGA-43-3394 TCGA-43-5668 TCGA-43-6647 
         474         1964         1176          822          349          757 
TCGA-43-6770 TCGA-43-6771 TCGA-43-8115 TCGA-43-8116 TCGA-43-A475 TCGA-43-A56U 
         310         1936          407          358          296          432 
TCGA-51-4080 TCGA-52-7810 TCGA-52-7812 TCGA-56-5897 TCGA-56-7221 TCGA-56-7731 
          12          923         1967            3           30         1961 
TCGA-56-8503 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BX 
          41           63           17           16           34           46 
TCGA-56-A4BY TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 TCGA-58-A46J TCGA-58-A46L 
          30            8          378          911         2589         1723 
TCGA-58-A46N TCGA-60-2696 TCGA-60-2706 TCGA-60-2709 TCGA-60-2710 TCGA-60-2712 
         910          109         1958         1505         1963          274 
TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 TCGA-60-2724 TCGA-60-2725 TCGA-63-6202 
        1731         1531         1475          717          816         1973 
TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-66-2734 TCGA-66-2744 TCGA-66-2753 
        1955         1947         1952         1311           30           31 
TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 
          61           28           30           61           31           61 
TCGA-66-2768 TCGA-66-2771 TCGA-66-2778 TCGA-66-2785 TCGA-66-2786 TCGA-66-2789 
          61          578          578           60          790         1955 
TCGA-66-2790 TCGA-66-2794 TCGA-66-2795 TCGA-68-7755 TCGA-68-7757 TCGA-68-A59J 
         699         1645          122           83          211          104 
TCGA-77-6843 TCGA-77-7335 TCGA-77-7337 TCGA-77-7463 TCGA-77-7465 TCGA-77-8128 
        1941         1954         1942         1954          479         1953 
TCGA-77-8131 TCGA-77-8138 TCGA-77-8139 TCGA-77-8144 TCGA-77-8148 TCGA-77-8150 
        1941         1946         1951          833          293         1961 
TCGA-77-8153 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-85-6560 TCGA-85-6561 
        1684         1092         1953         1942          364          395 
TCGA-85-7697 TCGA-85-7699 TCGA-85-7710 TCGA-85-7844 TCGA-85-8048 TCGA-85-8071 
          10            1         1965          911           26          428 
TCGA-85-8072 TCGA-85-8288 TCGA-85-8351 TCGA-85-8352 TCGA-85-8355 TCGA-85-8479 
         513           54           55           67           61           22 
TCGA-85-8580 TCGA-85-8582 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QR TCGA-85-A50Z 
         445          424           15         1972           25         1973 
TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-90-6837 TCGA-90-7766 TCGA-90-7964 
        1972         1987           24          758          289          428 
TCGA-90-A59Q TCGA-92-7340 TCGA-92-8063 TCGA-92-8065 TCGA-94-7033 TCGA-94-A4VJ 
         269           82          122           70           87          430 
TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8023 
        1213          189          211          183          256          308 
TCGA-NC-A5HE TCGA-NC-A5HG 
        1722         1548 

  AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE 
                             1                              1 
  AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE 
                          3724                           5287 
  AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE 
                         703.5                          509.5 
[1] "1.0 - 3724.0 (703.5)" "1.0 - 5287.0 (509.5)"
[1] "hr=" "1.3"
D27V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 27(20P12.2) MUTATED         1       34       84        1        24
  AMP PEAK 27(20P12.2) WILD-TYPE       0       38       53        0        28
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 27(20P12.2) MUTATED          42         31         10        5
  AMP PEAK 27(20P12.2) WILD-TYPE        29         26         10        1
D27V3, multiclass
            clus
vv           AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE
  STAGE I                               1                              0
  STAGE IA                             34                             38
  STAGE IB                             84                             53
  STAGE II                              1                              0
  STAGE IIA                            24                             28
  STAGE IIB                            42                             29
  STAGE IIIA                           31                             26
  STAGE IIIB                           10                             10
  STAGE IV                              5                              1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 27(20P12.2) MUTATED    46 149  28  11
  AMP PEAK 27(20P12.2) WILD-TYPE  52 105  20   9
D27V4, multiclass
    clus
vv   AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE
  T1                           46                             52
  T2                          149                            105
  T3                           28                             20
  T4                           11                              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK 27(20P12.2) MUTATED   149  63  17   2
  AMP PEAK 27(20P12.2) WILD-TYPE 112  50  18   3
D27V5, multiclass
    clus
vv   AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE
  N0                          149                            112
  N1                           63                             50
  N2                           17                             18
  N3                            2                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A  MX
  AMP PEAK 27(20P12.2) MUTATED   203   4   1  24
  AMP PEAK 27(20P12.2) WILD-TYPE 155   1   0  26
D27V6, multiclass
     clus
vv    AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE
  M0                           203                            155
  M1                             4                              1
  M1A                            1                              0
  MX                            24                             26
[1] 4 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(20P12.2) MUTATED    49 185
  AMP PEAK 27(20P12.2) WILD-TYPE  58 128
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(20P12.2) MUTATED     49  185
  AMP PEAK 27(20P12.2) WILD-TYPE   58  128
        clus
vv       AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE
  FEMALE                           49                             58
  MALE                            185                            128
[1] 2 2
[1] FALSE
D27V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK 27(20P12.2) MUTATED                                       7
  AMP PEAK 27(20P12.2) WILD-TYPE                                     5
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK 27(20P12.2) MUTATED                                        2
  AMP PEAK 27(20P12.2) WILD-TYPE                                      4
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 27(20P12.2) MUTATED                                         1
  AMP PEAK 27(20P12.2) WILD-TYPE                                       0
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 27(20P12.2) MUTATED                                                           224
  AMP PEAK 27(20P12.2) WILD-TYPE                                                         177
D27V9, multiclass
                                                             clus
vv                                                            AMP PEAK 27(20P12.2) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          224
                                                             clus
vv                                                            AMP PEAK 27(20P12.2) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            177
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V10, binary
                                cls
clus                               0   1
  AMP PEAK 27(20P12.2) MUTATED     7 227
  AMP PEAK 27(20P12.2) WILD-TYPE   6 180
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(20P12.2) MUTATED      7  227
  AMP PEAK 27(20P12.2) WILD-TYPE    6  180
     clus
vv    AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE
  NO                             7                              6
  YES                          227                            180
[1] 2 2
[1] FALSE
D27V11, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 27(20P12.2) MUTATED   191   5   3   9
  AMP PEAK 27(20P12.2) WILD-TYPE 151   3   1   9
D27V12, multiclass
    clus
vv   AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE
  R0                          191                            151
  R1                            5                              3
  R2                            3                              1
  RX                            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                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 27(20P12.2) MUTATED       6                         8   164
  AMP PEAK 27(20P12.2) WILD-TYPE     3                         9   134
D27V13, multiclass
                           clus
vv                          AMP PEAK 27(20P12.2) MUTATED
  ASIAN                                                6
  BLACK OR AFRICAN AMERICAN                            8
  WHITE                                              164
                           clus
vv                          AMP PEAK 27(20P12.2) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              9
  WHITE                                                134
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V14, binary
                                cls
clus                               0   1
  AMP PEAK 27(20P12.2) MUTATED     7 142
  AMP PEAK 27(20P12.2) WILD-TYPE   1 125
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(20P12.2) MUTATED      7  142
  AMP PEAK 27(20P12.2) WILD-TYPE    1  125
                        clus
vv                       AMP PEAK 27(20P12.2) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                          142
                        clus
vv                       AMP PEAK 27(20P12.2) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                            125
[1] 2 2
[1] FALSE

Clustering(28) Variable = AMP PEAK 28(20Q11.21) MUTATION ANALYSIS
D28V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 28(20Q11.21) MUTATED   159  79
  AMP PEAK 28(20Q11.21) WILD-TYPE 106  44
  AMP PEAK 28(20Q11.21) MUTATED AMP PEAK 28(20Q11.21) WILD-TYPE 
                            238                             150 
  AMP PEAK 28(20Q11.21) MUTATED AMP PEAK 28(20Q11.21) WILD-TYPE 
                             79                              44 
$`AMP PEAK 28(20Q11.21) MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 
         370          136         2417          146         1415          345 
TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-5592 TCGA-21-1070 
         396         1810          758           50           92         3636 
TCGA-21-1071 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1081 
        1426         1852         1058          474          965          284 
TCGA-21-1082 TCGA-21-1083 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI 
        3644          267         1268         1032          329          979 
TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 
          53          429          822          623         1067         1470 
TCGA-22-4595 TCGA-22-4604 TCGA-22-4605 TCGA-22-5471 TCGA-22-5472 TCGA-22-5477 
         734          399         1946          965         1964         1346 
TCGA-22-5478 TCGA-22-5480 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5491 
          24         1952          357          573          916         1713 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4538 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 
          29         2524         2979         1966         1941          428 
TCGA-33-4589 TCGA-33-6738 TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 
        1948          822           80         1874          958          881 
TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5239 TCGA-34-5240 TCGA-34-5928 
        1000          951         1528          707          365          552 
TCGA-37-3783 TCGA-37-3792 TCGA-37-4130 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 
         120           12          247          238          207           12 
TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5028 
         103         1454         2253         1361         1947           52 
TCGA-39-5029 TCGA-39-5031 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-43-2576 
         740          833         1084         1086          544         1223 
TCGA-43-2578 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-6771 
         684         1007          349          849          376         1936 
TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-46-6025 
         236         1970         1971          353          366          324 
TCGA-46-6026 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-56-1622 
         423          541         1948          923         1958          881 
TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 
         555           62           26           13           30           44 
TCGA-56-7580 TCGA-56-7582 TCGA-56-7822 TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 
          40           26            1          178           55           36 
TCGA-56-8625 TCGA-56-8626 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4ZJ 
          63           17           34           38            2           25 
TCGA-56-A4ZK TCGA-56-A5DR TCGA-58-8390 TCGA-58-8391 TCGA-58-8393 TCGA-58-A46M 
           4            4          911         2167         1058         1072 
TCGA-60-2695 TCGA-60-2696 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 
         642          109          311         1950         1943         1958 
TCGA-60-2707 TCGA-60-2708 TCGA-60-2711 TCGA-60-2714 TCGA-60-2715 TCGA-60-2719 
         661         1963         1260         1531         1075         1297 
TCGA-60-2720 TCGA-60-2722 TCGA-60-2726 TCGA-63-7020 TCGA-66-2737 TCGA-66-2742 
          97          908          358         1957           61          641 
TCGA-66-2744 TCGA-66-2753 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 
          30           31           30           30          639          762 
TCGA-66-2763 TCGA-66-2766 TCGA-66-2769 TCGA-66-2770 TCGA-66-2773 TCGA-66-2777 
          30           31         1947          700         1946           61 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2785 TCGA-66-2787 TCGA-66-2788 
        1956          121         1954           60         1217          699 
TCGA-66-2793 TCGA-66-2800 TCGA-68-7756 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I 
        1952         1492          202          244           96          121 
TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 
         104         1950         1941         1952         1959         1968 
TCGA-77-7141 TCGA-77-7142 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 
          15         1286         1942         1952         1954          479 
TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 
        1960         1945         1641         1945         1941         1947 
TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5G6 
         833         1943          293           10         1959         1955 
TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 
        1290         1280         1939          839          713          364 
TCGA-85-6561 TCGA-85-7696 TCGA-85-7698 TCGA-85-7843 TCGA-85-7844 TCGA-85-8049 
         395           18           49           35          911           60 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 
          16          960          428           13           11           13 
TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8481 
          60           55           67           54           61           21 
TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M 
         424            3          475         1960           25           19 
TCGA-85-A510 TCGA-85-A511 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7767 TCGA-90-7769 
        1967         1972           13          111           89          358 
TCGA-90-A4ED TCGA-90-A4EE TCGA-92-7341 TCGA-92-8064 TCGA-94-7943 TCGA-94-A4VJ 
         244          331          106          160          356          430 
TCGA-96-7545 TCGA-96-A4JK TCGA-98-8022 TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 
        1344          273          224          222           35          449 
TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HG TCGA-NC-A5HI 
          36           83         1548         1135 

$`AMP PEAK 28(20Q11.21) WILD-TYPE`
TCGA-18-3408 TCGA-18-3416 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 
        2464          862         1331          187           85         2754 
TCGA-18-5595 TCGA-21-1072 TCGA-21-1075 TCGA-21-1080 TCGA-21-5782 TCGA-22-0940 
         827         3016         2134         3724          962          608 
TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1017 TCGA-22-4596 
         223         1945          131         1952         1485           17 
TCGA-22-4599 TCGA-22-4601 TCGA-22-4607 TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 
        1161         1057          587          358         1933          445 
TCGA-22-5479 TCGA-22-5481 TCGA-22-5489 TCGA-22-5492 TCGA-33-4533 TCGA-33-4547 
        1651         1952         1912          506         1940         1311 
TCGA-33-4566 TCGA-33-4587 TCGA-34-5232 TCGA-34-5234 TCGA-34-5241 TCGA-34-5927 
        5287         1970         2062         1715          428          941 
TCGA-34-8454 TCGA-37-3789 TCGA-37-4129 TCGA-37-4132 TCGA-39-5022 TCGA-39-5024 
         166           13          200          227         1996         1964 
TCGA-39-5027 TCGA-39-5030 TCGA-39-5034 TCGA-39-5035 TCGA-39-5040 TCGA-43-2581 
        1849           59         1107          474         1964         1176 
TCGA-43-3394 TCGA-43-6647 TCGA-43-6770 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 
         822          757          310          212          407          358 
TCGA-43-A475 TCGA-43-A56U TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7812 
         296          432           12           12          911         1967 
TCGA-56-5897 TCGA-56-7221 TCGA-56-7730 TCGA-56-7731 TCGA-56-8503 TCGA-56-8628 
           3           30            6         1961           41           16 
TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A5DS TCGA-58-8388 TCGA-58-A46J TCGA-58-A46L 
          46           30            8          378         2589         1723 
TCGA-58-A46N TCGA-60-2709 TCGA-60-2710 TCGA-60-2712 TCGA-60-2713 TCGA-60-2716 
         910         1505         1963          274         1731         1475 
TCGA-60-2721 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-63-6202 TCGA-63-7021 
         983         1092          717          816         1973         1955 
TCGA-63-7022 TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 TCGA-66-2754 TCGA-66-2755 
        1947         1952         1967         1311           61           28 
TCGA-66-2765 TCGA-66-2767 TCGA-66-2768 TCGA-66-2771 TCGA-66-2778 TCGA-66-2783 
          61           61           61          578          578          759 
TCGA-66-2786 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 
         790         1955          699         1977          913         1645 
TCGA-66-2795 TCGA-68-7755 TCGA-68-7757 TCGA-77-6844 TCGA-77-7335 TCGA-77-8128 
         122           83          211         1942         1954         1953 
TCGA-77-8131 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8150 TCGA-77-8153 
        1941         1946         1951         1962         1961         1684 
TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G7 TCGA-85-6798 TCGA-85-7697 
        1092         1953         1942         1963           34           10 
TCGA-85-7699 TCGA-85-7710 TCGA-85-7950 TCGA-85-8048 TCGA-85-8072 TCGA-85-8288 
           1         1965           60           26          513           54 
TCGA-85-8355 TCGA-85-8479 TCGA-85-8580 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A50Z 
          61           22          445           15         1972         1973 
TCGA-85-A512 TCGA-85-A513 TCGA-90-6837 TCGA-90-7766 TCGA-90-7964 TCGA-90-A59Q 
        1987           24          758          289          428          269 
TCGA-92-7340 TCGA-92-8063 TCGA-92-8065 TCGA-94-7033 TCGA-96-7544 TCGA-96-8169 
          82          122           70           87         1213          189 
TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8023 TCGA-NC-A5HE 
         211          183          256          413          308         1722 

  AMP PEAK 28(20Q11.21) MUTATED AMP PEAK 28(20Q11.21) WILD-TYPE 
                              1                               1 
  AMP PEAK 28(20Q11.21) MUTATED AMP PEAK 28(20Q11.21) WILD-TYPE 
                           3644                            5287 
  AMP PEAK 28(20Q11.21) MUTATED AMP PEAK 28(20Q11.21) WILD-TYPE 
                          553.5                           774.5 
[1] "1.0 - 3644.0 (553.5)" "1.0 - 5287.0 (774.5)"
[1] "hr=" "1.6"
D28V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 28(20Q11.21) MUTATED         1       39       84        1        30
  AMP PEAK 28(20Q11.21) WILD-TYPE       0       33       53        0        22
                                 vv
clus                              STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 28(20Q11.21) MUTATED          46         39          9        5
  AMP PEAK 28(20Q11.21) WILD-TYPE        25         18         11        1
D28V3, multiclass
            clus
vv           AMP PEAK 28(20Q11.21) MUTATED AMP PEAK 28(20Q11.21) WILD-TYPE
  STAGE I                                1                               0
  STAGE IA                              39                              33
  STAGE IB                              84                              53
  STAGE II                               1                               0
  STAGE IIA                             30                              22
  STAGE IIB                             46                              25
  STAGE IIIA                            39                              18
  STAGE IIIB                             9                              11
  STAGE IV                               5                               1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  AMP PEAK 28(20Q11.21) MUTATED    54 159  30  13
  AMP PEAK 28(20Q11.21) WILD-TYPE  44  95  18   7
D28V4, multiclass
    clus
vv   AMP PEAK 28(20Q11.21) MUTATED AMP PEAK 28(20Q11.21) WILD-TYPE
  T1                            54                              44
  T2                           159                              95
  T3                            30                              18
  T4                            13                               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2  N3
  AMP PEAK 28(20Q11.21) MUTATED   158  72  22   0
  AMP PEAK 28(20Q11.21) WILD-TYPE 103  41  13   5
D28V5, multiclass
    clus
vv   AMP PEAK 28(20Q11.21) MUTATED AMP PEAK 28(20Q11.21) WILD-TYPE
  N0                           158                             103
  N1                            72                              41
  N2                            22                              13
  N3                             0                               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               M0  M1 M1A  MX
  AMP PEAK 28(20Q11.21) MUTATED   222   4   1  27
  AMP PEAK 28(20Q11.21) WILD-TYPE 136   1   0  23
D28V6, multiclass
     clus
vv    AMP PEAK 28(20Q11.21) MUTATED AMP PEAK 28(20Q11.21) WILD-TYPE
  M0                            222                             136
  M1                              4                               1
  M1A                             1                               0
  MX                             27                              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V7, binary
                                 cls
clus                                0   1
  AMP PEAK 28(20Q11.21) MUTATED    50 206
  AMP PEAK 28(20Q11.21) WILD-TYPE  57 107
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 28(20Q11.21) MUTATED     50  206
  AMP PEAK 28(20Q11.21) WILD-TYPE   57  107
        clus
vv       AMP PEAK 28(20Q11.21) MUTATED AMP PEAK 28(20Q11.21) WILD-TYPE
  FEMALE                            50                              57
  MALE                             206                             107
[1] 2 2
[1] FALSE
D28V8, continuous
                                 vv
clus                              LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK 28(20Q11.21) MUTATED                                       8
  AMP PEAK 28(20Q11.21) WILD-TYPE                                     4
                                 vv
clus                              LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK 28(20Q11.21) MUTATED                                        1
  AMP PEAK 28(20Q11.21) WILD-TYPE                                      5
                                 vv
clus                              LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 28(20Q11.21) MUTATED                                         0
  AMP PEAK 28(20Q11.21) WILD-TYPE                                       1
                                 vv
clus                              LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 28(20Q11.21) MUTATED                                                           247
  AMP PEAK 28(20Q11.21) WILD-TYPE                                                         154
D28V9, multiclass
                                                             clus
vv                                                            AMP PEAK 28(20Q11.21) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           247
                                                             clus
vv                                                            AMP PEAK 28(20Q11.21) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                     4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                    5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             154
[1] 4 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(20Q11.21) MUTATED     9 247
  AMP PEAK 28(20Q11.21) WILD-TYPE   4 160
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 28(20Q11.21) MUTATED      9  247
  AMP PEAK 28(20Q11.21) WILD-TYPE    4  160
     clus
vv    AMP PEAK 28(20Q11.21) MUTATED AMP PEAK 28(20Q11.21) WILD-TYPE
  NO                              9                               4
  YES                           247                             160
[1] 2 2
[1] FALSE
D28V11, continuous
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 28(20Q11.21) MUTATED   210   5   2  10
  AMP PEAK 28(20Q11.21) WILD-TYPE 132   3   2   8
D28V12, multiclass
    clus
vv   AMP PEAK 28(20Q11.21) MUTATED AMP PEAK 28(20Q11.21) WILD-TYPE
  R0                           210                             132
  R1                             5                               3
  R2                             2                               2
  RX                            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                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 28(20Q11.21) MUTATED       5                        10   184
  AMP PEAK 28(20Q11.21) WILD-TYPE     4                         7   114
D28V13, multiclass
                           clus
vv                          AMP PEAK 28(20Q11.21) MUTATED
  ASIAN                                                 5
  BLACK OR AFRICAN AMERICAN                            10
  WHITE                                               184
                           clus
vv                          AMP PEAK 28(20Q11.21) WILD-TYPE
  ASIAN                                                   4
  BLACK OR AFRICAN AMERICAN                               7
  WHITE                                                 114
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V14, binary
                                 cls
clus                                0   1
  AMP PEAK 28(20Q11.21) MUTATED     7 160
  AMP PEAK 28(20Q11.21) WILD-TYPE   1 107
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 28(20Q11.21) MUTATED      7  160
  AMP PEAK 28(20Q11.21) WILD-TYPE    1  107
                        clus
vv                       AMP PEAK 28(20Q11.21) MUTATED
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           160
                        clus
vv                       AMP PEAK 28(20Q11.21) WILD-TYPE
  HISPANIC OR LATINO                                   1
  NOT HISPANIC OR LATINO                             107
[1] 2 2
[1] FALSE

Clustering(29) Variable = AMP PEAK 29(22Q11.21) MUTATION ANALYSIS
D29V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 29(22Q11.21) MUTATED   130  65
  AMP PEAK 29(22Q11.21) WILD-TYPE 135  58
  AMP PEAK 29(22Q11.21) MUTATED AMP PEAK 29(22Q11.21) WILD-TYPE 
                            195                             193 
  AMP PEAK 29(22Q11.21) MUTATED AMP PEAK 29(22Q11.21) WILD-TYPE 
                             65                              58 
$`AMP PEAK 29(22Q11.21) MUTATED`
TCGA-18-3408 TCGA-18-3409 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3421 
        2464         2417         1415          345          396         1331 
TCGA-18-4721 TCGA-18-5595 TCGA-21-1070 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 
        2754          827         3636         3016         2134         1852 
TCGA-21-1077 TCGA-21-1079 TCGA-21-1081 TCGA-21-1083 TCGA-21-5784 TCGA-21-5786 
        1058          965          284          267         1268         1032 
TCGA-22-1002 TCGA-22-1011 TCGA-22-1012 TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 
         131           53          429          623         1067          734 
TCGA-22-4604 TCGA-22-4605 TCGA-22-4613 TCGA-22-5473 TCGA-22-5477 TCGA-22-5478 
         399         1946          358         1933         1346           24 
TCGA-22-5479 TCGA-22-5481 TCGA-22-5482 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 
        1651         1952          357         1713          506           29 
TCGA-33-4532 TCGA-33-4582 TCGA-33-4586 TCGA-33-4589 TCGA-34-2596 TCGA-34-2600 
        2524         1966          428         1948           80         1874 
TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5239 TCGA-34-5240 
         881         1000          951         1528          707          365 
TCGA-34-5241 TCGA-34-5928 TCGA-37-4130 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 
         428          552          247          238          207           12 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5029 TCGA-39-5034 TCGA-39-5036 
        2253         1361         1947          740         1107         1084 
TCGA-39-5037 TCGA-39-5039 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 
        1086          544         1007          349          849          376 
TCGA-43-6647 TCGA-43-6770 TCGA-43-7657 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 
         757          310          236         1971          353          296 
TCGA-46-6025 TCGA-51-4081 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-56-1622 
         324          911         1948          923         1958          881 
TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-7221 TCGA-56-7579 TCGA-56-7580 
           3          555           62           30           44           40 
TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 TCGA-56-8504 
          26            6         1961            1           41          178 
TCGA-56-8622 TCGA-56-8626 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX 
          55           17           34           38            2           46 
TCGA-56-A4ZJ TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8390 TCGA-58-A46M TCGA-58-A46N 
          25            4            8          911         1072          910 
TCGA-60-2695 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 
         642         1950         1943         1958          661         1963 
TCGA-60-2711 TCGA-60-2714 TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 
        1260         1531         1297           97          908         1092 
TCGA-60-2725 TCGA-60-2726 TCGA-63-7020 TCGA-63-7023 TCGA-66-2734 TCGA-66-2737 
         816          358         1957         1952         1311           61 
TCGA-66-2742 TCGA-66-2744 TCGA-66-2755 TCGA-66-2766 TCGA-66-2769 TCGA-66-2773 
         641           30           28           31         1947         1946 
TCGA-66-2777 TCGA-66-2781 TCGA-66-2788 TCGA-66-2791 TCGA-66-2792 TCGA-66-2800 
          61          121          699         1977          913         1492 
TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 TCGA-77-6845 TCGA-77-7139 TCGA-77-7141 
         121          104         1950         1952         1968           15 
TCGA-77-7142 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8008 
        1286         1942         1952         1954          479         1945 
TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8140 TCGA-77-8145 
        1953         1945         1941         1941         1962         1943 
TCGA-77-8150 TCGA-77-8153 TCGA-77-8156 TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 
        1961         1684           10         1942         1959         1955 
TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH 
        1963         1290         1280         1939          839          713 
TCGA-85-6561 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-8052 TCGA-85-8070 
         395           18           10           49           16          960 
TCGA-85-8276 TCGA-85-8277 TCGA-85-8350 TCGA-85-8354 TCGA-85-8580 TCGA-85-A4QQ 
          13           11           60           61          445         1960 
TCGA-85-A4QR TCGA-85-A50M TCGA-85-A510 TCGA-85-A511 TCGA-85-A5B5 TCGA-90-7767 
          25           19         1967         1972          111           89 
TCGA-90-7769 TCGA-92-7341 TCGA-94-7033 TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7545 
         358          106           87          356          430         1344 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-98-8022 TCGA-J1-A4AH TCGA-L3-A524 
         189          211          273          224          222          449 
TCGA-LA-A446 TCGA-NC-A5HG TCGA-NC-A5HI 
          36         1548         1135 

$`AMP PEAK 29(22Q11.21) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3410 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 
         370          136          146         1810          862          758 
TCGA-18-3419 TCGA-18-4083 TCGA-18-4086 TCGA-18-5592 TCGA-21-1071 TCGA-21-1078 
          50          187           85           92         1426          474 
TCGA-21-1080 TCGA-21-1082 TCGA-21-5782 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 
        3724         3644          962          329          979          608 
TCGA-22-0944 TCGA-22-1000 TCGA-22-1005 TCGA-22-1016 TCGA-22-1017 TCGA-22-4594 
         223         1945         1952          822         1485         1470 
TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4607 TCGA-22-5471 TCGA-22-5472 
          17         1161         1057          587          965         1964 
TCGA-22-5474 TCGA-22-5480 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-33-4533 
         445         1952          573          916         1912         1940 
TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4583 TCGA-33-4587 TCGA-33-6738 
        2979         1311         5287         1941         1970          822 
TCGA-34-2604 TCGA-34-5232 TCGA-34-5234 TCGA-34-5927 TCGA-34-8454 TCGA-37-3783 
         958         2062         1715          941          166          120 
TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 TCGA-37-5819 TCGA-39-5011 
          13           12          200          227          103         1454 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 TCGA-39-5031 
        1996         1964         1849           52           59          833 
TCGA-39-5035 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 
         474         1964         1223          684         1176          822 
TCGA-43-6771 TCGA-43-7656 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-A56U 
        1936          212         1970          407          358          432 
TCGA-43-A56V TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-52-7622 TCGA-52-7812 
         366          423           12           12          541         1967 
TCGA-56-6546 TCGA-56-7222 TCGA-56-7223 TCGA-56-8624 TCGA-56-8625 TCGA-56-8628 
          26           13           30           36           63           16 
TCGA-56-A4BY TCGA-56-A4ZK TCGA-58-8388 TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J 
          30            4          378         2167         1058         2589 
TCGA-58-A46L TCGA-60-2696 TCGA-60-2698 TCGA-60-2709 TCGA-60-2710 TCGA-60-2712 
        1723          109          311         1505         1963          274 
TCGA-60-2713 TCGA-60-2715 TCGA-60-2716 TCGA-60-2721 TCGA-60-2724 TCGA-63-6202 
        1731         1075         1475          983          717         1973 
TCGA-63-7021 TCGA-63-7022 TCGA-66-2727 TCGA-66-2753 TCGA-66-2754 TCGA-66-2756 
        1955         1947         1967           31           61           30 
TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2767 
          30          639          762           30           61           61 
TCGA-66-2768 TCGA-66-2770 TCGA-66-2771 TCGA-66-2778 TCGA-66-2780 TCGA-66-2782 
          61          700          578          578         1956         1954 
TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2789 TCGA-66-2790 
         759           60          790         1217         1955          699 
TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 
        1952         1645          122           83          202          211 
TCGA-68-8250 TCGA-68-8251 TCGA-77-6843 TCGA-77-6844 TCGA-77-7138 TCGA-77-7335 
         244           96         1941         1942         1959         1954 
TCGA-77-8007 TCGA-77-8009 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8144 
        1960         1641         1947         1946         1951          833 
TCGA-77-8148 TCGA-77-8154 TCGA-77-A5FZ TCGA-85-6560 TCGA-85-6798 TCGA-85-7699 
         293         1092         1953          364           34            1 
TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 
        1965           35          911           60           26           60 
TCGA-85-8071 TCGA-85-8072 TCGA-85-8287 TCGA-85-8288 TCGA-85-8351 TCGA-85-8352 
         428          513           13           54           55           67 
TCGA-85-8353 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8582 TCGA-85-8664 
          54           61           22           21          424            3 
TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A50Z TCGA-85-A512 TCGA-85-A513 
         475           15         1972         1973         1987           24 
TCGA-85-A53L TCGA-90-6837 TCGA-90-7766 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE 
          13          758          289          428          244          331 
TCGA-90-A59Q TCGA-92-7340 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-96-7544 
         269           82          122          160           70         1213 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8023 TCGA-L3-A4E7 TCGA-MF-A522 
         183          256          413          308           35           83 
TCGA-NC-A5HE 
        1722 

  AMP PEAK 29(22Q11.21) MUTATED AMP PEAK 29(22Q11.21) WILD-TYPE 
                              1                               1 
  AMP PEAK 29(22Q11.21) MUTATED AMP PEAK 29(22Q11.21) WILD-TYPE 
                           3636                            5287 
  AMP PEAK 29(22Q11.21) MUTATED AMP PEAK 29(22Q11.21) WILD-TYPE 
                            740                             541 
[1] "1.0 - 3636.0 (740.0)" "1.0 - 5287.0 (541.0)"
[1] "hr=" "1.1"
D29V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 29(22Q11.21) MUTATED         0       31       74        1        28
  AMP PEAK 29(22Q11.21) WILD-TYPE       1       41       63        0        24
                                 vv
clus                              STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 29(22Q11.21) MUTATED          46         24          8        4
  AMP PEAK 29(22Q11.21) WILD-TYPE        25         33         12        2
D29V3, multiclass
            clus
vv           AMP PEAK 29(22Q11.21) MUTATED AMP PEAK 29(22Q11.21) WILD-TYPE
  STAGE I                                0                               1
  STAGE IA                              31                              41
  STAGE IB                              74                              63
  STAGE II                               1                               0
  STAGE IIA                             28                              24
  STAGE IIB                             46                              25
  STAGE IIIA                            24                              33
  STAGE IIIB                             8                              12
  STAGE IV                               4                               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  AMP PEAK 29(22Q11.21) MUTATED    43 139  27   9
  AMP PEAK 29(22Q11.21) WILD-TYPE  55 115  21  11
D29V4, multiclass
    clus
vv   AMP PEAK 29(22Q11.21) MUTATED AMP PEAK 29(22Q11.21) WILD-TYPE
  T1                            43                              55
  T2                           139                             115
  T3                            27                              21
  T4                             9                              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 29(22Q11.21) MUTATED   139  60  13   1
  AMP PEAK 29(22Q11.21) WILD-TYPE 122  53  22   4
D29V5, multiclass
    clus
vv   AMP PEAK 29(22Q11.21) MUTATED AMP PEAK 29(22Q11.21) WILD-TYPE
  N0                           139                             122
  N1                            60                              53
  N2                            13                              22
  N3                             1                               4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               M0  M1 M1A  MX
  AMP PEAK 29(22Q11.21) MUTATED   191   3   1  21
  AMP PEAK 29(22Q11.21) WILD-TYPE 167   2   0  29
D29V6, multiclass
     clus
vv    AMP PEAK 29(22Q11.21) MUTATED AMP PEAK 29(22Q11.21) WILD-TYPE
  M0                            191                             167
  M1                              3                               2
  M1A                             1                               0
  MX                             21                              29
[1] 4 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(22Q11.21) MUTATED    53 165
  AMP PEAK 29(22Q11.21) WILD-TYPE  54 148
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 29(22Q11.21) MUTATED     53  165
  AMP PEAK 29(22Q11.21) WILD-TYPE   54  148
        clus
vv       AMP PEAK 29(22Q11.21) MUTATED AMP PEAK 29(22Q11.21) WILD-TYPE
  FEMALE                            53                              54
  MALE                             165                             148
[1] 2 2
[1] FALSE
D29V8, continuous
                                 vv
clus                              LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK 29(22Q11.21) MUTATED                                       8
  AMP PEAK 29(22Q11.21) WILD-TYPE                                     4
                                 vv
clus                              LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK 29(22Q11.21) MUTATED                                        1
  AMP PEAK 29(22Q11.21) WILD-TYPE                                      5
                                 vv
clus                              LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 29(22Q11.21) MUTATED                                         0
  AMP PEAK 29(22Q11.21) WILD-TYPE                                       1
                                 vv
clus                              LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 29(22Q11.21) MUTATED                                                           209
  AMP PEAK 29(22Q11.21) WILD-TYPE                                                         192
D29V9, multiclass
                                                             clus
vv                                                            AMP PEAK 29(22Q11.21) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           209
                                                             clus
vv                                                            AMP PEAK 29(22Q11.21) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                     4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                    5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             192
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V10, binary
                                 cls
clus                                0   1
  AMP PEAK 29(22Q11.21) MUTATED     5 213
  AMP PEAK 29(22Q11.21) WILD-TYPE   8 194
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 29(22Q11.21) MUTATED      5  213
  AMP PEAK 29(22Q11.21) WILD-TYPE    8  194
     clus
vv    AMP PEAK 29(22Q11.21) MUTATED AMP PEAK 29(22Q11.21) WILD-TYPE
  NO                              5                               8
  YES                           213                             194
[1] 2 2
[1] FALSE
D29V11, continuous
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 29(22Q11.21) MUTATED   182   6   0   6
  AMP PEAK 29(22Q11.21) WILD-TYPE 160   2   4  12
D29V12, multiclass
    clus
vv   AMP PEAK 29(22Q11.21) MUTATED AMP PEAK 29(22Q11.21) WILD-TYPE
  R0                           182                             160
  R1                             6                               2
  R2                             0                               4
  RX                             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                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 29(22Q11.21) MUTATED       4                         6   161
  AMP PEAK 29(22Q11.21) WILD-TYPE     5                        11   137
D29V13, multiclass
                           clus
vv                          AMP PEAK 29(22Q11.21) MUTATED
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                               161
                           clus
vv                          AMP PEAK 29(22Q11.21) WILD-TYPE
  ASIAN                                                   5
  BLACK OR AFRICAN AMERICAN                              11
  WHITE                                                 137
[1] 3 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(22Q11.21) MUTATED     4 140
  AMP PEAK 29(22Q11.21) WILD-TYPE   4 127
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 29(22Q11.21) MUTATED      4  140
  AMP PEAK 29(22Q11.21) WILD-TYPE    4  127
                        clus
vv                       AMP PEAK 29(22Q11.21) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           140
                        clus
vv                       AMP PEAK 29(22Q11.21) WILD-TYPE
  HISPANIC OR LATINO                                   4
  NOT HISPANIC OR LATINO                             127
[1] 2 2
[1] FALSE

Clustering(30) Variable = AMP PEAK 30(XQ28) MUTATION ANALYSIS
D30V1, survival
                             sevent
clus2                           0   1
  AMP PEAK 30(XQ28) MUTATED    64  33
  AMP PEAK 30(XQ28) WILD-TYPE 201  90
  AMP PEAK 30(XQ28) MUTATED AMP PEAK 30(XQ28) WILD-TYPE 
                         97                         291 
  AMP PEAK 30(XQ28) MUTATED AMP PEAK 30(XQ28) WILD-TYPE 
                         33                          90 
$`AMP PEAK 30(XQ28) MUTATED`
TCGA-18-3407 TCGA-18-3408 TCGA-18-3415 TCGA-18-3417 TCGA-18-3421 TCGA-18-5595 
         136         2464         1810          758         1331          827 
TCGA-21-1081 TCGA-22-0940 TCGA-22-1012 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 
         284          608          429          623         1067         1470 
TCGA-22-4595 TCGA-22-5473 TCGA-22-5477 TCGA-22-5478 TCGA-22-5480 TCGA-22-5481 
         734         1933         1346           24         1952         1952 
TCGA-22-5483 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4547 TCGA-33-4566 TCGA-34-2596 
         573           29         2524         1311         5287           80 
TCGA-34-2604 TCGA-34-2605 TCGA-34-2609 TCGA-34-5240 TCGA-34-5927 TCGA-34-5928 
         958          881          951          365          941          552 
TCGA-34-8454 TCGA-37-3792 TCGA-37-4133 TCGA-37-5819 TCGA-39-5011 TCGA-39-5019 
         166           12          238          103         1454         1361 
TCGA-39-5021 TCGA-39-5028 TCGA-39-5037 TCGA-43-5670 TCGA-43-7657 TCGA-43-8118 
        1947           52         1086          849          236         1971 
TCGA-43-A475 TCGA-51-4079 TCGA-56-7222 TCGA-56-7223 TCGA-56-8504 TCGA-56-8624 
         296           12           13           30          178           36 
TCGA-56-8629 TCGA-56-A49D TCGA-56-A5DR TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 
          34           38            4         1072          910          642 
TCGA-60-2708 TCGA-60-2709 TCGA-60-2724 TCGA-66-2753 TCGA-66-2756 TCGA-66-2758 
        1963         1505          717           31           30          639 
TCGA-66-2766 TCGA-66-2769 TCGA-66-2773 TCGA-66-2778 TCGA-66-2781 TCGA-66-2782 
          31         1947         1946          578          121         1954 
TCGA-66-2792 TCGA-66-2793 TCGA-68-7756 TCGA-77-6842 TCGA-77-6845 TCGA-77-7138 
         913         1952          202         1950         1952         1959 
TCGA-77-7141 TCGA-77-7338 TCGA-77-8009 TCGA-77-8136 TCGA-77-8144 TCGA-77-8156 
          15         1952         1641         1947          833           10 
TCGA-77-A5G3 TCGA-77-A5GA TCGA-77-A5GF TCGA-85-6561 TCGA-85-6798 TCGA-85-8070 
        1959         1280          839          395           34          960 
TCGA-85-8351 TCGA-85-8353 TCGA-85-8354 TCGA-85-A4QR TCGA-85-A50M TCGA-90-7769 
          55           54           61           25           19          358 
TCGA-90-A4EE TCGA-92-8064 TCGA-94-A4VJ TCGA-96-A4JK TCGA-98-8023 TCGA-J1-A4AH 
         331          160          430          273          308          222 
TCGA-LA-A446 
          36 

$`AMP PEAK 30(XQ28) WILD-TYPE`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
         370         2417          146         1415          345          396 
TCGA-18-3416 TCGA-18-3419 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 
         862           50          187           85         2754           92 
TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 
        3636         1426         3016         2134         1852         1058 
TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 
         474          965         3724         3644          267          962 
TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0944 TCGA-22-1000 
        1268         1032          329          979          223         1945 
TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1016 TCGA-22-1017 TCGA-22-4596 
         131         1952           53          822         1485           17 
TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 
        1161         1057          399         1946          587          358 
TCGA-22-5471 TCGA-22-5472 TCGA-22-5474 TCGA-22-5479 TCGA-22-5482 TCGA-22-5485 
         965         1964          445         1651          357          916 
TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4533 TCGA-33-4538 TCGA-33-4582 
        1912         1713          506         1940         2979         1966 
TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-33-6738 TCGA-34-2600 
        1941          428         1970         1948          822         1874 
TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5241 
        1000         1528         2062         1715          707          428 
TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4135 
         120           13          200          247          227          207 
TCGA-37-4141 TCGA-39-5016 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5029 
          12         2253         1996         1964         1849          740 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5039 
          59          833         1107          474         1084          544 
TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 
        1964         1223          684         1176          822         1007 
TCGA-43-5668 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 
         349          376          757          310         1936          212 
TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-A474 TCGA-43-A56U TCGA-43-A56V 
        1970          407          358          353          432          366 
TCGA-46-6025 TCGA-46-6026 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 
         324          423           12          911          541         1948 
TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 
         923         1958         1967          881            3          555 
TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 
          62           26           30           44           40           26 
TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 TCGA-56-8622 TCGA-56-8625 
           6         1961            1           41           55           63 
TCGA-56-8626 TCGA-56-8628 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ 
          17           16            2           46           30           25 
TCGA-56-A4ZK TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8393 
           4            8          378          911         2167         1058 
TCGA-58-A46J TCGA-58-A46L TCGA-60-2696 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 
        2589         1723          109          311         1950         1943 
TCGA-60-2706 TCGA-60-2707 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 
        1958          661         1963         1260          274         1731 
TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 
        1531         1075         1475         1297           97          983 
TCGA-60-2722 TCGA-60-2723 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 
         908         1092          816          358         1973         1957 
TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 
        1955         1947         1952         1967         1311           61 
TCGA-66-2742 TCGA-66-2744 TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 TCGA-66-2759 
         641           30           61           28           30          762 
TCGA-66-2763 TCGA-66-2765 TCGA-66-2767 TCGA-66-2768 TCGA-66-2770 TCGA-66-2771 
          30           61           61           61          700          578 
TCGA-66-2777 TCGA-66-2780 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 
          61         1956          759           60          790         1217 
TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2794 TCGA-66-2795 
         699         1955          699         1977         1645          122 
TCGA-66-2800 TCGA-68-7755 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I 
        1492           83          211          244           96          121 
TCGA-68-A59J TCGA-77-6843 TCGA-77-6844 TCGA-77-7139 TCGA-77-7142 TCGA-77-7335 
         104         1941         1942         1968         1286         1954 
TCGA-77-7337 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8128 
        1942         1954          479         1960         1945         1953 
TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 
        1945         1941         1941         1946         1951         1962 
TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-A5FZ 
        1943          293         1961         1684         1092         1953 
TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GB TCGA-77-A5GH 
        1942         1955         1963         1290         1939          713 
TCGA-85-6560 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 
         364           18           10           49            1         1965 
TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 
          35          911           60           26           60           16 
TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 
         428          513           13           11           13           54 
TCGA-85-8350 TCGA-85-8352 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 
          60           67           61           22           21          445 
TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QQ 
         424            3          475           15         1972         1960 
TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L 
        1973         1967         1972         1987           24           13 
TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7964 TCGA-90-A4ED 
         111          758          289           89          428          244 
TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8065 TCGA-94-7033 
         269           82          106          122           70           87 
TCGA-94-7943 TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL 
         356         1213         1344          189          211          183 
TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-L3-A4E7 TCGA-L3-A524 TCGA-MF-A522 
         256          413          224           35          449           83 
TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HI 
        1722         1548         1135 

  AMP PEAK 30(XQ28) MUTATED AMP PEAK 30(XQ28) WILD-TYPE 
                          4                           1 
  AMP PEAK 30(XQ28) MUTATED AMP PEAK 30(XQ28) WILD-TYPE 
                       5287                        3724 
  AMP PEAK 30(XQ28) MUTATED AMP PEAK 30(XQ28) WILD-TYPE 
                        623                         684 
[1] "4.0 - 5287.0 (623.0)" "1.0 - 3724.0 (684.0)"
[1] "hr=" "1.3"
D30V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 30(XQ28) MUTATED         0        9       36        0        14
  AMP PEAK 30(XQ28) WILD-TYPE       1       63      101        1        38
                             vv
clus                          STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 30(XQ28) MUTATED          21         13          7        2
  AMP PEAK 30(XQ28) WILD-TYPE        50         44         13        4
D30V3, multiclass
            clus
vv           AMP PEAK 30(XQ28) MUTATED AMP PEAK 30(XQ28) WILD-TYPE
  STAGE I                            0                           1
  STAGE IA                           9                          63
  STAGE IB                          36                         101
  STAGE II                           0                           1
  STAGE IIA                         14                          38
  STAGE IIB                         21                          50
  STAGE IIIA                        13                          44
  STAGE IIIB                         7                          13
  STAGE IV                           2                           4
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2  T3  T4
  AMP PEAK 30(XQ28) MUTATED    12  66  17   8
  AMP PEAK 30(XQ28) WILD-TYPE  86 188  31  12
D30V4, multiclass
    clus
vv   AMP PEAK 30(XQ28) MUTATED AMP PEAK 30(XQ28) WILD-TYPE
  T1                        12                          86
  T2                        66                         188
  T3                        17                          31
  T4                         8                          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 30(XQ28) MUTATED    61  33   6   1
  AMP PEAK 30(XQ28) WILD-TYPE 200  80  29   4
D30V5, multiclass
    clus
vv   AMP PEAK 30(XQ28) MUTATED AMP PEAK 30(XQ28) WILD-TYPE
  N0                        61                         200
  N1                        33                          80
  N2                         6                          29
  N3                         1                           4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           M0  M1 M1A  MX
  AMP PEAK 30(XQ28) MUTATED    84   2   0  14
  AMP PEAK 30(XQ28) WILD-TYPE 274   3   1  36
D30V6, multiclass
     clus
vv    AMP PEAK 30(XQ28) MUTATED AMP PEAK 30(XQ28) WILD-TYPE
  M0                         84                         274
  M1                          2                           3
  M1A                         0                           1
  MX                         14                          36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V7, binary
                             cls
clus                            0   1
  AMP PEAK 30(XQ28) MUTATED    22  81
  AMP PEAK 30(XQ28) WILD-TYPE  85 232
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 30(XQ28) MUTATED     22   81
  AMP PEAK 30(XQ28) WILD-TYPE   85  232
        clus
vv       AMP PEAK 30(XQ28) MUTATED AMP PEAK 30(XQ28) WILD-TYPE
  FEMALE                        22                          85
  MALE                          81                         232
[1] 2 2
[1] FALSE
D30V8, continuous
                             vv
clus                          LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK 30(XQ28) MUTATED                                       3
  AMP PEAK 30(XQ28) WILD-TYPE                                     9
                             vv
clus                          LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK 30(XQ28) MUTATED                                        1
  AMP PEAK 30(XQ28) WILD-TYPE                                      5
                             vv
clus                          LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 30(XQ28) MUTATED                                         0
  AMP PEAK 30(XQ28) WILD-TYPE                                       1
                             vv
clus                          LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 30(XQ28) MUTATED                                                            99
  AMP PEAK 30(XQ28) WILD-TYPE                                                         302
D30V9, multiclass
                                                             clus
vv                                                            AMP PEAK 30(XQ28) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                               3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                              1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                             0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                        99
                                                             clus
vv                                                            AMP PEAK 30(XQ28) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         302
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V10, binary
                             cls
clus                            0   1
  AMP PEAK 30(XQ28) MUTATED     3 100
  AMP PEAK 30(XQ28) WILD-TYPE  10 307
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 30(XQ28) MUTATED      3  100
  AMP PEAK 30(XQ28) WILD-TYPE   10  307
     clus
vv    AMP PEAK 30(XQ28) MUTATED AMP PEAK 30(XQ28) WILD-TYPE
  NO                          3                          10
  YES                       100                         307
[1] 2 2
[1] FALSE
D30V11, continuous
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK 30(XQ28) MUTATED    85   4   1   2
  AMP PEAK 30(XQ28) WILD-TYPE 257   4   3  16
D30V12, multiclass
    clus
vv   AMP PEAK 30(XQ28) MUTATED AMP PEAK 30(XQ28) WILD-TYPE
  R0                        85                         257
  R1                         4                           4
  R2                         1                           3
  RX                         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                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 30(XQ28) MUTATED       3                         4    71
  AMP PEAK 30(XQ28) WILD-TYPE     6                        13   227
D30V13, multiclass
                           clus
vv                          AMP PEAK 30(XQ28) MUTATED
  ASIAN                                             3
  BLACK OR AFRICAN AMERICAN                         4
  WHITE                                            71
                           clus
vv                          AMP PEAK 30(XQ28) WILD-TYPE
  ASIAN                                               6
  BLACK OR AFRICAN AMERICAN                          13
  WHITE                                             227
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V14, binary
                             cls
clus                            0   1
  AMP PEAK 30(XQ28) MUTATED     0  65
  AMP PEAK 30(XQ28) WILD-TYPE   8 202
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 30(XQ28) MUTATED      0   65
  AMP PEAK 30(XQ28) WILD-TYPE    8  202
                        clus
vv                       AMP PEAK 30(XQ28) MUTATED AMP PEAK 30(XQ28) WILD-TYPE
  HISPANIC OR LATINO                             0                           8
  NOT HISPANIC OR LATINO                        65                         202
[1] 2 2
[1] FALSE

Clustering(31) Variable = DEL PEAK  1(1P36.11) MUTATION ANALYSIS
D31V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  1(1P36.11) MUTATED   123  53
  DEL PEAK  1(1P36.11) WILD-TYPE 142  70
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           176                            212 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            53                             70 
$`DEL PEAK  1(1P36.11) MUTATED`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 
         370         2464         1415          345          396         1810 
TCGA-18-4083 TCGA-18-4721 TCGA-18-5592 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 
         187         2754           92         1426         3016         2134 
TCGA-21-1077 TCGA-21-1079 TCGA-21-1082 TCGA-21-1083 TCGA-21-5786 TCGA-21-5787 
        1058          965         3644          267         1032          329 
TCGA-22-0940 TCGA-22-0944 TCGA-22-1017 TCGA-22-4593 TCGA-22-4596 TCGA-22-4599 
         608          223         1485         1067           17         1161 
TCGA-22-4601 TCGA-22-4604 TCGA-22-5471 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 
        1057          399          965         1933          445         1346 
TCGA-22-5479 TCGA-22-5483 TCGA-22-5491 TCGA-33-4533 TCGA-33-4538 TCGA-33-4582 
        1651          573         1713         1940         2979         1966 
TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-34-2596 TCGA-34-2600 TCGA-34-2605 
        1941          428         1970           80         1874          881 
TCGA-34-2608 TCGA-34-5231 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4133 
        1000         1528           12          200          247          238 
TCGA-37-5819 TCGA-39-5016 TCGA-39-5027 TCGA-39-5031 TCGA-39-5036 TCGA-39-5037 
         103         2253         1849          833         1084         1086 
TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-6770 TCGA-43-7657 TCGA-43-8118 
        1223         1176          822          310          236         1971 
TCGA-43-A474 TCGA-43-A56V TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 
         353          366          324          423           12           12 
TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 
         911          541         1948          923         1958         1967 
TCGA-56-1622 TCGA-56-5898 TCGA-56-6545 TCGA-56-7221 TCGA-56-7223 TCGA-56-7580 
         881          555           62           30           30           40 
TCGA-56-7582 TCGA-56-7730 TCGA-56-7822 TCGA-56-A4BX TCGA-56-A4ZK TCGA-58-8390 
          26            6            1           46            4          911 
TCGA-58-8391 TCGA-58-8393 TCGA-58-A46L TCGA-58-A46M TCGA-60-2698 TCGA-60-2706 
        2167         1058         1723         1072          311         1958 
TCGA-60-2707 TCGA-60-2708 TCGA-60-2711 TCGA-60-2713 TCGA-60-2714 TCGA-60-2722 
         661         1963         1260         1731         1531          908 
TCGA-60-2726 TCGA-63-7023 TCGA-66-2737 TCGA-66-2742 TCGA-66-2755 TCGA-66-2758 
         358         1952           61          641           28          639 
TCGA-66-2766 TCGA-66-2767 TCGA-66-2770 TCGA-66-2773 TCGA-66-2777 TCGA-66-2780 
          31           61          700         1946           61         1956 
TCGA-66-2781 TCGA-66-2785 TCGA-66-2787 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 
         121           60         1217          699         1977          913 
TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7757 
        1952         1645          122         1492           83          211 
TCGA-68-A59J TCGA-77-6843 TCGA-77-6845 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 
         104         1941         1952         1968           15         1286 
TCGA-77-7338 TCGA-77-7465 TCGA-77-8009 TCGA-77-8128 TCGA-77-8133 TCGA-77-8144 
        1952          479         1641         1953         1941          833 
TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-A5G3 TCGA-77-A5G8 
        1943          293         1961         1684         1959         1290 
TCGA-77-A5GF TCGA-85-6561 TCGA-85-7696 TCGA-85-7698 TCGA-85-7699 TCGA-85-8049 
         839          395           18           49            1           60 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8277 TCGA-85-8287 
          16          960          428          513           11           13 
TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8580 TCGA-85-A4CL TCGA-85-A4QR 
          55           67           54          445           15           25 
TCGA-85-A511 TCGA-85-A512 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-A4ED TCGA-90-A4EE 
        1972         1987           13          111          244          331 
TCGA-92-7341 TCGA-92-8064 TCGA-94-7943 TCGA-96-7545 TCGA-96-A4JK TCGA-98-8021 
         106          160          356         1344          273          413 
TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE 
         308          222          449           36           83         1722 
TCGA-NC-A5HG TCGA-NC-A5HI 
        1548         1135 

$`DEL PEAK  1(1P36.11) WILD-TYPE`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 
         136         2417          146          862          758           50 
TCGA-18-3421 TCGA-18-4086 TCGA-18-5595 TCGA-21-1070 TCGA-21-1076 TCGA-21-1078 
        1331           85          827         3636         1852          474 
TCGA-21-1080 TCGA-21-1081 TCGA-21-5782 TCGA-21-5784 TCGA-21-A5DI TCGA-22-1000 
        3724          284          962         1268          979         1945 
TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 
         131         1952           53          429          822          623 
TCGA-22-4594 TCGA-22-4595 TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 TCGA-22-5472 
        1470          734         1946          587          358         1964 
TCGA-22-5478 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 
          24         1952         1952          357          916         1912 
TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4547 TCGA-33-4566 TCGA-33-4589 
         506           29         2524         1311         5287         1948 
TCGA-33-6738 TCGA-34-2604 TCGA-34-2609 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 
         822          958          951         2062         1715          707 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 
         365          428          941          552          166          120 
TCGA-37-3789 TCGA-37-4132 TCGA-37-4135 TCGA-37-4141 TCGA-39-5011 TCGA-39-5019 
          13          227          207           12         1454         1361 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 
        1947         1996         1964           52          740           59 
TCGA-39-5034 TCGA-39-5035 TCGA-39-5039 TCGA-39-5040 TCGA-43-2578 TCGA-43-3920 
        1107          474          544         1964          684         1007 
TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6771 TCGA-43-7656 
         349          849          376          757         1936          212 
TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-A475 TCGA-43-A56U TCGA-56-5897 
        1970          407          358          296          432            3 
TCGA-56-6546 TCGA-56-7222 TCGA-56-7579 TCGA-56-7731 TCGA-56-8503 TCGA-56-8504 
          26           13           44         1961           41          178 
TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 
          55           36           63           17           16           34 
TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR TCGA-56-A5DS 
          38            2           30           25            4            8 
TCGA-58-8388 TCGA-58-A46J TCGA-58-A46N TCGA-60-2695 TCGA-60-2696 TCGA-60-2703 
         378         2589          910          642          109         1950 
TCGA-60-2704 TCGA-60-2709 TCGA-60-2710 TCGA-60-2712 TCGA-60-2715 TCGA-60-2716 
        1943         1505         1963          274         1075         1475 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 
        1297           97          983         1092          717          816 
TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-66-2727 TCGA-66-2734 
        1973         1957         1955         1947         1967         1311 
TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2756 TCGA-66-2757 TCGA-66-2759 
          30           31           61           30           30          762 
TCGA-66-2763 TCGA-66-2765 TCGA-66-2768 TCGA-66-2769 TCGA-66-2771 TCGA-66-2778 
          30           61           61         1947          578          578 
TCGA-66-2782 TCGA-66-2783 TCGA-66-2786 TCGA-66-2788 TCGA-66-2789 TCGA-68-7756 
        1954          759          790          699         1955          202 
TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-77-6842 TCGA-77-6844 TCGA-77-7138 
         244           96          121         1950         1942         1959 
TCGA-77-7335 TCGA-77-7337 TCGA-77-7463 TCGA-77-8007 TCGA-77-8008 TCGA-77-8130 
        1954         1942         1954         1960         1945         1945 
TCGA-77-8131 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8154 
        1941         1947         1946         1951         1962         1092 
TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5GA 
          10         1953         1942         1955         1963         1280 
TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6560 TCGA-85-6798 TCGA-85-7697 TCGA-85-7710 
        1939          713          364           34           10         1965 
TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8276 TCGA-85-8288 
          35          911           60           26           13           54 
TCGA-85-8350 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8582 
          60           61           61           22           21          424 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A50Z 
           3          475         1972         1960           19         1973 
TCGA-85-A510 TCGA-85-A513 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 
        1967           24          758          289           89          358 
TCGA-90-7964 TCGA-90-A59Q TCGA-92-7340 TCGA-92-8063 TCGA-92-8065 TCGA-94-7033 
         428          269           82          122           70           87 
TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 
         430         1213          189          211          183          256 
TCGA-98-8022 TCGA-L3-A4E7 
         224           35 

  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                             1                              2 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                          3644                           5287 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           680                            605 
[1] "1.0 - 3644.0 (680.0)" "2.0 - 5287.0 (605.0)"
[1] "hr=" "1.1"
D31V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  1(1P36.11) MUTATED         0       29       64        1        26
  DEL PEAK  1(1P36.11) WILD-TYPE       1       43       73        0        26
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK  1(1P36.11) MUTATED          28         28         10        2
  DEL PEAK  1(1P36.11) WILD-TYPE        43         29         10        4
D31V3, multiclass
            clus
vv           DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  STAGE I                               0                              1
  STAGE IA                             29                             43
  STAGE IB                             64                             73
  STAGE II                              1                              0
  STAGE IIA                            26                             26
  STAGE IIB                            28                             43
  STAGE IIIA                           28                             29
  STAGE IIIB                           10                             10
  STAGE IV                              2                              4
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK  1(1P36.11) MUTATED    42 115  21  11
  DEL PEAK  1(1P36.11) WILD-TYPE  56 139  27   9
D31V4, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  T1                           42                             56
  T2                          115                            139
  T3                           21                             27
  T4                           11                              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  1(1P36.11) MUTATED   113  57  15   2
  DEL PEAK  1(1P36.11) WILD-TYPE 148  56  20   3
D31V5, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  N0                          113                            148
  N1                           57                             56
  N2                           15                             20
  N3                            2                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A  MX
  DEL PEAK  1(1P36.11) MUTATED   168   2   0  16
  DEL PEAK  1(1P36.11) WILD-TYPE 190   3   1  34
D31V6, multiclass
     clus
vv    DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  M0                           168                            190
  M1                             2                              3
  M1A                            0                              1
  MX                            16                             34
[1] 4 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  1(1P36.11) MUTATED    36 153
  DEL PEAK  1(1P36.11) WILD-TYPE  71 160
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED     36  153
  DEL PEAK  1(1P36.11) WILD-TYPE   71  160
        clus
vv       DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  FEMALE                           36                             71
  MALE                            153                            160
[1] 2 2
[1] FALSE
D31V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK  1(1P36.11) MUTATED                                       6
  DEL PEAK  1(1P36.11) WILD-TYPE                                     6
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK  1(1P36.11) MUTATED                                        1
  DEL PEAK  1(1P36.11) WILD-TYPE                                      5
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK  1(1P36.11) MUTATED                                         1
  DEL PEAK  1(1P36.11) WILD-TYPE                                       0
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  1(1P36.11) MUTATED                                                           181
  DEL PEAK  1(1P36.11) WILD-TYPE                                                         220
D31V9, multiclass
                                                             clus
vv                                                            DEL PEAK  1(1P36.11) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          181
                                                             clus
vv                                                            DEL PEAK  1(1P36.11) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V10, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED     7 182
  DEL PEAK  1(1P36.11) WILD-TYPE   6 225
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED      7  182
  DEL PEAK  1(1P36.11) WILD-TYPE    6  225
     clus
vv    DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  NO                             7                              6
  YES                          182                            225
[1] 2 2
[1] FALSE
D31V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK  1(1P36.11) MUTATED   160   4   2   7
  DEL PEAK  1(1P36.11) WILD-TYPE 182   4   2  11
D31V12, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  R0                          160                            182
  R1                            4                              4
  R2                            2                              2
  RX                            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                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1P36.11) MUTATED       4                         8   137
  DEL PEAK  1(1P36.11) WILD-TYPE     5                         9   161
D31V13, multiclass
                           clus
vv                          DEL PEAK  1(1P36.11) MUTATED
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                            8
  WHITE                                              137
                           clus
vv                          DEL PEAK  1(1P36.11) WILD-TYPE
  ASIAN                                                  5
  BLACK OR AFRICAN AMERICAN                              9
  WHITE                                                161
[1] 3 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  1(1P36.11) MUTATED     5 118
  DEL PEAK  1(1P36.11) WILD-TYPE   3 149
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED      5  118
  DEL PEAK  1(1P36.11) WILD-TYPE    3  149
                        clus
vv                       DEL PEAK  1(1P36.11) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          118
                        clus
vv                       DEL PEAK  1(1P36.11) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            149
[1] 2 2
[1] FALSE

Clustering(32) Variable = DEL PEAK  2(1P13.1) MUTATION ANALYSIS
D32V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  2(1P13.1) MUTATED   120  55
  DEL PEAK  2(1P13.1) WILD-TYPE 145  68
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                          175                           213 
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                           55                            68 
$`DEL PEAK  2(1P13.1) MUTATED`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3421 
         370         2464          345          396         1810         1331 
TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 
        2754           92         3636         1426         3016         2134 
TCGA-21-1076 TCGA-21-1077 TCGA-21-1079 TCGA-21-5786 TCGA-22-0940 TCGA-22-0944 
        1852         1058          965         1032          608          223 
TCGA-22-1012 TCGA-22-1017 TCGA-22-4593 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 
         429         1485         1067           17         1161         1057 
TCGA-22-4604 TCGA-22-5471 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 
         399          965         1933          445         1346         1651 
TCGA-22-5481 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-A5C4 TCGA-33-4538 
        1952          573          916         1912           29         2979 
TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-34-2596 TCGA-34-2600 TCGA-34-2605 
        1966         1941          428           80         1874          881 
TCGA-34-2608 TCGA-34-5231 TCGA-37-4129 TCGA-37-5819 TCGA-39-5016 TCGA-39-5029 
        1000         1528          200          103         2253          740 
TCGA-39-5034 TCGA-39-5037 TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 
        1107         1086          684         1176          822         1007 
TCGA-43-6143 TCGA-43-7657 TCGA-43-7658 TCGA-43-A474 TCGA-43-A56V TCGA-46-6025 
         376          236         1970          353          366          324 
TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 
         423           12           12          911          541         1948 
TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5898 TCGA-56-6545 
         923         1958         1967          881          555           62 
TCGA-56-7221 TCGA-56-7223 TCGA-56-7730 TCGA-56-7822 TCGA-56-8625 TCGA-56-A49D 
          30           30            6            1           63           38 
TCGA-56-A4BX TCGA-56-A4ZK TCGA-58-8391 TCGA-58-8393 TCGA-58-A46L TCGA-58-A46M 
          46            4         2167         1058         1723         1072 
TCGA-60-2698 TCGA-60-2707 TCGA-60-2708 TCGA-60-2714 TCGA-60-2719 TCGA-60-2721 
         311          661         1963         1531         1297          983 
TCGA-60-2722 TCGA-60-2726 TCGA-66-2727 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 
         908          358         1967           61           28           30 
TCGA-66-2758 TCGA-66-2763 TCGA-66-2766 TCGA-66-2767 TCGA-66-2770 TCGA-66-2771 
         639           30           31           61          700          578 
TCGA-66-2773 TCGA-66-2777 TCGA-66-2781 TCGA-66-2787 TCGA-66-2790 TCGA-66-2791 
        1946           61          121         1217          699         1977 
TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 
         913         1952         1645          122         1492           83 
TCGA-68-A59J TCGA-77-6843 TCGA-77-6845 TCGA-77-7139 TCGA-77-7141 TCGA-77-7338 
         104         1941         1952         1968           15         1952 
TCGA-77-7463 TCGA-77-7465 TCGA-77-8009 TCGA-77-8128 TCGA-77-8133 TCGA-77-8136 
        1954          479         1641         1953         1941         1947 
TCGA-77-8145 TCGA-77-8148 TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5G8 TCGA-77-A5GA 
        1943          293           10         1959         1290         1280 
TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6561 TCGA-85-7696 TCGA-85-7710 TCGA-85-7843 
         839          713          395           18         1965           35 
TCGA-85-7950 TCGA-85-8049 TCGA-85-8052 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 
          60           60           16          428          513           13 
TCGA-85-8277 TCGA-85-8287 TCGA-85-8352 TCGA-85-8353 TCGA-85-8664 TCGA-85-A4CL 
          11           13           67           54            3           15 
TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A511 TCGA-85-A512 TCGA-85-A53L TCGA-85-A5B5 
          25         1973         1972         1987           13          111 
TCGA-90-7767 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7341 TCGA-92-8064 TCGA-94-7943 
          89          331          269          106          160          356 
TCGA-94-A4VJ TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-A4JK TCGA-98-8021 
         430         1213         1344          189          273          413 
TCGA-98-8022 TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A524 TCGA-MF-A522 TCGA-NC-A5HE 
         224          308          222          449           83         1722 
TCGA-NC-A5HG 
        1548 

$`DEL PEAK  2(1P13.1) WILD-TYPE`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3416 TCGA-18-3417 
         136         2417          146         1415          862          758 
TCGA-18-3419 TCGA-18-4083 TCGA-18-4086 TCGA-18-5595 TCGA-21-1078 TCGA-21-1080 
          50          187           85          827          474         3724 
TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 TCGA-21-5787 
         284         3644          267          962         1268          329 
TCGA-21-A5DI TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1016 
         979         1945          131         1952           53          822 
TCGA-22-4591 TCGA-22-4594 TCGA-22-4595 TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 
         623         1470          734         1946          587          358 
TCGA-22-5472 TCGA-22-5478 TCGA-22-5480 TCGA-22-5482 TCGA-22-5491 TCGA-22-5492 
        1964           24         1952          357         1713          506 
TCGA-33-4532 TCGA-33-4533 TCGA-33-4547 TCGA-33-4566 TCGA-33-4587 TCGA-33-4589 
        2524         1940         1311         5287         1970         1948 
TCGA-33-6738 TCGA-34-2604 TCGA-34-2609 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 
         822          958          951         2062         1715          707 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 
         365          428          941          552          166          120 
TCGA-37-3789 TCGA-37-3792 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 
          13           12          247          227          238          207 
TCGA-37-4141 TCGA-39-5011 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 
          12         1454         1361         1947         1996         1964 
TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 
        1849           52           59          833          474         1084 
TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-5668 TCGA-43-5670 TCGA-43-6647 
         544         1964         1223          349          849          757 
TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 
         310         1936          212          407          358         1971 
TCGA-43-A475 TCGA-43-A56U TCGA-56-5897 TCGA-56-6546 TCGA-56-7222 TCGA-56-7579 
         296          432            3           26           13           44 
TCGA-56-7580 TCGA-56-7582 TCGA-56-7731 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 
          40           26         1961           41          178           55 
TCGA-56-8624 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BY 
          36           17           16           34            2           30 
TCGA-56-A4ZJ TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 TCGA-58-A46J 
          25            4            8          378          911         2589 
TCGA-58-A46N TCGA-60-2695 TCGA-60-2696 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 
         910          642          109         1950         1943         1958 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2715 
        1505         1963         1260          274         1731         1075 
TCGA-60-2716 TCGA-60-2720 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-63-6202 
        1475           97         1092          717          816         1973 
TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-66-2734 TCGA-66-2737 
        1957         1955         1947         1952         1311           61 
TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2757 TCGA-66-2759 TCGA-66-2765 
         641           30           31           30          762           61 
TCGA-66-2768 TCGA-66-2769 TCGA-66-2778 TCGA-66-2780 TCGA-66-2782 TCGA-66-2783 
          61         1947          578         1956         1954          759 
TCGA-66-2785 TCGA-66-2786 TCGA-66-2788 TCGA-66-2789 TCGA-68-7756 TCGA-68-7757 
          60          790          699         1955          202          211 
TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-77-6842 TCGA-77-6844 TCGA-77-7138 
         244           96          121         1950         1942         1959 
TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-8007 TCGA-77-8008 TCGA-77-8130 
        1286         1954         1942         1960         1945         1945 
TCGA-77-8131 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8150 
        1941         1946         1951         1962          833         1961 
TCGA-77-8153 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 
        1684         1092         1953         1942         1955         1963 
TCGA-77-A5GB TCGA-85-6560 TCGA-85-6798 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 
        1939          364           34           10           49            1 
TCGA-85-7844 TCGA-85-8048 TCGA-85-8070 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 
         911           26          960           54           60           55 
TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 
          61           61           22           21          445          424 
TCGA-85-8666 TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A510 TCGA-85-A513 
         475         1972         1960           19         1967           24 
TCGA-90-6837 TCGA-90-7766 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED TCGA-92-7340 
         758          289          358          428          244           82 
TCGA-92-8063 TCGA-92-8065 TCGA-94-7033 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 
         122           70           87          211          183          256 
TCGA-L3-A4E7 TCGA-LA-A446 TCGA-NC-A5HI 
          35           36         1135 

  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                            1                             1 
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                         3636                          5287 
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                          661                           641 
[1] "1.0 - 3636.0 (661.0)" "1.0 - 5287.0 (641.0)"
[1] "hr=" "1"  
D32V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  2(1P13.1) MUTATED         0       30       56        1        28
  DEL PEAK  2(1P13.1) WILD-TYPE       1       42       81        0        24
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK  2(1P13.1) MUTATED          34         26         10        1
  DEL PEAK  2(1P13.1) WILD-TYPE        37         31         10        5
D32V3, multiclass
            clus
vv           DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  STAGE I                              0                             1
  STAGE IA                            30                            42
  STAGE IB                            56                            81
  STAGE II                             1                             0
  STAGE IIA                           28                            24
  STAGE IIB                           34                            37
  STAGE IIIA                          26                            31
  STAGE IIIB                          10                            10
  STAGE IV                             1                             5
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK  2(1P13.1) MUTATED    43 111  23  10
  DEL PEAK  2(1P13.1) WILD-TYPE  55 143  25  10
D32V4, multiclass
    clus
vv   DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  T1                          43                            55
  T2                         111                           143
  T3                          23                            25
  T4                          10                            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   108  61  14   2
  DEL PEAK  2(1P13.1) WILD-TYPE 153  52  21   3
D32V5, multiclass
    clus
vv   DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  N0                         108                           153
  N1                          61                            52
  N2                          14                            21
  N3                           2                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A  MX
  DEL PEAK  2(1P13.1) MUTATED   167   1   0  16
  DEL PEAK  2(1P13.1) WILD-TYPE 191   4   1  34
D32V6, multiclass
     clus
vv    DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  M0                          167                           191
  M1                            1                             4
  M1A                           0                             1
  MX                           16                            34
[1] 4 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  2(1P13.1) MUTATED    41 146
  DEL PEAK  2(1P13.1) WILD-TYPE  66 167
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.1) MUTATED     41  146
  DEL PEAK  2(1P13.1) WILD-TYPE   66  167
        clus
vv       DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  FEMALE                          41                            66
  MALE                           146                           167
[1] 2 2
[1] FALSE
D32V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK  2(1P13.1) MUTATED                                       6
  DEL PEAK  2(1P13.1) WILD-TYPE                                     6
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK  2(1P13.1) MUTATED                                        2
  DEL PEAK  2(1P13.1) WILD-TYPE                                      4
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK  2(1P13.1) MUTATED                                         0
  DEL PEAK  2(1P13.1) WILD-TYPE                                       1
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  2(1P13.1) MUTATED                                                           179
  DEL PEAK  2(1P13.1) WILD-TYPE                                                         222
D32V9, multiclass
                                                             clus
vv                                                            DEL PEAK  2(1P13.1) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         179
                                                             clus
vv                                                            DEL PEAK  2(1P13.1) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           222
[1] 4 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  2(1P13.1) MUTATED     4 183
  DEL PEAK  2(1P13.1) WILD-TYPE   9 224
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.1) MUTATED      4  183
  DEL PEAK  2(1P13.1) WILD-TYPE    9  224
     clus
vv    DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  NO                            4                             9
  YES                         183                           224
[1] 2 2
[1] FALSE
D32V11, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  2(1P13.1) MUTATED   156   4   2   8
  DEL PEAK  2(1P13.1) WILD-TYPE 186   4   2  10
D32V12, multiclass
    clus
vv   DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  R0                         156                           186
  R1                           4                             4
  R2                           2                             2
  RX                           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                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(1P13.1) MUTATED       3                         6   139
  DEL PEAK  2(1P13.1) WILD-TYPE     6                        11   159
D32V13, multiclass
                           clus
vv                          DEL PEAK  2(1P13.1) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           6
  WHITE                                             139
                           clus
vv                          DEL PEAK  2(1P13.1) WILD-TYPE
  ASIAN                                                 6
  BLACK OR AFRICAN AMERICAN                            11
  WHITE                                               159
[1] 3 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  2(1P13.1) MUTATED     6 114
  DEL PEAK  2(1P13.1) WILD-TYPE   2 153
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.1) MUTATED      6  114
  DEL PEAK  2(1P13.1) WILD-TYPE    2  153
                        clus
vv                       DEL PEAK  2(1P13.1) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                         114
                        clus
vv                       DEL PEAK  2(1P13.1) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           153
[1] 2 2
[1] FALSE

Clustering(33) Variable = DEL PEAK  3(2P25.3) MUTATION ANALYSIS
D33V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  3(2P25.3) MUTATED    24  15
  DEL PEAK  3(2P25.3) WILD-TYPE 241 108
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                           39                           349 
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                           15                           108 
$`DEL PEAK  3(2P25.3) MUTATED`
TCGA-18-3406 TCGA-18-3414 TCGA-18-3421 TCGA-22-4594 TCGA-22-4601 TCGA-22-5489 
         370          396         1331         1470         1057         1912 
TCGA-33-4587 TCGA-37-4135 TCGA-37-5819 TCGA-39-5011 TCGA-39-5028 TCGA-39-5029 
        1970          207          103         1454           52          740 
TCGA-39-5031 TCGA-39-5034 TCGA-43-2578 TCGA-43-7657 TCGA-52-7810 TCGA-56-1622 
         833         1107          684          236          923          881 
TCGA-56-A49D TCGA-60-2713 TCGA-60-2722 TCGA-60-2726 TCGA-66-2756 TCGA-66-2766 
          38         1731          908          358           30           31 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2791 TCGA-68-A59J TCGA-77-7337 TCGA-77-8130 
        1956          121         1977          104         1942         1945 
TCGA-77-8153 TCGA-77-A5GH TCGA-85-7699 TCGA-85-7710 TCGA-85-8352 TCGA-85-8354 
        1684          713            1         1965           67           61 
TCGA-85-A511 TCGA-92-8063 TCGA-96-A4JL 
        1972          122          183 

$`DEL PEAK  3(2P25.3) WILD-TYPE`
TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 
         136         2464         2417          146         1415          345 
TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-4083 TCGA-18-4086 
        1810          862          758           50          187           85 
TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 
        2754           92          827         3636         1426         3016 
TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 
        2134         1852         1058          474          965         3724 
TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 
         284         3644          267          962         1268         1032 
TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 
         329          979          608          223         1945          131 
TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 
        1952           53          429          822         1485          623 
TCGA-22-4593 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4604 TCGA-22-4605 
        1067          734           17         1161          399         1946 
TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 
         587          358          965         1964         1933          445 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 
        1346           24         1651         1952         1952          357 
TCGA-22-5483 TCGA-22-5485 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 
         573          916         1713          506           29         2524 
TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 
        1940         2979         1311         5287         1966         1941 
TCGA-33-4586 TCGA-33-4589 TCGA-33-6738 TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 
         428         1948          822           80         1874          958 
TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 
         881         1000          951         1528         2062         1715 
TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-8454 
         707          365          428          941          552          166 
TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 
         120           13           12          200          247          227 
TCGA-37-4133 TCGA-37-4141 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 
         238           12         2253         1361         1947         1996 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5030 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 
        1964         1849           59          474         1084         1086 
TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 
         544         1964         1223         1176          822         1007 
TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 
         349          849          376          757          310         1936 
TCGA-43-7656 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 
         212         1970          407          358         1971          353 
TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 
         296          432          366          324          423           12 
TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7811 TCGA-52-7812 
          12          911          541         1948         1958         1967 
TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 
           3          555           62           26           30           13 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 
          30           44           40           26            6         1961 
TCGA-56-7822 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 
           1           41          178           55           36           63 
TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY 
          17           16           34            2           46           30 
TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 
          25            4            4            8          378          911 
TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N 
        2167         1058         2589         1723         1072          910 
TCGA-60-2695 TCGA-60-2696 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 
         642          109          311         1950         1943         1958 
TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 
         661         1963         1505         1963         1260          274 
TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 
        1531         1075         1475         1297           97          983 
TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 
        1092          717          816         1973         1957         1955 
TCGA-63-7022 TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 
        1947         1952         1967         1311           61          641 
TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 TCGA-66-2758 
          30           31           61           28           30          639 
TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 
         762           30           61           61           61         1947 
TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2782 
         700          578         1946           61          578         1954 
TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 
         759           60          790         1217          699         1955 
TCGA-66-2790 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 
         699          913         1952         1645          122         1492 
TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I 
          83          202          211          244           96          121 
TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 
        1950         1941         1942         1952         1959         1968 
TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 
          15         1286         1954         1952         1954          479 
TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8131 TCGA-77-8133 
        1960         1945         1641         1953         1941         1941 
TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 
        1947         1946         1951         1962          833         1943 
TCGA-77-8148 TCGA-77-8150 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 
         293         1961         1092           10         1953         1942 
TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB 
        1959         1955         1963         1290         1280         1939 
TCGA-77-A5GF TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 
         839          364          395           34           18           10 
TCGA-85-7698 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 
          49           35          911           60           26           60 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 
          16          960          428          513           13           11 
TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 TCGA-85-8355 
          13           54           60           55           54           61 
TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 
          22           21          445          424            3          475 
TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z 
          15         1972         1960           25           19         1973 
TCGA-85-A510 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 
        1967         1987           24           13          111          758 
TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE 
         289           89          358          428          244          331 
TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 
         269           82          106          160           70           87 
TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 
         356          430         1213         1344          189          211 
TCGA-96-A4JK TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-J1-A4AH 
         273          256          413          224          308          222 
TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HG 
          35          449           36           83         1722         1548 
TCGA-NC-A5HI 
        1135 

  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                            1                             1 
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                         1977                          5287 
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                          740                           623 
[1] "1.0 - 1977.0 (740.0)" "1.0 - 5287.0 (623.0)"
[1] "hr=" "1.4"
D33V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  3(2P25.3) MUTATED         0        7       11        0         2
  DEL PEAK  3(2P25.3) WILD-TYPE       1       65      126        1        50
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK  3(2P25.3) MUTATED           7         10          3        1
  DEL PEAK  3(2P25.3) WILD-TYPE        64         47         17        5
D33V3, multiclass
            clus
vv           DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE
  STAGE I                              0                             1
  STAGE IA                             7                            65
  STAGE IB                            11                           126
  STAGE II                             0                             1
  STAGE IIA                            2                            50
  STAGE IIB                            7                            64
  STAGE IIIA                          10                            47
  STAGE IIIB                           3                            17
  STAGE IV                             1                             5
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK  3(2P25.3) MUTATED     8  24   4   5
  DEL PEAK  3(2P25.3) WILD-TYPE  90 230  44  15
D33V4, multiclass
    clus
vv   DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE
  T1                           8                            90
  T2                          24                           230
  T3                           4                            44
  T4                           5                            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  3(2P25.3) MUTATED    24  10   6   1
  DEL PEAK  3(2P25.3) WILD-TYPE 237 103  29   4
D33V5, multiclass
    clus
vv   DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE
  N0                          24                           237
  N1                          10                           103
  N2                           6                            29
  N3                           1                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A  MX
  DEL PEAK  3(2P25.3) MUTATED    35   1   0   5
  DEL PEAK  3(2P25.3) WILD-TYPE 323   4   1  45
D33V6, multiclass
     clus
vv    DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE
  M0                           35                           323
  M1                            1                             4
  M1A                           0                             1
  MX                            5                            45
[1] 4 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  3(2P25.3) MUTATED    14  27
  DEL PEAK  3(2P25.3) WILD-TYPE  93 286
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2P25.3) MUTATED     14   27
  DEL PEAK  3(2P25.3) WILD-TYPE   93  286
        clus
vv       DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE
  FEMALE                          14                            93
  MALE                            27                           286
[1] 2 2
[1] FALSE
D33V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK  3(2P25.3) MUTATED                                       0
  DEL PEAK  3(2P25.3) WILD-TYPE                                    12
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK  3(2P25.3) MUTATED                                        0
  DEL PEAK  3(2P25.3) WILD-TYPE                                      6
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK  3(2P25.3) MUTATED                                         1
  DEL PEAK  3(2P25.3) WILD-TYPE                                       0
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  3(2P25.3) MUTATED                                                            40
  DEL PEAK  3(2P25.3) WILD-TYPE                                                         361
D33V9, multiclass
                                                             clus
vv                                                            DEL PEAK  3(2P25.3) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          40
                                                             clus
vv                                                            DEL PEAK  3(2P25.3) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  12
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           361
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V10, binary
                               cls
clus                              0   1
  DEL PEAK  3(2P25.3) MUTATED     1  40
  DEL PEAK  3(2P25.3) WILD-TYPE  12 367
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2P25.3) MUTATED      1   40
  DEL PEAK  3(2P25.3) WILD-TYPE   12  367
     clus
vv    DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE
  NO                            1                            12
  YES                          40                           367
[1] 2 2
[1] FALSE
D33V11, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  3(2P25.3) MUTATED    36   1   0   1
  DEL PEAK  3(2P25.3) WILD-TYPE 306   7   4  17
D33V12, multiclass
    clus
vv   DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE
  R0                          36                           306
  R1                           1                             7
  R2                           0                             4
  RX                           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                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  3(2P25.3) MUTATED       2                         0    29
  DEL PEAK  3(2P25.3) WILD-TYPE     7                        17   269
D33V13, multiclass
                           clus
vv                          DEL PEAK  3(2P25.3) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              29
                           clus
vv                          DEL PEAK  3(2P25.3) WILD-TYPE
  ASIAN                                                 7
  BLACK OR AFRICAN AMERICAN                            17
  WHITE                                               269
[1] 3 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  3(2P25.3) MUTATED     1  25
  DEL PEAK  3(2P25.3) WILD-TYPE   7 242
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2P25.3) MUTATED      1   25
  DEL PEAK  3(2P25.3) WILD-TYPE    7  242
                        clus
vv                       DEL PEAK  3(2P25.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          25
                        clus
vv                       DEL PEAK  3(2P25.3) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           242
[1] 2 2
[1] FALSE

Clustering(34) Variable = DEL PEAK  4(2Q22.1) MUTATION ANALYSIS
D34V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  4(2Q22.1) MUTATED    72  28
  DEL PEAK  4(2Q22.1) WILD-TYPE 193  95
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                          100                           288 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                           28                            95 
$`DEL PEAK  4(2Q22.1) MUTATED`
TCGA-18-3406 TCGA-18-3412 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-21-1075 
         370          345         1810          862          758         2134 
TCGA-21-1077 TCGA-21-1082 TCGA-21-5782 TCGA-21-5786 TCGA-21-5787 TCGA-22-0940 
        1058         3644          962         1032          329          608 
TCGA-22-0944 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4604 TCGA-22-5474 
         223         1067         1470          734          399          445 
TCGA-22-5477 TCGA-22-5481 TCGA-22-A5C4 TCGA-33-4538 TCGA-33-4587 TCGA-34-5231 
        1346         1952           29         2979         1970         1528 
TCGA-37-3783 TCGA-37-4130 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 
         120          247          207           12          103         1454 
TCGA-39-5035 TCGA-39-5037 TCGA-43-6770 TCGA-43-7657 TCGA-43-8115 TCGA-43-8116 
         474         1086          310          236          407          358 
TCGA-43-A474 TCGA-46-6025 TCGA-51-4081 TCGA-52-7810 TCGA-56-7223 TCGA-56-7822 
         353          324          911          923           30            1 
TCGA-56-8503 TCGA-56-8629 TCGA-56-A5DR TCGA-58-8391 TCGA-58-A46M TCGA-60-2698 
          41           34            4         2167         1072          311 
TCGA-60-2713 TCGA-60-2715 TCGA-60-2722 TCGA-60-2724 TCGA-60-2726 TCGA-63-6202 
        1731         1075          908          717          358         1973 
TCGA-66-2754 TCGA-66-2758 TCGA-66-2763 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 
          61          639           30           31           61           61 
TCGA-66-2770 TCGA-66-2781 TCGA-66-2786 TCGA-66-2787 TCGA-66-2790 TCGA-66-2791 
         700          121          790         1217          699         1977 
TCGA-66-2793 TCGA-66-2800 TCGA-68-A59J TCGA-77-6843 TCGA-77-7138 TCGA-77-7338 
        1952         1492          104         1941         1959         1952 
TCGA-77-7465 TCGA-77-8007 TCGA-77-8009 TCGA-77-8136 TCGA-77-8148 TCGA-85-7696 
         479         1960         1641         1947          293           18 
TCGA-85-7697 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-8071 TCGA-85-8072 
          10            1         1965           35          428          513 
TCGA-85-8276 TCGA-85-8277 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8354 
          13           11           54           60           55           61 
TCGA-85-8664 TCGA-85-A4CL TCGA-85-A512 TCGA-90-A4EE TCGA-92-8064 TCGA-92-8065 
           3           15         1987          331          160           70 
TCGA-96-7544 TCGA-98-8023 TCGA-LA-A446 TCGA-MF-A522 
        1213          308           36           83 

$`DEL PEAK  4(2Q22.1) WILD-TYPE`
TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3414 
         136         2464         2417          146         1415          396 
TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 
          50         1331          187           85         2754           92 
TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1076 TCGA-21-1078 
         827         3636         1426         3016         1852          474 
TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1083 TCGA-21-5784 TCGA-21-A5DI 
         965         3724          284          267         1268          979 
TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 
        1945          131         1952           53          429          822 
TCGA-22-1017 TCGA-22-4591 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4605 
        1485          623           17         1161         1057         1946 
TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5478 
         587          358          965         1964         1933           24 
TCGA-22-5479 TCGA-22-5480 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 
        1651         1952          357          573          916         1912 
TCGA-22-5491 TCGA-22-5492 TCGA-33-4532 TCGA-33-4533 TCGA-33-4547 TCGA-33-4566 
        1713          506         2524         1940         1311         5287 
TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4589 TCGA-33-6738 TCGA-34-2596 
        1966         1941          428         1948          822           80 
TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5232 
        1874          958          881         1000          951         2062 
TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 
        1715          707          365          428          941          552 
TCGA-34-8454 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 TCGA-37-4133 
         166           13           12          200          227          238 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 
        2253         1361         1947         1996         1964         1849 
TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5036 
          52          740           59          833         1107         1084 
TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 
         544         1964         1223          684         1176          822 
TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6771 
        1007          349          849          376          757         1936 
TCGA-43-7656 TCGA-43-7658 TCGA-43-8118 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V 
         212         1970         1971          296          432          366 
TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-52-7622 TCGA-52-7809 TCGA-52-7811 
         423           12           12          541         1948         1958 
TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 
        1967          881            3          555           62           26 
TCGA-56-7221 TCGA-56-7222 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 
          30           13           44           40           26            6 
TCGA-56-7731 TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 
        1961          178           55           36           63           17 
TCGA-56-8628 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ 
          16           38            2           46           30           25 
TCGA-56-A4ZK TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 TCGA-58-8393 TCGA-58-A46J 
           4            8          378          911         1058         2589 
TCGA-58-A46L TCGA-58-A46N TCGA-60-2695 TCGA-60-2696 TCGA-60-2703 TCGA-60-2704 
        1723          910          642          109         1950         1943 
TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 
        1958          661         1963         1505         1963         1260 
TCGA-60-2712 TCGA-60-2714 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 
         274         1531         1475         1297           97          983 
TCGA-60-2723 TCGA-60-2725 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 
        1092          816         1957         1955         1947         1952 
TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 
        1967         1311           61          641           30           31 
TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2759 TCGA-66-2765 TCGA-66-2769 
          28           30           30          762           61         1947 
TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2782 
         578         1946           61          578         1956         1954 
TCGA-66-2783 TCGA-66-2785 TCGA-66-2788 TCGA-66-2789 TCGA-66-2792 TCGA-66-2794 
         759           60          699         1955          913         1645 
TCGA-66-2795 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 
         122           83          202          211          244           96 
TCGA-68-A59I TCGA-77-6842 TCGA-77-6844 TCGA-77-6845 TCGA-77-7139 TCGA-77-7141 
         121         1950         1942         1952         1968           15 
TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7463 TCGA-77-8008 TCGA-77-8128 
        1286         1954         1942         1954         1945         1953 
TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 
        1945         1941         1941         1946         1951         1962 
TCGA-77-8144 TCGA-77-8145 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 
         833         1943         1961         1684         1092           10 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 
        1953         1942         1959         1955         1963         1290 
TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 TCGA-85-6561 
        1280         1939          839          713          364          395 
TCGA-85-6798 TCGA-85-7698 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 
          34           49          911           60           26           60 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8287 TCGA-85-8352 TCGA-85-8353 TCGA-85-8355 
          16          960           13           67           54           61 
TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8666 TCGA-85-A4PA 
          22           21          445          424          475         1972 
TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 
        1960           25           19         1973         1967         1972 
TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 
          24           13          111          758          289           89 
TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 
         358          428          244          269           82          106 
TCGA-92-8063 TCGA-94-7033 TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7545 TCGA-96-8169 
         122           87          356          430         1344          189 
TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 
         211          273          183          256          413          224 
TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HI 
         222           35          449         1722         1548         1135 

  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                            1                             2 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                         3644                          5287 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                        417.5                         748.5 
[1] "1.0 - 3644.0 (417.5)" "2.0 - 5287.0 (748.5)"
[1] "hr=" "1"  
D34V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  4(2Q22.1) MUTATED         0       18       24        0        21
  DEL PEAK  4(2Q22.1) WILD-TYPE       1       54      113        1        31
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK  4(2Q22.1) MUTATED          21         17          5        1
  DEL PEAK  4(2Q22.1) WILD-TYPE        50         40         15        5
D34V3, multiclass
            clus
vv           DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  STAGE I                              0                             1
  STAGE IA                            18                            54
  STAGE IB                            24                           113
  STAGE II                             0                             1
  STAGE IIA                           21                            31
  STAGE IIB                           21                            50
  STAGE IIIA                          17                            40
  STAGE IIIB                           5                            15
  STAGE IV                             1                             5
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK  4(2Q22.1) MUTATED    26  64  14   3
  DEL PEAK  4(2Q22.1) WILD-TYPE  72 190  34  17
D34V4, multiclass
    clus
vv   DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  T1                          26                            72
  T2                          64                           190
  T3                          14                            34
  T4                           3                            17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK  4(2Q22.1) MUTATED    55  40  10   2
  DEL PEAK  4(2Q22.1) WILD-TYPE 206  73  25   3
D34V5, multiclass
    clus
vv   DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  N0                          55                           206
  N1                          40                            73
  N2                          10                            25
  N3                           2                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A  MX
  DEL PEAK  4(2Q22.1) MUTATED    91   1   0  14
  DEL PEAK  4(2Q22.1) WILD-TYPE 267   4   1  36
D34V6, multiclass
     clus
vv    DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  M0                           91                           267
  M1                            1                             4
  M1A                           0                             1
  MX                           14                            36
[1] 4 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  4(2Q22.1) MUTATED    19  88
  DEL PEAK  4(2Q22.1) WILD-TYPE  88 225
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q22.1) MUTATED     19   88
  DEL PEAK  4(2Q22.1) WILD-TYPE   88  225
        clus
vv       DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  FEMALE                          19                            88
  MALE                            88                           225
[1] 2 2
[1] FALSE
D34V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK  4(2Q22.1) MUTATED                                       1
  DEL PEAK  4(2Q22.1) WILD-TYPE                                    11
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK  4(2Q22.1) MUTATED                                        1
  DEL PEAK  4(2Q22.1) WILD-TYPE                                      5
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK  4(2Q22.1) MUTATED                                         1
  DEL PEAK  4(2Q22.1) WILD-TYPE                                       0
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  4(2Q22.1) MUTATED                                                           104
  DEL PEAK  4(2Q22.1) WILD-TYPE                                                         297
D34V9, multiclass
                                                             clus
vv                                                            DEL PEAK  4(2Q22.1) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         104
                                                             clus
vv                                                            DEL PEAK  4(2Q22.1) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  11
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           297
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V10, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q22.1) MUTATED     2 105
  DEL PEAK  4(2Q22.1) WILD-TYPE  11 302
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q22.1) MUTATED      2  105
  DEL PEAK  4(2Q22.1) WILD-TYPE   11  302
     clus
vv    DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  NO                            2                            11
  YES                         105                           302
[1] 2 2
[1] FALSE
D34V11, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  4(2Q22.1) MUTATED    90   2   0   7
  DEL PEAK  4(2Q22.1) WILD-TYPE 252   6   4  11
D34V12, multiclass
    clus
vv   DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  R0                          90                           252
  R1                           2                             6
  R2                           0                             4
  RX                           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                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(2Q22.1) MUTATED       1                         3    77
  DEL PEAK  4(2Q22.1) WILD-TYPE     8                        14   221
D34V13, multiclass
                           clus
vv                          DEL PEAK  4(2Q22.1) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           3
  WHITE                                              77
                           clus
vv                          DEL PEAK  4(2Q22.1) WILD-TYPE
  ASIAN                                                 8
  BLACK OR AFRICAN AMERICAN                            14
  WHITE                                               221
[1] 3 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  4(2Q22.1) MUTATED     1  70
  DEL PEAK  4(2Q22.1) WILD-TYPE   7 197
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q22.1) MUTATED      1   70
  DEL PEAK  4(2Q22.1) WILD-TYPE    7  197
                        clus
vv                       DEL PEAK  4(2Q22.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          70
                        clus
vv                       DEL PEAK  4(2Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           197
[1] 2 2
[1] FALSE

Clustering(35) Variable = DEL PEAK  5(2Q37.1) MUTATION ANALYSIS
D35V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  5(2Q37.1) MUTATED    84  38
  DEL PEAK  5(2Q37.1) WILD-TYPE 181  85
  DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE 
                          122                           266 
  DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE 
                           38                            85 
$`DEL PEAK  5(2Q37.1) MUTATED`
TCGA-18-3415 TCGA-18-3417 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-21-1070 
        1810          758         1331          187           85         3636 
TCGA-21-1075 TCGA-21-1083 TCGA-21-5786 TCGA-22-0940 TCGA-22-0944 TCGA-22-1011 
        2134          267         1032          608          223           53 
TCGA-22-1012 TCGA-22-1016 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4613 
         429          822         1057          399         1946          358 
TCGA-22-5474 TCGA-22-5477 TCGA-22-5481 TCGA-22-5482 TCGA-22-5491 TCGA-33-4532 
         445         1346         1952          357         1713         2524 
TCGA-33-4533 TCGA-33-4538 TCGA-33-4582 TCGA-34-2605 TCGA-34-5231 TCGA-34-5240 
        1940         2979         1966          881         1528          365 
TCGA-34-5241 TCGA-37-4141 TCGA-39-5029 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 
         428           12          740          474         1084         1086 
TCGA-43-2578 TCGA-43-3394 TCGA-43-6143 TCGA-43-7657 TCGA-43-8115 TCGA-43-8118 
         684          822          376          236          407         1971 
TCGA-43-A56U TCGA-51-4081 TCGA-52-7810 TCGA-52-7811 TCGA-56-7579 TCGA-56-7582 
         432          911          923         1958           44           26 
TCGA-56-8504 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BY TCGA-56-A4ZK TCGA-58-8393 
         178           34           38           30            4         1058 
TCGA-58-A46L TCGA-60-2696 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2722 
        1723          109         1260          274         1731          908 
TCGA-63-7023 TCGA-66-2727 TCGA-66-2755 TCGA-66-2758 TCGA-66-2763 TCGA-66-2766 
        1952         1967           28          639           30           31 
TCGA-66-2767 TCGA-66-2769 TCGA-66-2777 TCGA-66-2787 TCGA-66-2792 TCGA-66-2793 
          61         1947           61         1217          913         1952 
TCGA-66-2800 TCGA-68-7755 TCGA-68-8250 TCGA-68-A59J TCGA-77-6845 TCGA-77-7141 
        1492           83          244          104         1952           15 
TCGA-77-7142 TCGA-77-7337 TCGA-77-7465 TCGA-77-8007 TCGA-77-8009 TCGA-77-8136 
        1286         1942          479         1960         1641         1947 
TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-85-6798 
         293         1961         1684         1092           10           34 
TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 
          18           10           49            1         1965           35 
TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8288 TCGA-85-8352 TCGA-85-8479 
         513           13           11           54           67           22 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4QR TCGA-85-A511 TCGA-85-A53L TCGA-90-7767 
           3          475           25         1972           13           89 
TCGA-90-7769 TCGA-90-A4EE TCGA-92-7340 TCGA-92-7341 TCGA-92-8064 TCGA-92-8065 
         358          331           82          106          160           70 
TCGA-96-7544 TCGA-96-7545 TCGA-96-A4JK TCGA-J1-A4AH TCGA-L3-A524 TCGA-LA-A446 
        1213         1344          273          222          449           36 
TCGA-NC-A5HE TCGA-NC-A5HG 
        1722         1548 

$`DEL PEAK  5(2Q37.1) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
         370          136         2464         2417          146         1415 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3416 TCGA-18-3419 TCGA-18-4721 TCGA-18-5592 
         345          396          862           50         2754           92 
TCGA-18-5595 TCGA-21-1071 TCGA-21-1072 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 
         827         1426         3016         1852         1058          474 
TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-5782 TCGA-21-5784 
         965         3724          284         3644          962         1268 
TCGA-21-5787 TCGA-21-A5DI TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1017 
         329          979         1945          131         1952         1485 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 
         623         1067         1470          734           17         1161 
TCGA-22-4607 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5478 TCGA-22-5479 
         587          965         1964         1933           24         1651 
TCGA-22-5480 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5492 TCGA-22-A5C4 
        1952          573          916         1912          506           29 
TCGA-33-4547 TCGA-33-4566 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 
        1311         5287         1941          428         1970         1948 
TCGA-33-6738 TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2608 TCGA-34-2609 
         822           80         1874          958         1000          951 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5927 TCGA-34-5928 TCGA-34-8454 
        2062         1715          707          941          552          166 
TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 
         120           13           12          200          247          227 
TCGA-37-4133 TCGA-37-4135 TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 
         238          207          103         1454         2253         1361 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 
        1947         1996         1964         1849           52           59 
TCGA-39-5031 TCGA-39-5034 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 
         833         1107          544         1964         1223         1176 
TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 
        1007          349          849          757          310         1936 
TCGA-43-7656 TCGA-43-7658 TCGA-43-8116 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56V 
         212         1970          358          353          296          366 
TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-52-7622 TCGA-52-7809 
         324          423           12           12          541         1948 
TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 
        1967          881            3          555           62           26 
TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7580 TCGA-56-7730 TCGA-56-7731 
          30           13           30           40            6         1961 
TCGA-56-7822 TCGA-56-8503 TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 
           1           41           55           36           63           17 
TCGA-56-8628 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZJ TCGA-56-A5DR TCGA-56-A5DS 
          16            2           46           25            4            8 
TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-A46J TCGA-58-A46M TCGA-58-A46N 
         378          911         2167         2589         1072          910 
TCGA-60-2695 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 
         642          311         1950         1943         1958          661 
TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 
        1963         1505         1963         1531         1075         1475 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 
        1297           97          983         1092          717          816 
TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-66-2734 
         358         1973         1957         1955         1947         1311 
TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2756 
          61          641           30           31           61           30 
TCGA-66-2757 TCGA-66-2759 TCGA-66-2765 TCGA-66-2768 TCGA-66-2770 TCGA-66-2771 
          30          762           61           61          700          578 
TCGA-66-2773 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 
        1946          578         1956          121         1954          759 
TCGA-66-2785 TCGA-66-2786 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 
          60          790          699         1955          699         1977 
TCGA-66-2794 TCGA-66-2795 TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I 
        1645          122          202          211           96          121 
TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-7138 TCGA-77-7139 TCGA-77-7335 
        1950         1941         1942         1959         1968         1954 
TCGA-77-7338 TCGA-77-7463 TCGA-77-8008 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 
        1952         1954         1945         1953         1945         1941 
TCGA-77-8133 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 
        1941         1946         1951         1962          833         1943 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 
        1953         1942         1959         1955         1963         1290 
TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 TCGA-85-6561 
        1280         1939          839          713          364          395 
TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 
         911           60           26           60           16          960 
TCGA-85-8071 TCGA-85-8287 TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 TCGA-85-8354 
         428           13           60           55           54           61 
TCGA-85-8355 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-A4CL TCGA-85-A4PA 
          61           21          445          424           15         1972 
TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A512 TCGA-85-A513 
        1960           19         1973         1967         1987           24 
TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A59Q 
         111          758          289          428          244          269 
TCGA-92-8063 TCGA-94-7033 TCGA-94-7943 TCGA-94-A4VJ TCGA-96-8169 TCGA-96-8170 
         122           87          356          430          189          211 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-L3-A4E7 
         183          256          413          224          308           35 
TCGA-MF-A522 TCGA-NC-A5HI 
          83         1135 

  DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE 
                            1                             1 
  DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE 
                         3636                          5287 
  DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE 
                          447                           715 
[1] "1.0 - 3636.0 (447.0)" "1.0 - 5287.0 (715.0)"
[1] "hr=" "1.2"
D35V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  5(2Q37.1) MUTATED         0       21       43        1        19
  DEL PEAK  5(2Q37.1) WILD-TYPE       1       51       94        0        33
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK  5(2Q37.1) MUTATED          24         17          6        1
  DEL PEAK  5(2Q37.1) WILD-TYPE        47         40         14        5
D35V3, multiclass
            clus
vv           DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE
  STAGE I                              0                             1
  STAGE IA                            21                            51
  STAGE IB                            43                            94
  STAGE II                             1                             0
  STAGE IIA                           19                            33
  STAGE IIB                           24                            47
  STAGE IIIA                          17                            40
  STAGE IIIB                           6                            14
  STAGE IV                             1                             5
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK  5(2Q37.1) MUTATED    30  81  15   6
  DEL PEAK  5(2Q37.1) WILD-TYPE  68 173  33  14
D35V4, multiclass
    clus
vv   DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE
  T1                          30                            68
  T2                          81                           173
  T3                          15                            33
  T4                           6                            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  5(2Q37.1) MUTATED    81  42   8   1
  DEL PEAK  5(2Q37.1) WILD-TYPE 180  71  27   4
D35V5, multiclass
    clus
vv   DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE
  N0                          81                           180
  N1                          42                            71
  N2                           8                            27
  N3                           1                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A  MX
  DEL PEAK  5(2Q37.1) MUTATED   111   1   0  20
  DEL PEAK  5(2Q37.1) WILD-TYPE 247   4   1  30
D35V6, multiclass
     clus
vv    DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE
  M0                          111                           247
  M1                            1                             4
  M1A                           0                             1
  MX                           20                            30
[1] 4 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  5(2Q37.1) MUTATED    35  97
  DEL PEAK  5(2Q37.1) WILD-TYPE  72 216
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.1) MUTATED     35   97
  DEL PEAK  5(2Q37.1) WILD-TYPE   72  216
        clus
vv       DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE
  FEMALE                          35                            72
  MALE                            97                           216
[1] 2 2
[1] FALSE
D35V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK  5(2Q37.1) MUTATED                                       5
  DEL PEAK  5(2Q37.1) WILD-TYPE                                     7
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK  5(2Q37.1) MUTATED                                        2
  DEL PEAK  5(2Q37.1) WILD-TYPE                                      4
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK  5(2Q37.1) MUTATED                                         0
  DEL PEAK  5(2Q37.1) WILD-TYPE                                       1
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  5(2Q37.1) MUTATED                                                           125
  DEL PEAK  5(2Q37.1) WILD-TYPE                                                         276
D35V9, multiclass
                                                             clus
vv                                                            DEL PEAK  5(2Q37.1) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         125
                                                             clus
vv                                                            DEL PEAK  5(2Q37.1) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           276
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V10, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q37.1) MUTATED     2 130
  DEL PEAK  5(2Q37.1) WILD-TYPE  11 277
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.1) MUTATED      2  130
  DEL PEAK  5(2Q37.1) WILD-TYPE   11  277
     clus
vv    DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE
  NO                            2                            11
  YES                         130                           277
[1] 2 2
[1] FALSE
D35V11, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  5(2Q37.1) MUTATED   108   3   0   7
  DEL PEAK  5(2Q37.1) WILD-TYPE 234   5   4  11
D35V12, multiclass
    clus
vv   DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE
  R0                         108                           234
  R1                           3                             5
  R2                           0                             4
  RX                           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                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(2Q37.1) MUTATED       2                         6    96
  DEL PEAK  5(2Q37.1) WILD-TYPE     7                        11   202
D35V13, multiclass
                           clus
vv                          DEL PEAK  5(2Q37.1) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           6
  WHITE                                              96
                           clus
vv                          DEL PEAK  5(2Q37.1) WILD-TYPE
  ASIAN                                                 7
  BLACK OR AFRICAN AMERICAN                            11
  WHITE                                               202
[1] 3 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  5(2Q37.1) MUTATED     3  85
  DEL PEAK  5(2Q37.1) WILD-TYPE   5 182
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.1) MUTATED      3   85
  DEL PEAK  5(2Q37.1) WILD-TYPE    5  182
                        clus
vv                       DEL PEAK  5(2Q37.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          85
                        clus
vv                       DEL PEAK  5(2Q37.1) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           182
[1] 2 2
[1] FALSE

Clustering(36) Variable = DEL PEAK  6(3P25.3) MUTATION ANALYSIS
D36V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  6(3P25.3) MUTATED   214  97
  DEL PEAK  6(3P25.3) WILD-TYPE  51  26
  DEL PEAK  6(3P25.3) MUTATED DEL PEAK  6(3P25.3) WILD-TYPE 
                          311                            77 
  DEL PEAK  6(3P25.3) MUTATED DEL PEAK  6(3P25.3) WILD-TYPE 
                           97                            26 
$`DEL PEAK  6(3P25.3) MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
         370          136         2464         2417          146         1415 
TCGA-18-3412 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-4083 TCGA-18-4086 
         345         1810          862          758          187           85 
TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1075 TCGA-21-1077 
        2754           92         3636         1426         2134         1058 
TCGA-21-1079 TCGA-21-1080 TCGA-21-1083 TCGA-21-5782 TCGA-21-5786 TCGA-21-5787 
         965         3724          267          962         1032          329 
TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1012 
         979          608          223         1945          131          429 
TCGA-22-1016 TCGA-22-4591 TCGA-22-4594 TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 
         822          623         1470          734         1161         1057 
TCGA-22-4604 TCGA-22-4605 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 
         399         1946          358          965         1964         1933 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 
        1346           24         1651         1952         1952          357 
TCGA-22-5483 TCGA-22-5485 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 
         573          916         1713          506           29         2524 
TCGA-33-4538 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 
        2979         1966         1941          428         1970         1948 
TCGA-33-6738 TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 
         822           80         1874          958          881         1000 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5239 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 
        1528         2062          707          428          941          552 
TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 
         166          120           13          200          247          227 
TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 
         238          207           12         1454         2253         1361 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 
        1947         1996         1964         1849           52           59 
TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-43-2576 
         833         1107          474         1084         1086         1223 
TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-6143 TCGA-43-6770 TCGA-43-7656 
        1176          822         1007          376          310          212 
TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 
         236         1970          407          358         1971          353 
TCGA-43-A56V TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 
         366          423           12           12          911          541 
TCGA-52-7809 TCGA-52-7811 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-7221 
        1948         1958          881            3          555           30 
TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 
          13           30           44           40           26            6 
TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 
        1961            1           41          178           55           36 
TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX 
          17           16           34           38            2           46 
TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 
          30           25            4            8          378          911 
TCGA-58-8391 TCGA-58-8393 TCGA-60-2695 TCGA-60-2696 TCGA-60-2698 TCGA-60-2703 
        2167         1058          642          109          311         1950 
TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 
        1943         1958          661         1963         1505         1963 
TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2715 TCGA-60-2719 TCGA-60-2720 
        1260          274         1731         1075         1297           97 
TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 
         983          908         1092          717          816          358 
TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 
        1957         1955         1947         1952         1967         1311 
TCGA-66-2737 TCGA-66-2742 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 
          61          641           61           28           30           30 
TCGA-66-2758 TCGA-66-2763 TCGA-66-2765 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 
         639           30           61           61           61         1947 
TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 
         700          578         1946           61          578         1956 
TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 
         121         1954          759           60          790         1217 
TCGA-66-2788 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2795 
         699          699         1977          913         1952          122 
TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 
        1492           83          202          211          244           96 
TCGA-68-A59I TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 
         121         1950         1941         1942         1952         1959 
TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 
        1968           15         1286         1954         1942         1952 
TCGA-77-7463 TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 
        1954          479         1945         1641         1953         1945 
TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 
        1941         1947         1946         1951         1962          833 
TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 
        1943          293         1961         1684         1092           10 
TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA 
        1942         1959         1955         1963         1290         1280 
TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 
        1939          839          713          364          395           34 
TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 
          10           49            1         1965          911           60 
TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 
          26           60           16          960          428          513 
TCGA-85-8276 TCGA-85-8277 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 
          13           11           54           60           55           54 
TCGA-85-8355 TCGA-85-8481 TCGA-85-8580 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL 
          61           21          445            3          475           15 
TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 
        1960           25         1973         1967         1972         1987 
TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7766 TCGA-90-7767 TCGA-90-7964 TCGA-90-A4ED 
          13          111          289           89          428          244 
TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 
         331          269          106          122          160           70 
TCGA-94-7033 TCGA-94-7943 TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 
          87          356         1213         1344          189          211 
TCGA-96-A4JK TCGA-96-A4JL TCGA-98-8021 TCGA-98-8022 TCGA-J1-A4AH TCGA-L3-A4E7 
         273          183          413          224          222           35 
TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HI 
          36           83         1722         1548         1135 

$`DEL PEAK  6(3P25.3) WILD-TYPE`
TCGA-18-3414 TCGA-18-3419 TCGA-18-3421 TCGA-18-5595 TCGA-21-1072 TCGA-21-1076 
         396           50         1331          827         3016         1852 
TCGA-21-1078 TCGA-21-1081 TCGA-21-1082 TCGA-21-5784 TCGA-22-1005 TCGA-22-1011 
         474          284         3644         1268         1952           53 
TCGA-22-1017 TCGA-22-4593 TCGA-22-4596 TCGA-22-4607 TCGA-22-5474 TCGA-22-5489 
        1485         1067           17          587          445         1912 
TCGA-33-4533 TCGA-33-4547 TCGA-33-4566 TCGA-34-2609 TCGA-34-5234 TCGA-34-5240 
        1940         1311         5287          951         1715          365 
TCGA-37-3792 TCGA-37-5819 TCGA-39-5029 TCGA-39-5039 TCGA-39-5040 TCGA-43-2578 
          12          103          740          544         1964          684 
TCGA-43-5668 TCGA-43-5670 TCGA-43-6647 TCGA-43-6771 TCGA-43-A475 TCGA-43-A56U 
         349          849          757         1936          296          432 
TCGA-46-6025 TCGA-52-7810 TCGA-52-7812 TCGA-56-6545 TCGA-56-6546 TCGA-56-8625 
         324          923         1967           62           26           63 
TCGA-56-A5DR TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2714 
           4         2589         1723         1072          910         1531 
TCGA-60-2716 TCGA-63-6202 TCGA-66-2744 TCGA-66-2753 TCGA-66-2759 TCGA-66-2766 
        1475         1973           30           31          762           31 
TCGA-66-2789 TCGA-66-2794 TCGA-68-A59J TCGA-77-8007 TCGA-77-8131 TCGA-77-A5FZ 
        1955         1645          104         1960         1941         1953 
TCGA-85-7696 TCGA-85-7843 TCGA-85-8287 TCGA-85-8352 TCGA-85-8354 TCGA-85-8479 
          18           35           13           67           61           22 
TCGA-85-8582 TCGA-85-A4PA TCGA-85-A50M TCGA-85-A513 TCGA-90-6837 TCGA-90-7769 
         424         1972           19           24          758          358 
TCGA-92-7340 TCGA-94-A4VJ TCGA-98-7454 TCGA-98-8023 TCGA-L3-A524 
          82          430          256          308          449 

  DEL PEAK  6(3P25.3) MUTATED DEL PEAK  6(3P25.3) WILD-TYPE 
                            1                             4 
  DEL PEAK  6(3P25.3) MUTATED DEL PEAK  6(3P25.3) WILD-TYPE 
                         3724                          5287 
  DEL PEAK  6(3P25.3) MUTATED DEL PEAK  6(3P25.3) WILD-TYPE 
                          642                           587 
[1] "1.0 - 3724.0 (642.0)" "4.0 - 5287.0 (587.0)"
[1] "hr=" "1.1"
D36V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  6(3P25.3) MUTATED         1       59      112        1        39
  DEL PEAK  6(3P25.3) WILD-TYPE       0       13       25        0        13
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK  6(3P25.3) MUTATED          51         46         17        5
  DEL PEAK  6(3P25.3) WILD-TYPE        20         11          3        1
D36V3, multiclass
            clus
vv           DEL PEAK  6(3P25.3) MUTATED DEL PEAK  6(3P25.3) WILD-TYPE
  STAGE I                              1                             0
  STAGE IA                            59                            13
  STAGE IB                           112                            25
  STAGE II                             1                             0
  STAGE IIA                           39                            13
  STAGE IIB                           51                            20
  STAGE IIIA                          46                            11
  STAGE IIIB                          17                             3
  STAGE IV                             5                             1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK  6(3P25.3) MUTATED    80 197  41  16
  DEL PEAK  6(3P25.3) WILD-TYPE  18  57   7   4
D36V4, multiclass
    clus
vv   DEL PEAK  6(3P25.3) MUTATED DEL PEAK  6(3P25.3) WILD-TYPE
  T1                          80                            18
  T2                         197                            57
  T3                          41                             7
  T4                          16                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK  6(3P25.3) MUTATED   212  90  24   4
  DEL PEAK  6(3P25.3) WILD-TYPE  49  23  11   1
D36V5, multiclass
    clus
vv   DEL PEAK  6(3P25.3) MUTATED DEL PEAK  6(3P25.3) WILD-TYPE
  N0                         212                            49
  N1                          90                            23
  N2                          24                            11
  N3                           4                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A  MX
  DEL PEAK  6(3P25.3) MUTATED   284   4   1  39
  DEL PEAK  6(3P25.3) WILD-TYPE  74   1   0  11
D36V6, multiclass
     clus
vv    DEL PEAK  6(3P25.3) MUTATED DEL PEAK  6(3P25.3) WILD-TYPE
  M0                          284                            74
  M1                            4                             1
  M1A                           1                             0
  MX                           39                            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"
D36V7, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P25.3) MUTATED    85 249
  DEL PEAK  6(3P25.3) WILD-TYPE  22  64
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P25.3) MUTATED     85  249
  DEL PEAK  6(3P25.3) WILD-TYPE   22   64
        clus
vv       DEL PEAK  6(3P25.3) MUTATED DEL PEAK  6(3P25.3) WILD-TYPE
  FEMALE                          85                            22
  MALE                           249                            64
[1] 2 2
[1] FALSE
D36V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK  6(3P25.3) MUTATED                                       9
  DEL PEAK  6(3P25.3) WILD-TYPE                                     3
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK  6(3P25.3) MUTATED                                        2
  DEL PEAK  6(3P25.3) WILD-TYPE                                      4
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK  6(3P25.3) MUTATED                                         1
  DEL PEAK  6(3P25.3) WILD-TYPE                                       0
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  6(3P25.3) MUTATED                                                           322
  DEL PEAK  6(3P25.3) WILD-TYPE                                                          79
D36V9, multiclass
                                                             clus
vv                                                            DEL PEAK  6(3P25.3) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         322
                                                             clus
vv                                                            DEL PEAK  6(3P25.3) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            79
[1] 4 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  6(3P25.3) MUTATED    12 322
  DEL PEAK  6(3P25.3) WILD-TYPE   1  85
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P25.3) MUTATED     12  322
  DEL PEAK  6(3P25.3) WILD-TYPE    1   85
     clus
vv    DEL PEAK  6(3P25.3) MUTATED DEL PEAK  6(3P25.3) WILD-TYPE
  NO                           12                             1
  YES                         322                            85
[1] 2 2
[1] FALSE
D36V11, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  6(3P25.3) MUTATED   271   5   4  14
  DEL PEAK  6(3P25.3) WILD-TYPE  71   3   0   4
D36V12, multiclass
    clus
vv   DEL PEAK  6(3P25.3) MUTATED DEL PEAK  6(3P25.3) WILD-TYPE
  R0                         271                            71
  R1                           5                             3
  R2                           4                             0
  RX                          14                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(3P25.3) MUTATED       6                        14   231
  DEL PEAK  6(3P25.3) WILD-TYPE     3                         3    67
D36V13, multiclass
                           clus
vv                          DEL PEAK  6(3P25.3) MUTATED
  ASIAN                                               6
  BLACK OR AFRICAN AMERICAN                          14
  WHITE                                             231
                           clus
vv                          DEL PEAK  6(3P25.3) WILD-TYPE
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                             3
  WHITE                                                67
[1] 3 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  6(3P25.3) MUTATED     6 207
  DEL PEAK  6(3P25.3) WILD-TYPE   2  60
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P25.3) MUTATED      6  207
  DEL PEAK  6(3P25.3) WILD-TYPE    2   60
                        clus
vv                       DEL PEAK  6(3P25.3) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                         207
                        clus
vv                       DEL PEAK  6(3P25.3) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            60
[1] 2 2
[1] FALSE

Clustering(37) Variable = DEL PEAK  7(3P13) MUTATION ANALYSIS
D37V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  7(3P13) MUTATED   232 106
  DEL PEAK  7(3P13) WILD-TYPE  33  17
  DEL PEAK  7(3P13) MUTATED DEL PEAK  7(3P13) WILD-TYPE 
                        338                          50 
  DEL PEAK  7(3P13) MUTATED DEL PEAK  7(3P13) WILD-TYPE 
                        106                          17 
$`DEL PEAK  7(3P13) MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
         370          136         2464         2417          146         1415 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 
         345          396         1810          862          758           50 
TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 
        1331          187           85         2754           92         3636 
TCGA-21-1071 TCGA-21-1075 TCGA-21-1077 TCGA-21-1079 TCGA-21-1080 TCGA-21-1082 
        1426         2134         1058          965         3724         3644 
TCGA-21-1083 TCGA-21-5782 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 
         267          962         1032          329          979          608 
TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 
         223         1945          131          429          822         1485 
TCGA-22-4591 TCGA-22-4594 TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 
         623         1470          734         1161         1057          399 
TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 
        1946          587          358          965         1964         1933 
TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 
         445         1346           24         1651         1952         1952 
TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 
         357          573          916         1912         1713          506 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4582 
          29         2524         1940         2979         1311         1966 
TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-33-6738 TCGA-34-2596 
        1941          428         1970         1948          822           80 
TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 
        1874          958          881         1000          951         1528 
TCGA-34-5232 TCGA-34-5239 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-8454 
        2062          707          428          941          552          166 
TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 
         120           13          200          247          227          238 
TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 
         207           12          103         1454         2253         1361 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 
        1947         1996         1964         1849           52          740 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-43-2576 
          59          833         1107          474         1084         1223 
TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 
         684         1176          822         1007          849          376 
TCGA-43-6770 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 
         310          212          236         1970          407          358 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 
        1971          353          366          324          423           12 
TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 
          12          911          541         1948          923         1958 
TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-7221 
        1967          881            3          555           62           30 
TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 
          13           30           44           40           26            6 
TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 TCGA-56-8504 TCGA-56-8624 TCGA-56-8625 
        1961            1           41          178           36           63 
TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX 
          17           16           34           38            2           46 
TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8388 
          30           25            4            4            8          378 
TCGA-58-8390 TCGA-58-8391 TCGA-58-8393 TCGA-58-A46L TCGA-58-A46M TCGA-60-2695 
         911         2167         1058         1723         1072          642 
TCGA-60-2696 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 
         109          311         1950         1943         1958          661 
TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 
        1963         1505         1963         1260          274         1731 
TCGA-60-2719 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 
        1297          983          908         1092          717          816 
TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 
         358         1973         1957         1955         1947         1952 
TCGA-66-2727 TCGA-66-2734 TCGA-66-2742 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 
        1967         1311          641           61           28           30 
TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 
          30          639          762           61           31           61 
TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 
          61         1947          700          578         1946           61 
TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 
         578         1956          121         1954          759           60 
TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 
         790         1217          699         1955          699         1977 
TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-68-7755 TCGA-68-7756 
         913         1952         1645          122           83          202 
TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 
         211          244           96          121          104         1950 
TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 
        1941         1942         1952         1959         1968           15 
TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 
        1286         1954         1942         1952         1954          479 
TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 
        1945         1641         1953         1945         1941         1947 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 
        1946         1951         1962          833         1943          293 
TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5G1 TCGA-77-A5G3 
        1961         1684         1092           10         1942         1959 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF 
        1955         1963         1290         1280         1939          839 
TCGA-77-A5GH TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 
         713          364          395           34           18           10 
TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 
          49            1         1965           35          911           60 
TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 
          60           16          960          428          513           13 
TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 
          11           13           54           60           55           54 
TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8664 
          61           61           22           21          445            3 
TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A510 
         475           15         1960           25         1973         1967 
TCGA-85-A511 TCGA-85-A512 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7766 TCGA-90-7767 
        1972         1987           13          111          289           89 
TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7341 TCGA-92-8063 
         428          244          331          269          106          122 
TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7544 
         160           70           87          356          430         1213 
TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-98-8021 TCGA-98-8022 
        1344          189          211          273          413          224 
TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE 
         308          222           35           36           83         1722 
TCGA-NC-A5HG TCGA-NC-A5HI 
        1548         1135 

$`DEL PEAK  7(3P13) WILD-TYPE`
TCGA-18-5595 TCGA-21-1072 TCGA-21-1076 TCGA-21-1078 TCGA-21-1081 TCGA-21-5784 
         827         3016         1852          474          284         1268 
TCGA-22-1005 TCGA-22-1011 TCGA-22-4593 TCGA-22-4596 TCGA-33-4566 TCGA-34-5234 
        1952           53         1067           17         5287         1715 
TCGA-34-5240 TCGA-37-3792 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-5668 
         365           12         1086          544         1964          349 
TCGA-43-6647 TCGA-43-6771 TCGA-43-A475 TCGA-43-A56U TCGA-56-6546 TCGA-56-8622 
         757         1936          296          432           26           55 
TCGA-58-A46J TCGA-58-A46N TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2720 
        2589          910         1531         1075         1475           97 
TCGA-66-2737 TCGA-66-2744 TCGA-66-2753 TCGA-66-2763 TCGA-66-2800 TCGA-77-8007 
          61           30           31           30         1492         1960 
TCGA-77-8131 TCGA-77-A5FZ TCGA-85-8048 TCGA-85-8352 TCGA-85-8582 TCGA-85-A4PA 
        1941         1953           26           67          424         1972 
TCGA-85-A50M TCGA-85-A513 TCGA-90-6837 TCGA-90-7769 TCGA-92-7340 TCGA-96-A4JL 
          19           24          758          358           82          183 
TCGA-98-7454 TCGA-L3-A524 
         256          449 

  DEL PEAK  7(3P13) MUTATED DEL PEAK  7(3P13) WILD-TYPE 
                          1                          12 
  DEL PEAK  7(3P13) MUTATED DEL PEAK  7(3P13) WILD-TYPE 
                       3724                        5287 
  DEL PEAK  7(3P13) MUTATED DEL PEAK  7(3P13) WILD-TYPE 
                      672.5                       461.5 
[1] "1.0 - 3724.0 (672.5)"  "12.0 - 5287.0 (461.5)"
[1] "hr=" "1.1"
D37V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  7(3P13) MUTATED         1       65      119        1        42
  DEL PEAK  7(3P13) WILD-TYPE       0        7       18        0        10
                             vv
clus                          STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK  7(3P13) MUTATED          55         54         18        6
  DEL PEAK  7(3P13) WILD-TYPE        16          3          2        0
D37V3, multiclass
            clus
vv           DEL PEAK  7(3P13) MUTATED DEL PEAK  7(3P13) WILD-TYPE
  STAGE I                            1                           0
  STAGE IA                          65                           7
  STAGE IB                         119                          18
  STAGE II                           1                           0
  STAGE IIA                         42                          10
  STAGE IIB                         55                          16
  STAGE IIIA                        54                           3
  STAGE IIIB                        18                           2
  STAGE IV                           6                           0
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2  T3  T4
  DEL PEAK  7(3P13) MUTATED    88 215  44  17
  DEL PEAK  7(3P13) WILD-TYPE  10  39   4   3
D37V4, multiclass
    clus
vv   DEL PEAK  7(3P13) MUTATED DEL PEAK  7(3P13) WILD-TYPE
  T1                        88                          10
  T2                       215                          39
  T3                        44                           4
  T4                        17                           3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           N0  N1  N2  N3
  DEL PEAK  7(3P13) MUTATED   228  95  32   5
  DEL PEAK  7(3P13) WILD-TYPE  33  18   3   0
D37V5, multiclass
    clus
vv   DEL PEAK  7(3P13) MUTATED DEL PEAK  7(3P13) WILD-TYPE
  N0                       228                          33
  N1                        95                          18
  N2                        32                           3
  N3                         5                           0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           M0  M1 M1A  MX
  DEL PEAK  7(3P13) MUTATED   310   5   1  42
  DEL PEAK  7(3P13) WILD-TYPE  48   0   0   8
D37V6, multiclass
     clus
vv    DEL PEAK  7(3P13) MUTATED DEL PEAK  7(3P13) WILD-TYPE
  M0                        310                          48
  M1                          5                           0
  M1A                         1                           0
  MX                         42                           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"
D37V7, binary
                             cls
clus                            0   1
  DEL PEAK  7(3P13) MUTATED    91 273
  DEL PEAK  7(3P13) WILD-TYPE  16  40
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  7(3P13) MUTATED     91  273
  DEL PEAK  7(3P13) WILD-TYPE   16   40
        clus
vv       DEL PEAK  7(3P13) MUTATED DEL PEAK  7(3P13) WILD-TYPE
  FEMALE                        91                          16
  MALE                         273                          40
[1] 2 2
[1] FALSE
D37V8, continuous
                             vv
clus                          LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK  7(3P13) MUTATED                                      10
  DEL PEAK  7(3P13) WILD-TYPE                                     2
                             vv
clus                          LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK  7(3P13) MUTATED                                        3
  DEL PEAK  7(3P13) WILD-TYPE                                      3
                             vv
clus                          LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK  7(3P13) MUTATED                                         1
  DEL PEAK  7(3P13) WILD-TYPE                                       0
                             vv
clus                          LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  7(3P13) MUTATED                                                           350
  DEL PEAK  7(3P13) WILD-TYPE                                                          51
D37V9, multiclass
                                                             clus
vv                                                            DEL PEAK  7(3P13) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                              10
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                              3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                             1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                       350
                                                             clus
vv                                                            DEL PEAK  7(3P13) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          51
[1] 4 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  7(3P13) MUTATED    12 352
  DEL PEAK  7(3P13) WILD-TYPE   1  55
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  7(3P13) MUTATED     12  352
  DEL PEAK  7(3P13) WILD-TYPE    1   55
     clus
vv    DEL PEAK  7(3P13) MUTATED DEL PEAK  7(3P13) WILD-TYPE
  NO                         12                           1
  YES                       352                          55
[1] 2 2
[1] FALSE
D37V11, continuous
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK  7(3P13) MUTATED   298   5   4  14
  DEL PEAK  7(3P13) WILD-TYPE  44   3   0   4
D37V12, multiclass
    clus
vv   DEL PEAK  7(3P13) MUTATED DEL PEAK  7(3P13) WILD-TYPE
  R0                       298                          44
  R1                         5                           3
  R2                         4                           0
  RX                        14                           4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(3P13) MUTATED       6                        17   255
  DEL PEAK  7(3P13) WILD-TYPE     3                         0    43
D37V13, multiclass
                           clus
vv                          DEL PEAK  7(3P13) MUTATED
  ASIAN                                             6
  BLACK OR AFRICAN AMERICAN                        17
  WHITE                                           255
                           clus
vv                          DEL PEAK  7(3P13) WILD-TYPE
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              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"
D37V14, binary
                             cls
clus                            0   1
  DEL PEAK  7(3P13) MUTATED     8 228
  DEL PEAK  7(3P13) WILD-TYPE   0  39
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  7(3P13) MUTATED      8  228
  DEL PEAK  7(3P13) WILD-TYPE    0   39
                        clus
vv                       DEL PEAK  7(3P13) MUTATED DEL PEAK  7(3P13) WILD-TYPE
  HISPANIC OR LATINO                             8                           0
  NOT HISPANIC OR LATINO                       228                          39
[1] 2 2
[1] FALSE

Clustering(38) Variable = DEL PEAK  8(3P12.3) MUTATION ANALYSIS
D38V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  8(3P12.3) MUTATED   229 104
  DEL PEAK  8(3P12.3) WILD-TYPE  36  19
  DEL PEAK  8(3P12.3) MUTATED DEL PEAK  8(3P12.3) WILD-TYPE 
                          333                            55 
  DEL PEAK  8(3P12.3) MUTATED DEL PEAK  8(3P12.3) WILD-TYPE 
                          104                            19 
$`DEL PEAK  8(3P12.3) MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
         370          136         2464         2417          146         1415 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 
         345          396         1810          862          758           50 
TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 
        1331          187           85         2754           92         3636 
TCGA-21-1071 TCGA-21-1075 TCGA-21-1079 TCGA-21-1080 TCGA-21-1082 TCGA-21-1083 
        1426         2134          965         3724         3644          267 
TCGA-21-5782 TCGA-21-5786 TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 
         962         1032          979          608          223         1945 
TCGA-22-1002 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 
         131          429          822         1485          623         1067 
TCGA-22-4594 TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 
        1470          734         1161         1057          399         1946 
TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 
         587          358          965         1964         1933          445 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 
        1346           24         1651         1952         1952          357 
TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 
         573          916         1912         1713          506           29 
TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4582 TCGA-33-4583 
        2524         1940         2979         1311         1966         1941 
TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-33-6738 TCGA-34-2596 TCGA-34-2600 
         428         1970         1948          822           80         1874 
TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 
         958          881         1000          951         1528         2062 
TCGA-34-5239 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 
         707          428          941          552          166          120 
TCGA-37-3789 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4141 
          13          200          247          227          238           12 
TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 
         103         1454         2253         1361         1947         1996 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5034 
        1964         1849           52          740           59         1107 
TCGA-39-5035 TCGA-39-5036 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 
         474         1084         1223          684         1176          822 
TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 TCGA-43-6770 TCGA-43-7656 TCGA-43-7657 
        1007          849          376          310          212          236 
TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V 
        1970          407          358         1971          353          366 
TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 
         324          423           12           12          911          541 
TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 
        1948          923         1958         1967          881            3 
TCGA-56-5898 TCGA-56-6545 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 
         555           62           30           13           30           44 
TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 
          40           26            6         1961            1           41 
TCGA-56-8504 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 
         178           36           63           17           16           34 
TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK 
          38            2           46           30           25            4 
TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-A46L 
           4            8          378          911         2167         1723 
TCGA-58-A46M TCGA-60-2695 TCGA-60-2696 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 
        1072          642          109          311         1950         1943 
TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 
        1958          661         1963         1505         1963         1260 
TCGA-60-2712 TCGA-60-2713 TCGA-60-2719 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 
         274         1731         1297          983          908         1092 
TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 
         717          816          358         1973         1957         1955 
TCGA-63-7022 TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 TCGA-66-2742 TCGA-66-2754 
        1947         1952         1967         1311          641           61 
TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2765 
          28           30           30          639          762           61 
TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 
          31           61           61         1947          700          578 
TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 
        1946           61          578         1956          121         1954 
TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 
         759           60          790         1217          699         1955 
TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 
         699         1977          913         1952         1645          122 
TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 
        1492           83          202          211          244           96 
TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 
         121          104         1950         1941         1942         1952 
TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 
        1959         1968           15         1286         1954         1942 
TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 TCGA-77-8130 
        1952         1954          479         1945         1641         1945 
TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 
        1941         1947         1946         1951         1962          833 
TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 
        1943          293         1961         1684         1092           10 
TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA 
        1942         1959         1955         1963         1290         1280 
TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 
        1939          839          713          364          395           34 
TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 
          18           10           49            1         1965           35 
TCGA-85-7844 TCGA-85-7950 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 
         911           60           60           16          960          428 
TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 
         513           13           11           13           54           60 
TCGA-85-8351 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 
          55           54           61           61           22           21 
TCGA-85-8580 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4QQ TCGA-85-A4QR 
         445            3          475           15         1960           25 
TCGA-85-A50Z TCGA-85-A510 TCGA-85-A512 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7766 
        1973         1967         1987           13          111          289 
TCGA-90-7767 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7341 
          89          428          244          331          269          106 
TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 TCGA-94-A4VJ 
         122          160           70           87          356          430 
TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-98-8021 
        1213         1344          189          211          273          413 
TCGA-98-8022 TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-LA-A446 TCGA-MF-A522 
         224          308          222           35           36           83 
TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HI 
        1722         1548         1135 

$`DEL PEAK  8(3P12.3) WILD-TYPE`
TCGA-18-5595 TCGA-21-1072 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1081 
         827         3016         1852         1058          474          284 
TCGA-21-5784 TCGA-21-5787 TCGA-22-1005 TCGA-22-1011 TCGA-22-4596 TCGA-33-4566 
        1268          329         1952           53           17         5287 
TCGA-34-5234 TCGA-34-5240 TCGA-37-3792 TCGA-37-4135 TCGA-39-5031 TCGA-39-5037 
        1715          365           12          207          833         1086 
TCGA-39-5039 TCGA-39-5040 TCGA-43-5668 TCGA-43-6647 TCGA-43-6771 TCGA-43-A475 
         544         1964          349          757         1936          296 
TCGA-43-A56U TCGA-56-6546 TCGA-56-8622 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46N 
         432           26           55         1058         2589          910 
TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2720 TCGA-66-2737 TCGA-66-2744 
        1531         1075         1475           97           61           30 
TCGA-66-2753 TCGA-66-2763 TCGA-77-8007 TCGA-77-8128 TCGA-77-8131 TCGA-77-A5FZ 
          31           30         1960         1953         1941         1953 
TCGA-85-8048 TCGA-85-8352 TCGA-85-8582 TCGA-85-A4PA TCGA-85-A50M TCGA-85-A511 
          26           67          424         1972           19         1972 
TCGA-85-A513 TCGA-90-6837 TCGA-90-7769 TCGA-92-7340 TCGA-96-A4JL TCGA-98-7454 
          24          758          358           82          183          256 
TCGA-L3-A524 
         449 

  DEL PEAK  8(3P12.3) MUTATED DEL PEAK  8(3P12.3) WILD-TYPE 
                            1                            12 
  DEL PEAK  8(3P12.3) MUTATED DEL PEAK  8(3P12.3) WILD-TYPE 
                         3724                          5287 
  DEL PEAK  8(3P12.3) MUTATED DEL PEAK  8(3P12.3) WILD-TYPE 
                          661                           474 
[1] "1.0 - 3724.0 (661.0)"  "12.0 - 5287.0 (474.0)"
[1] "hr=" "1"  
D38V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  8(3P12.3) MUTATED         1       64      118        1        43
  DEL PEAK  8(3P12.3) WILD-TYPE       0        8       19        0         9
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK  8(3P12.3) MUTATED          53         51         18        6
  DEL PEAK  8(3P12.3) WILD-TYPE        18          6          2        0
D38V3, multiclass
            clus
vv           DEL PEAK  8(3P12.3) MUTATED DEL PEAK  8(3P12.3) WILD-TYPE
  STAGE I                              1                             0
  STAGE IA                            64                             8
  STAGE IB                           118                            19
  STAGE II                             1                             0
  STAGE IIA                           43                             9
  STAGE IIB                           53                            18
  STAGE IIIA                          51                             6
  STAGE IIIB                          18                             2
  STAGE IV                             6                             0
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK  8(3P12.3) MUTATED    87 209  44  18
  DEL PEAK  8(3P12.3) WILD-TYPE  11  45   4   2
D38V4, multiclass
    clus
vv   DEL PEAK  8(3P12.3) MUTATED DEL PEAK  8(3P12.3) WILD-TYPE
  T1                          87                            11
  T2                         209                            45
  T3                          44                             4
  T4                          18                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK  8(3P12.3) MUTATED   227  93  29   5
  DEL PEAK  8(3P12.3) WILD-TYPE  34  20   6   0
D38V5, multiclass
    clus
vv   DEL PEAK  8(3P12.3) MUTATED DEL PEAK  8(3P12.3) WILD-TYPE
  N0                         227                            34
  N1                          93                            20
  N2                          29                             6
  N3                           5                             0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A  MX
  DEL PEAK  8(3P12.3) MUTATED   304   5   1  42
  DEL PEAK  8(3P12.3) WILD-TYPE  54   0   0   8
D38V6, multiclass
     clus
vv    DEL PEAK  8(3P12.3) MUTATED DEL PEAK  8(3P12.3) WILD-TYPE
  M0                          304                            54
  M1                            5                             0
  M1A                           1                             0
  MX                           42                             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"
D38V7, binary
                               cls
clus                              0   1
  DEL PEAK  8(3P12.3) MUTATED    89 269
  DEL PEAK  8(3P12.3) WILD-TYPE  18  44
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P12.3) MUTATED     89  269
  DEL PEAK  8(3P12.3) WILD-TYPE   18   44
        clus
vv       DEL PEAK  8(3P12.3) MUTATED DEL PEAK  8(3P12.3) WILD-TYPE
  FEMALE                          89                            18
  MALE                           269                            44
[1] 2 2
[1] FALSE
D38V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK  8(3P12.3) MUTATED                                      10
  DEL PEAK  8(3P12.3) WILD-TYPE                                     2
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK  8(3P12.3) MUTATED                                        3
  DEL PEAK  8(3P12.3) WILD-TYPE                                      3
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK  8(3P12.3) MUTATED                                         1
  DEL PEAK  8(3P12.3) WILD-TYPE                                       0
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  8(3P12.3) MUTATED                                                           344
  DEL PEAK  8(3P12.3) WILD-TYPE                                                          57
D38V9, multiclass
                                                             clus
vv                                                            DEL PEAK  8(3P12.3) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                10
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         344
                                                             clus
vv                                                            DEL PEAK  8(3P12.3) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            57
[1] 4 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  8(3P12.3) MUTATED    11 347
  DEL PEAK  8(3P12.3) WILD-TYPE   2  60
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P12.3) MUTATED     11  347
  DEL PEAK  8(3P12.3) WILD-TYPE    2   60
     clus
vv    DEL PEAK  8(3P12.3) MUTATED DEL PEAK  8(3P12.3) WILD-TYPE
  NO                           11                             2
  YES                         347                            60
[1] 2 2
[1] FALSE
D38V11, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  8(3P12.3) MUTATED   292   5   4  14
  DEL PEAK  8(3P12.3) WILD-TYPE  50   3   0   4
D38V12, multiclass
    clus
vv   DEL PEAK  8(3P12.3) MUTATED DEL PEAK  8(3P12.3) WILD-TYPE
  R0                         292                            50
  R1                           5                             3
  R2                           4                             0
  RX                          14                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(3P12.3) MUTATED       6                        16   252
  DEL PEAK  8(3P12.3) WILD-TYPE     3                         1    46
D38V13, multiclass
                           clus
vv                          DEL PEAK  8(3P12.3) MUTATED
  ASIAN                                               6
  BLACK OR AFRICAN AMERICAN                          16
  WHITE                                             252
                           clus
vv                          DEL PEAK  8(3P12.3) WILD-TYPE
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                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"
D38V14, binary
                               cls
clus                              0   1
  DEL PEAK  8(3P12.3) MUTATED     8 223
  DEL PEAK  8(3P12.3) WILD-TYPE   0  44
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P12.3) MUTATED      8  223
  DEL PEAK  8(3P12.3) WILD-TYPE    0   44
                        clus
vv                       DEL PEAK  8(3P12.3) MUTATED
  HISPANIC OR LATINO                               8
  NOT HISPANIC OR LATINO                         223
                        clus
vv                       DEL PEAK  8(3P12.3) WILD-TYPE
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                            44
[1] 2 2
[1] FALSE

Clustering(39) Variable = DEL PEAK  9(3P12.3) MUTATION ANALYSIS
D39V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  9(3P12.3) MUTATED   225 103
  DEL PEAK  9(3P12.3) WILD-TYPE  40  20
  DEL PEAK  9(3P12.3) MUTATED DEL PEAK  9(3P12.3) WILD-TYPE 
                          328                            60 
  DEL PEAK  9(3P12.3) MUTATED DEL PEAK  9(3P12.3) WILD-TYPE 
                          103                            20 
$`DEL PEAK  9(3P12.3) MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
         370          136         2464         2417          146         1415 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 
         345          396         1810          862          758           50 
TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 
        1331          187           85         2754           92         3636 
TCGA-21-1071 TCGA-21-1075 TCGA-21-1079 TCGA-21-1080 TCGA-21-1082 TCGA-21-1083 
        1426         2134          965         3724         3644          267 
TCGA-21-5782 TCGA-21-5786 TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 
         962         1032          979          608          223         1945 
TCGA-22-1002 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4594 
         131          429          822         1485          623         1470 
TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 
         734         1161         1057          399         1946          587 
TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 
         358          965         1964         1933          445         1346 
TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 
          24         1651         1952         1952          357          573 
TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 
         916         1912         1713          506           29         2524 
TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 
        1940         2979         1311         1966         1941          428 
TCGA-33-4587 TCGA-33-4589 TCGA-33-6738 TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 
        1970         1948          822           80         1874          958 
TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5239 
         881         1000          951         1528         2062          707 
TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 
         428          941          552          166          120           13 
TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 
         200          247          227          238          207           12 
TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 
         103         1454         2253         1361         1947         1996 
TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5034 TCGA-39-5035 
        1849           52          740           59         1107          474 
TCGA-39-5036 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 
        1084         1223          684         1176          822         1007 
TCGA-43-5670 TCGA-43-6143 TCGA-43-6770 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 
         849          376          310          212          236         1970 
TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-46-6025 
         407          358         1971          353          366          324 
TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 
         423           12           12          911          541         1948 
TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 
         923         1958         1967          881            3          555 
TCGA-56-6545 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 
          62           30           13           30           44           40 
TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 TCGA-56-8504 
          26            6         1961            1           41          178 
TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D 
          36           63           17           16           34           38 
TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR 
           2           46           30           25            4            4 
TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-A46L TCGA-58-A46M 
           8          378          911         2167         1723         1072 
TCGA-60-2695 TCGA-60-2696 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 
         642          109          311         1950         1943         1958 
TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 
         661         1963         1505         1963         1260          274 
TCGA-60-2713 TCGA-60-2719 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 
        1731         1297          983          908         1092          717 
TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 
         816          358         1973         1957         1955         1947 
TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 TCGA-66-2742 TCGA-66-2754 TCGA-66-2755 
        1952         1967         1311          641           61           28 
TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2765 TCGA-66-2767 
          30           30          639          762           61           61 
TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 
          61         1947          700          578         1946           61 
TCGA-66-2778 TCGA-66-2780 TCGA-66-2782 TCGA-66-2783 TCGA-66-2786 TCGA-66-2787 
         578         1956         1954          759          790         1217 
TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 
         699         1955          699         1977          913         1952 
TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 
        1645          122         1492           83          202          211 
TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 
         244           96          121          104         1950         1941 
TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 
        1942         1952         1959         1968           15         1286 
TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8008 
        1954         1942         1952         1954          479         1945 
TCGA-77-8009 TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 
        1641         1945         1941         1947         1946         1951 
TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 
        1962          833         1943          293         1961         1684 
TCGA-77-8154 TCGA-77-8156 TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 
        1092           10         1942         1959         1955         1963 
TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 
        1290         1280         1939          839          713          364 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 
         395           34           18           10           49            1 
TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8049 TCGA-85-8052 
        1965           35          911           60           60           16 
TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 
         428          513           13           11           13           54 
TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 
          60           55           54           61           61           22 
TCGA-85-8481 TCGA-85-8580 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4QQ 
          21          445            3          475           15         1960 
TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A510 TCGA-85-A512 TCGA-85-A53L TCGA-85-A5B5 
          25         1973         1967         1987           13          111 
TCGA-90-7766 TCGA-90-7767 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q 
         289           89          428          244          331          269 
TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 
         106          122          160           70           87          356 
TCGA-94-A4VJ TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK 
         430         1213         1344          189          211          273 
TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-LA-A446 
         413          224          308          222           35           36 
TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HI 
          83         1722         1548         1135 

$`DEL PEAK  9(3P12.3) WILD-TYPE`
TCGA-18-5595 TCGA-21-1072 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1081 
         827         3016         1852         1058          474          284 
TCGA-21-5784 TCGA-21-5787 TCGA-22-1005 TCGA-22-1011 TCGA-22-4593 TCGA-22-4596 
        1268          329         1952           53         1067           17 
TCGA-33-4566 TCGA-34-5234 TCGA-34-5240 TCGA-37-3792 TCGA-39-5024 TCGA-39-5031 
        5287         1715          365           12         1964          833 
TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-5668 TCGA-43-6647 TCGA-43-6771 
        1086          544         1964          349          757         1936 
TCGA-43-A475 TCGA-43-A56U TCGA-56-6546 TCGA-56-8622 TCGA-58-8393 TCGA-58-A46J 
         296          432           26           55         1058         2589 
TCGA-58-A46N TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2720 TCGA-66-2737 
         910         1531         1075         1475           97           61 
TCGA-66-2744 TCGA-66-2753 TCGA-66-2763 TCGA-66-2766 TCGA-66-2781 TCGA-66-2785 
          30           31           30           31          121           60 
TCGA-77-8007 TCGA-77-8128 TCGA-77-8131 TCGA-77-A5FZ TCGA-85-8048 TCGA-85-8070 
        1960         1953         1941         1953           26          960 
TCGA-85-8352 TCGA-85-8582 TCGA-85-A4PA TCGA-85-A50M TCGA-85-A511 TCGA-85-A513 
          67          424         1972           19         1972           24 
TCGA-90-6837 TCGA-90-7769 TCGA-92-7340 TCGA-96-A4JL TCGA-98-7454 TCGA-L3-A524 
         758          358           82          183          256          449 

  DEL PEAK  9(3P12.3) MUTATED DEL PEAK  9(3P12.3) WILD-TYPE 
                            1                            12 
  DEL PEAK  9(3P12.3) MUTATED DEL PEAK  9(3P12.3) WILD-TYPE 
                         3724                          5287 
  DEL PEAK  9(3P12.3) MUTATED DEL PEAK  9(3P12.3) WILD-TYPE 
                        651.5                         509.0 
[1] "1.0 - 3724.0 (651.5)"  "12.0 - 5287.0 (509.0)"
[1] "hr=" "1"  
D39V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  9(3P12.3) MUTATED         1       64      115        1        42
  DEL PEAK  9(3P12.3) WILD-TYPE       0        8       22        0        10
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK  9(3P12.3) MUTATED          53         49         19        6
  DEL PEAK  9(3P12.3) WILD-TYPE        18          8          1        0
D39V3, multiclass
            clus
vv           DEL PEAK  9(3P12.3) MUTATED DEL PEAK  9(3P12.3) WILD-TYPE
  STAGE I                              1                             0
  STAGE IA                            64                             8
  STAGE IB                           115                            22
  STAGE II                             1                             0
  STAGE IIA                           42                            10
  STAGE IIB                           53                            18
  STAGE IIIA                          49                             8
  STAGE IIIB                          19                             1
  STAGE IV                             6                             0
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK  9(3P12.3) MUTATED    87 204  44  18
  DEL PEAK  9(3P12.3) WILD-TYPE  11  50   4   2
D39V4, multiclass
    clus
vv   DEL PEAK  9(3P12.3) MUTATED DEL PEAK  9(3P12.3) WILD-TYPE
  T1                          87                            11
  T2                         204                            50
  T3                          44                             4
  T4                          18                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK  9(3P12.3) MUTATED   224  93  27   5
  DEL PEAK  9(3P12.3) WILD-TYPE  37  20   8   0
D39V5, multiclass
    clus
vv   DEL PEAK  9(3P12.3) MUTATED DEL PEAK  9(3P12.3) WILD-TYPE
  N0                         224                            37
  N1                          93                            20
  N2                          27                             8
  N3                           5                             0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A  MX
  DEL PEAK  9(3P12.3) MUTATED   299   5   1  42
  DEL PEAK  9(3P12.3) WILD-TYPE  59   0   0   8
D39V6, multiclass
     clus
vv    DEL PEAK  9(3P12.3) MUTATED DEL PEAK  9(3P12.3) WILD-TYPE
  M0                          299                            59
  M1                            5                             0
  M1A                           1                             0
  MX                           42                             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"
D39V7, binary
                               cls
clus                              0   1
  DEL PEAK  9(3P12.3) MUTATED    88 265
  DEL PEAK  9(3P12.3) WILD-TYPE  19  48
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3P12.3) MUTATED     88  265
  DEL PEAK  9(3P12.3) WILD-TYPE   19   48
        clus
vv       DEL PEAK  9(3P12.3) MUTATED DEL PEAK  9(3P12.3) WILD-TYPE
  FEMALE                          88                            19
  MALE                           265                            48
[1] 2 2
[1] FALSE
D39V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK  9(3P12.3) MUTATED                                      10
  DEL PEAK  9(3P12.3) WILD-TYPE                                     2
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK  9(3P12.3) MUTATED                                        3
  DEL PEAK  9(3P12.3) WILD-TYPE                                      3
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK  9(3P12.3) MUTATED                                         1
  DEL PEAK  9(3P12.3) WILD-TYPE                                       0
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  9(3P12.3) MUTATED                                                           339
  DEL PEAK  9(3P12.3) WILD-TYPE                                                          62
D39V9, multiclass
                                                             clus
vv                                                            DEL PEAK  9(3P12.3) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                10
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         339
                                                             clus
vv                                                            DEL PEAK  9(3P12.3) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            62
[1] 4 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  9(3P12.3) MUTATED    11 342
  DEL PEAK  9(3P12.3) WILD-TYPE   2  65
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3P12.3) MUTATED     11  342
  DEL PEAK  9(3P12.3) WILD-TYPE    2   65
     clus
vv    DEL PEAK  9(3P12.3) MUTATED DEL PEAK  9(3P12.3) WILD-TYPE
  NO                           11                             2
  YES                         342                            65
[1] 2 2
[1] FALSE
D39V11, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  9(3P12.3) MUTATED   287   5   4  14
  DEL PEAK  9(3P12.3) WILD-TYPE  55   3   0   4
D39V12, multiclass
    clus
vv   DEL PEAK  9(3P12.3) MUTATED DEL PEAK  9(3P12.3) WILD-TYPE
  R0                         287                            55
  R1                           5                             3
  R2                           4                             0
  RX                          14                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(3P12.3) MUTATED       6                        16   250
  DEL PEAK  9(3P12.3) WILD-TYPE     3                         1    48
D39V13, multiclass
                           clus
vv                          DEL PEAK  9(3P12.3) MUTATED
  ASIAN                                               6
  BLACK OR AFRICAN AMERICAN                          16
  WHITE                                             250
                           clus
vv                          DEL PEAK  9(3P12.3) WILD-TYPE
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                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"
D39V14, binary
                               cls
clus                              0   1
  DEL PEAK  9(3P12.3) MUTATED     8 222
  DEL PEAK  9(3P12.3) WILD-TYPE   0  45
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3P12.3) MUTATED      8  222
  DEL PEAK  9(3P12.3) WILD-TYPE    0   45
                        clus
vv                       DEL PEAK  9(3P12.3) MUTATED
  HISPANIC OR LATINO                               8
  NOT HISPANIC OR LATINO                         222
                        clus
vv                       DEL PEAK  9(3P12.3) WILD-TYPE
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                            45
[1] 2 2
[1] FALSE

Clustering(40) Variable = DEL PEAK 10(3Q11.1) MUTATION ANALYSIS
D40V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 10(3Q11.1) MUTATED    45  14
  DEL PEAK 10(3Q11.1) WILD-TYPE 220 109
  DEL PEAK 10(3Q11.1) MUTATED DEL PEAK 10(3Q11.1) WILD-TYPE 
                           59                           329 
  DEL PEAK 10(3Q11.1) MUTATED DEL PEAK 10(3Q11.1) WILD-TYPE 
                           14                           109 
$`DEL PEAK 10(3Q11.1) MUTATED`
TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3417 TCGA-18-5592 TCGA-21-1079 
        2464         1415          345          758           92          965 
TCGA-21-1082 TCGA-22-0940 TCGA-22-1016 TCGA-22-1017 TCGA-22-4594 TCGA-33-4533 
        3644          608          822         1485         1470         1940 
TCGA-33-4583 TCGA-33-4589 TCGA-33-6738 TCGA-34-5232 TCGA-37-4129 TCGA-37-4132 
        1941         1948          822         2062          200          227 
TCGA-37-5819 TCGA-39-5019 TCGA-43-8115 TCGA-43-A474 TCGA-46-6025 TCGA-46-6026 
         103         1361          407          353          324          423 
TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-7579 TCGA-56-8504 TCGA-56-A4BX 
        1958         1967          881           44          178           46 
TCGA-56-A5DS TCGA-60-2711 TCGA-60-2719 TCGA-66-2754 TCGA-66-2767 TCGA-66-2781 
           8         1260         1297           61           61          121 
TCGA-66-2794 TCGA-66-2800 TCGA-68-7755 TCGA-68-8251 TCGA-68-A59J TCGA-77-6842 
        1645         1492           83           96          104         1950 
TCGA-77-8130 TCGA-77-8138 TCGA-77-A5G1 TCGA-77-A5GB TCGA-77-A5GH TCGA-85-7697 
        1945         1946         1942         1939          713           10 
TCGA-85-8049 TCGA-85-8071 TCGA-85-8072 TCGA-85-8354 TCGA-85-8481 TCGA-85-8666 
          60          428          513           61           21          475 
TCGA-90-A4ED TCGA-92-7341 TCGA-96-7545 TCGA-98-8022 TCGA-98-8023 
         244          106         1344          224          308 

$`DEL PEAK 10(3Q11.1) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3414 TCGA-18-3415 
         370          136         2417          146          396         1810 
TCGA-18-3416 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 
         862           50         1331          187           85         2754 
TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 
         827         3636         1426         3016         2134         1852 
TCGA-21-1077 TCGA-21-1078 TCGA-21-1080 TCGA-21-1081 TCGA-21-1083 TCGA-21-5782 
        1058          474         3724          284          267          962 
TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0944 TCGA-22-1000 
        1268         1032          329          979          223         1945 
TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-4591 TCGA-22-4593 
         131         1952           53          429          623         1067 
TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 
         734           17         1161         1057          399         1946 
TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 
         587          358          965         1964         1933          445 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 
        1346           24         1651         1952         1952          357 
TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 
         573          916         1912         1713          506           29 
TCGA-33-4532 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4586 
        2524         2979         1311         5287         1966          428 
TCGA-33-4587 TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 
        1970           80         1874          958          881         1000 
TCGA-34-2609 TCGA-34-5231 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 
         951         1528         1715          707          365          428 
TCGA-34-5927 TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 
         941          552          166          120           13           12 
TCGA-37-4130 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-39-5011 TCGA-39-5016 
         247          238          207           12         1454         2253 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 
        1947         1996         1964         1849           52          740 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 
          59          833         1107          474         1084         1086 
TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 
         544         1964         1223          684         1176          822 
TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 
        1007          349          849          376          757          310 
TCGA-43-6771 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8116 TCGA-43-8118 
        1936          212          236         1970          358         1971 
TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 
         296          432          366           12           12          911 
TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 
         541         1948          923            3          555           62 
TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7580 TCGA-56-7582 
          26           30           13           30           40           26 
TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 TCGA-56-8622 TCGA-56-8624 
           6         1961            1           41           55           36 
TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW 
          63           17           16           34           38            2 
TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-58-8388 TCGA-58-8390 
          30           25            4            4          378          911 
TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N 
        2167         1058         2589         1723         1072          910 
TCGA-60-2695 TCGA-60-2696 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 
         642          109          311         1950         1943         1958 
TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2712 TCGA-60-2713 
         661         1963         1505         1963          274         1731 
TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 
        1531         1075         1475           97          983          908 
TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 
        1092          717          816          358         1973         1957 
TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 
        1955         1947         1952         1967         1311           61 
TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 
         641           30           31           28           30           30 
TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2768 
         639          762           30           61           31           61 
TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 
        1947          700          578         1946           61          578 
TCGA-66-2780 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 
        1956         1954          759           60          790         1217 
TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 
         699         1955          699         1977          913         1952 
TCGA-66-2795 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-A59I TCGA-77-6843 
         122          202          211          244          121         1941 
TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 
        1942         1952         1959         1968           15         1286 
TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 
        1954         1942         1952         1954          479         1960 
TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 
        1945         1641         1953         1941         1941         1947 
TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 
        1951         1962          833         1943          293         1961 
TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G3 TCGA-77-A5G6 
        1684         1092           10         1953         1959         1955 
TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GF TCGA-85-6560 TCGA-85-6561 
        1963         1290         1280          839          364          395 
TCGA-85-6798 TCGA-85-7696 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 
          34           18           49            1         1965           35 
TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8052 TCGA-85-8070 TCGA-85-8276 
         911           60           26           16          960           13 
TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 
          11           13           54           60           55           67 
TCGA-85-8353 TCGA-85-8355 TCGA-85-8479 TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 
          54           61           22          445          424            3 
TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z 
          15         1972         1960           25           19         1973 
TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 
        1967         1972         1987           24           13          111 
TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4EE 
         758          289           89          358          428          331 
TCGA-90-A59Q TCGA-92-7340 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 
         269           82          122          160           70           87 
TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK 
         356          430         1213          189          211          273 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 
         183          256          413          222           35          449 
TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HI 
          36           83         1722         1548         1135 

  DEL PEAK 10(3Q11.1) MUTATED DEL PEAK 10(3Q11.1) WILD-TYPE 
                            8                             1 
  DEL PEAK 10(3Q11.1) MUTATED DEL PEAK 10(3Q11.1) WILD-TYPE 
                         3644                          5287 
  DEL PEAK 10(3Q11.1) MUTATED DEL PEAK 10(3Q11.1) WILD-TYPE 
                          513                           661 
[1] "8.0 - 3644.0 (513.0)" "1.0 - 5287.0 (661.0)"
[1] "hr=" "1.2"
D40V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 10(3Q11.1) MUTATED         0        7       24        0         9
  DEL PEAK 10(3Q11.1) WILD-TYPE       1       65      113        1        43
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 10(3Q11.1) MUTATED           9          9          3        2
  DEL PEAK 10(3Q11.1) WILD-TYPE        62         48         17        4
D40V3, multiclass
            clus
vv           DEL PEAK 10(3Q11.1) MUTATED DEL PEAK 10(3Q11.1) WILD-TYPE
  STAGE I                              0                             1
  STAGE IA                             7                            65
  STAGE IB                            24                           113
  STAGE II                             0                             1
  STAGE IIA                            9                            43
  STAGE IIB                            9                            62
  STAGE IIIA                           9                            48
  STAGE IIIB                           3                            17
  STAGE IV                             2                             4
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 10(3Q11.1) MUTATED    13  38  10   2
  DEL PEAK 10(3Q11.1) WILD-TYPE  85 216  38  18
D40V4, multiclass
    clus
vv   DEL PEAK 10(3Q11.1) MUTATED DEL PEAK 10(3Q11.1) WILD-TYPE
  T1                          13                            85
  T2                          38                           216
  T3                          10                            38
  T4                           2                            18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 10(3Q11.1) MUTATED    39  15   7   1
  DEL PEAK 10(3Q11.1) WILD-TYPE 222  98  28   4
D40V5, multiclass
    clus
vv   DEL PEAK 10(3Q11.1) MUTATED DEL PEAK 10(3Q11.1) WILD-TYPE
  N0                          39                           222
  N1                          15                            98
  N2                           7                            28
  N3                           1                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A  MX
  DEL PEAK 10(3Q11.1) MUTATED    52   2   0   9
  DEL PEAK 10(3Q11.1) WILD-TYPE 306   3   1  41
D40V6, multiclass
     clus
vv    DEL PEAK 10(3Q11.1) MUTATED DEL PEAK 10(3Q11.1) WILD-TYPE
  M0                           52                           306
  M1                            2                             3
  M1A                           0                             1
  MX                            9                            41
[1] 4 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 10(3Q11.1) MUTATED    16  47
  DEL PEAK 10(3Q11.1) WILD-TYPE  91 266
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(3Q11.1) MUTATED     16   47
  DEL PEAK 10(3Q11.1) WILD-TYPE   91  266
        clus
vv       DEL PEAK 10(3Q11.1) MUTATED DEL PEAK 10(3Q11.1) WILD-TYPE
  FEMALE                          16                            91
  MALE                            47                           266
[1] 2 2
[1] FALSE
D40V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 10(3Q11.1) MUTATED                                       0
  DEL PEAK 10(3Q11.1) WILD-TYPE                                    12
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 10(3Q11.1) MUTATED                                        2
  DEL PEAK 10(3Q11.1) WILD-TYPE                                      4
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 10(3Q11.1) MUTATED                                         0
  DEL PEAK 10(3Q11.1) WILD-TYPE                                       1
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 10(3Q11.1) MUTATED                                                            61
  DEL PEAK 10(3Q11.1) WILD-TYPE                                                         340
D40V9, multiclass
                                                             clus
vv                                                            DEL PEAK 10(3Q11.1) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          61
                                                             clus
vv                                                            DEL PEAK 10(3Q11.1) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  12
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           340
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V10, binary
                               cls
clus                              0   1
  DEL PEAK 10(3Q11.1) MUTATED     1  62
  DEL PEAK 10(3Q11.1) WILD-TYPE  12 345
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(3Q11.1) MUTATED      1   62
  DEL PEAK 10(3Q11.1) WILD-TYPE   12  345
     clus
vv    DEL PEAK 10(3Q11.1) MUTATED DEL PEAK 10(3Q11.1) WILD-TYPE
  NO                            1                            12
  YES                          62                           345
[1] 2 2
[1] FALSE
D40V11, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 10(3Q11.1) MUTATED    54   0   1   1
  DEL PEAK 10(3Q11.1) WILD-TYPE 288   8   3  17
D40V12, multiclass
    clus
vv   DEL PEAK 10(3Q11.1) MUTATED DEL PEAK 10(3Q11.1) WILD-TYPE
  R0                          54                           288
  R1                           0                             8
  R2                           1                             3
  RX                           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                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(3Q11.1) MUTATED       1                         2    46
  DEL PEAK 10(3Q11.1) WILD-TYPE     8                        15   252
D40V13, multiclass
                           clus
vv                          DEL PEAK 10(3Q11.1) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              46
                           clus
vv                          DEL PEAK 10(3Q11.1) WILD-TYPE
  ASIAN                                                 8
  BLACK OR AFRICAN AMERICAN                            15
  WHITE                                               252
[1] 3 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 10(3Q11.1) MUTATED     4  43
  DEL PEAK 10(3Q11.1) WILD-TYPE   4 224
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(3Q11.1) MUTATED      4   43
  DEL PEAK 10(3Q11.1) WILD-TYPE    4  224
                        clus
vv                       DEL PEAK 10(3Q11.1) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          43
                        clus
vv                       DEL PEAK 10(3Q11.1) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           224
[1] 2 2
[1] FALSE

Clustering(41) Variable = DEL PEAK 11(4P15.2) MUTATION ANALYSIS
D41V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 11(4P15.2) MUTATED   171  71
  DEL PEAK 11(4P15.2) WILD-TYPE  94  52
  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                          242                           146 
  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                           71                            52 
$`DEL PEAK 11(4P15.2) MUTATED`
TCGA-18-3407 TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 
         136         1415          345         1810          862          758 
TCGA-18-3421 TCGA-18-4086 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1076 
        1331           85           92         3636         1426         1852 
TCGA-21-1077 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 
        1058          965         3724          284         3644          267 
TCGA-21-5782 TCGA-21-5786 TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 
         962         1032          329          608          223         1945 
TCGA-22-1011 TCGA-22-1012 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4599 
          53          429         1067         1470          734         1161 
TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 
         399         1946          587          358          965         1964 
TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 TCGA-22-5482 TCGA-22-5483 
        1933          445         1346         1651          357          573 
TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 
         916         1912         1713         2524         1940         2979 
TCGA-33-4547 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 
        1311         1966         1941          428         1970         1948 
TCGA-33-6738 TCGA-34-2600 TCGA-34-2605 TCGA-34-5231 TCGA-34-5232 TCGA-34-5241 
         822         1874          881         1528         2062          428 
TCGA-34-5927 TCGA-34-5928 TCGA-37-3783 TCGA-37-3789 TCGA-37-4133 TCGA-37-4135 
         941          552          120           13          238          207 
TCGA-37-4141 TCGA-37-5819 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5027 
          12          103         2253         1361         1947         1849 
TCGA-39-5031 TCGA-39-5035 TCGA-39-5037 TCGA-39-5040 TCGA-43-2578 TCGA-43-3394 
         833          474         1086         1964          684          822 
TCGA-43-5670 TCGA-43-6143 TCGA-43-6771 TCGA-43-7656 TCGA-43-7657 TCGA-43-8115 
         849          376         1936          212          236          407 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A56U TCGA-43-A56V TCGA-46-6025 TCGA-46-6026 
        1971          353          432          366          324          423 
TCGA-51-4081 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 
         911         1948          923         1958         1967          881 
TCGA-56-5898 TCGA-56-6545 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 
         555           62           30           13           30           44 
TCGA-56-7582 TCGA-56-7730 TCGA-56-8625 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX 
          26            6           63           38            2           46 
TCGA-56-A4ZK TCGA-56-A5DR TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M 
           4            4         1058         2589         1723         1072 
TCGA-60-2695 TCGA-60-2696 TCGA-60-2698 TCGA-60-2703 TCGA-60-2706 TCGA-60-2707 
         642          109          311         1950         1958          661 
TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 
        1963         1505         1963         1260          274         1731 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 
        1297           97          983          908         1092          717 
TCGA-60-2726 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-66-2727 
         358         1957         1955         1947         1952         1967 
TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2753 TCGA-66-2754 TCGA-66-2758 
        1311           61          641           31           61          639 
TCGA-66-2759 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2771 TCGA-66-2773 
         762           61           31           61          578         1946 
TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2783 TCGA-66-2785 
          61          578         1956          121          759           60 
TCGA-66-2786 TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 
         790         1977          913         1645          122         1492 
TCGA-68-7755 TCGA-68-7756 TCGA-68-A59J TCGA-77-6845 TCGA-77-7139 TCGA-77-7142 
          83          202          104         1952         1968         1286 
TCGA-77-7335 TCGA-77-7337 TCGA-77-7463 TCGA-77-7465 TCGA-77-8009 TCGA-77-8128 
        1954         1942         1954          479         1641         1953 
TCGA-77-8130 TCGA-77-8133 TCGA-77-8138 TCGA-77-8139 TCGA-77-8144 TCGA-77-8145 
        1945         1941         1946         1951          833         1943 
TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-A5G3 TCGA-77-A5G7 
         293         1961         1684         1092         1959         1963 
TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 
        1290         1280         1939          839          713          364 
TCGA-85-6561 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7843 
         395           18           10           49            1           35 
TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 
          26           60           16          428          513           13 
TCGA-85-8277 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 
          11           54           60           55           67           54 
TCGA-85-8354 TCGA-85-8481 TCGA-85-8580 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL 
          61           21          445            3          475           15 
TCGA-85-A4QR TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A53L TCGA-85-A5B5 
          25         1967         1972         1987           13          111 
TCGA-90-7766 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 
         289          428          244          331          269           82 
TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7943 TCGA-96-A4JK 
         106          122          160           70          356          273 
TCGA-98-7454 TCGA-98-8021 TCGA-L3-A4E7 TCGA-L3-A524 TCGA-MF-A522 TCGA-NC-A5HE 
         256          413           35          449           83         1722 
TCGA-NC-A5HG TCGA-NC-A5HI 
        1548         1135 

$`DEL PEAK 11(4P15.2) WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3414 TCGA-18-3419 
         370         2464         2417          146          396           50 
TCGA-18-4083 TCGA-18-4721 TCGA-18-5595 TCGA-21-1072 TCGA-21-1075 TCGA-21-1078 
         187         2754          827         3016         2134          474 
TCGA-21-5784 TCGA-21-A5DI TCGA-22-1002 TCGA-22-1005 TCGA-22-1016 TCGA-22-1017 
        1268          979          131         1952          822         1485 
TCGA-22-4591 TCGA-22-4596 TCGA-22-4601 TCGA-22-5478 TCGA-22-5480 TCGA-22-5481 
         623           17         1057           24         1952         1952 
TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4566 TCGA-34-2596 TCGA-34-2604 TCGA-34-2608 
         506           29         5287           80          958         1000 
TCGA-34-2609 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-8454 TCGA-37-3792 
         951         1715          707          365          166           12 
TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-39-5011 TCGA-39-5022 TCGA-39-5024 
         200          247          227         1454         1996         1964 
TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5034 TCGA-39-5036 TCGA-39-5039 
          52          740           59         1107         1084          544 
TCGA-43-2576 TCGA-43-2581 TCGA-43-3920 TCGA-43-5668 TCGA-43-6647 TCGA-43-6770 
        1223         1176         1007          349          757          310 
TCGA-43-7658 TCGA-43-8116 TCGA-43-A475 TCGA-51-4079 TCGA-51-4080 TCGA-52-7622 
        1970          358          296           12           12          541 
TCGA-56-5897 TCGA-56-6546 TCGA-56-7580 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 
           3           26           40         1961            1           41 
TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 
         178           55           36           17           16           34 
TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 
          30           25            8          378          911         2167 
TCGA-58-A46N TCGA-60-2704 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2725 
         910         1943         1531         1075         1475          816 
TCGA-63-6202 TCGA-66-2744 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2763 
        1973           30           28           30           30           30 
TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2782 TCGA-66-2787 TCGA-66-2788 
          61         1947          700         1954         1217          699 
TCGA-66-2789 TCGA-66-2790 TCGA-66-2793 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 
        1955          699         1952          211          244           96 
TCGA-68-A59I TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-7138 TCGA-77-7141 
         121         1950         1941         1942         1959           15 
TCGA-77-7338 TCGA-77-8007 TCGA-77-8008 TCGA-77-8131 TCGA-77-8136 TCGA-77-8140 
        1952         1960         1945         1941         1947         1962 
TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 TCGA-85-6798 TCGA-85-7710 
          10         1953         1942         1955           34         1965 
TCGA-85-7844 TCGA-85-7950 TCGA-85-8070 TCGA-85-8287 TCGA-85-8355 TCGA-85-8479 
         911           60          960           13           61           22 
TCGA-85-8582 TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A50Z TCGA-85-A513 
         424         1972         1960           19         1973           24 
TCGA-90-6837 TCGA-90-7767 TCGA-90-7769 TCGA-94-7033 TCGA-94-A4VJ TCGA-96-7544 
         758           89          358           87          430         1213 
TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-8022 TCGA-98-8023 
        1344          189          211          183          224          308 
TCGA-J1-A4AH TCGA-LA-A446 
         222           36 

  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                            1                             1 
  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                         3724                          5287 
  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                        672.5                         542.5 
[1] "1.0 - 3724.0 (672.5)" "1.0 - 5287.0 (542.5)"
[1] "hr=" "1.1"
D41V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 11(4P15.2) MUTATED         0       40       91        1        36
  DEL PEAK 11(4P15.2) WILD-TYPE       1       32       46        0        16
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 11(4P15.2) MUTATED          39         38         12        3
  DEL PEAK 11(4P15.2) WILD-TYPE        32         19          8        3
D41V3, multiclass
            clus
vv           DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE
  STAGE I                              0                             1
  STAGE IA                            40                            32
  STAGE IB                            91                            46
  STAGE II                             1                             0
  STAGE IIA                           36                            16
  STAGE IIB                           39                            32
  STAGE IIIA                          38                            19
  STAGE IIIB                          12                             8
  STAGE IV                             3                             3
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 11(4P15.2) MUTATED    56 167  30   9
  DEL PEAK 11(4P15.2) WILD-TYPE  42  87  18  11
D41V4, multiclass
    clus
vv   DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE
  T1                          56                            42
  T2                         167                            87
  T3                          30                            18
  T4                           9                            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(4P15.2) MUTATED   156  73  25   4
  DEL PEAK 11(4P15.2) WILD-TYPE 105  40  10   1
D41V5, multiclass
    clus
vv   DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE
  N0                         156                           105
  N1                          73                            40
  N2                          25                            10
  N3                           4                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A  MX
  DEL PEAK 11(4P15.2) MUTATED   227   3   0  28
  DEL PEAK 11(4P15.2) WILD-TYPE 131   2   1  22
D41V6, multiclass
     clus
vv    DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE
  M0                          227                           131
  M1                            3                             2
  M1A                           0                             1
  MX                           28                            22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V7, binary
                               cls
clus                              0   1
  DEL PEAK 11(4P15.2) MUTATED    62 200
  DEL PEAK 11(4P15.2) WILD-TYPE  45 113
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4P15.2) MUTATED     62  200
  DEL PEAK 11(4P15.2) WILD-TYPE   45  113
        clus
vv       DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE
  FEMALE                          62                            45
  MALE                           200                           113
[1] 2 2
[1] FALSE
D41V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 11(4P15.2) MUTATED                                       7
  DEL PEAK 11(4P15.2) WILD-TYPE                                     5
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 11(4P15.2) MUTATED                                        2
  DEL PEAK 11(4P15.2) WILD-TYPE                                      4
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 11(4P15.2) MUTATED                                         1
  DEL PEAK 11(4P15.2) WILD-TYPE                                       0
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 11(4P15.2) MUTATED                                                           252
  DEL PEAK 11(4P15.2) WILD-TYPE                                                         149
D41V9, multiclass
                                                             clus
vv                                                            DEL PEAK 11(4P15.2) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         252
                                                             clus
vv                                                            DEL PEAK 11(4P15.2) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           149
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V10, binary
                               cls
clus                              0   1
  DEL PEAK 11(4P15.2) MUTATED    11 251
  DEL PEAK 11(4P15.2) WILD-TYPE   2 156
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4P15.2) MUTATED     11  251
  DEL PEAK 11(4P15.2) WILD-TYPE    2  156
     clus
vv    DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE
  NO                           11                             2
  YES                         251                           156
[1] 2 2
[1] FALSE
D41V11, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 11(4P15.2) MUTATED   213   4   4  11
  DEL PEAK 11(4P15.2) WILD-TYPE 129   4   0   7
D41V12, multiclass
    clus
vv   DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE
  R0                         213                           129
  R1                           4                             4
  R2                           4                             0
  RX                          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                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(4P15.2) MUTATED       3                        10   186
  DEL PEAK 11(4P15.2) WILD-TYPE     6                         7   112
D41V13, multiclass
                           clus
vv                          DEL PEAK 11(4P15.2) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                          10
  WHITE                                             186
                           clus
vv                          DEL PEAK 11(4P15.2) WILD-TYPE
  ASIAN                                                 6
  BLACK OR AFRICAN AMERICAN                             7
  WHITE                                               112
[1] 3 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 11(4P15.2) MUTATED     5 159
  DEL PEAK 11(4P15.2) WILD-TYPE   3 108
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4P15.2) MUTATED      5  159
  DEL PEAK 11(4P15.2) WILD-TYPE    3  108
                        clus
vv                       DEL PEAK 11(4P15.2) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         159
                        clus
vv                       DEL PEAK 11(4P15.2) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           108
[1] 2 2
[1] FALSE

Clustering(42) Variable = DEL PEAK 12(4Q22.1) MUTATION ANALYSIS
D42V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 12(4Q22.1) MUTATED   155  69
  DEL PEAK 12(4Q22.1) WILD-TYPE 110  54
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                          224                           164 
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                           69                            54 
$`DEL PEAK 12(4Q22.1) MUTATED`
TCGA-18-3407 TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 TCGA-18-4083 TCGA-18-4086 
         136         1415          345         1810          187           85 
TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 
        2754           92         3636         1426         3016         2134 
TCGA-21-1076 TCGA-21-1077 TCGA-21-1079 TCGA-21-1080 TCGA-21-1082 TCGA-21-1083 
        1852         1058          965         3724         3644          267 
TCGA-21-5786 TCGA-21-5787 TCGA-22-0944 TCGA-22-1000 TCGA-22-1011 TCGA-22-1012 
        1032          329          223         1945           53          429 
TCGA-22-4594 TCGA-22-4595 TCGA-22-4599 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 
        1470          734         1161          399         1946          587 
TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5479 
         358          965         1964         1933          445         1651 
TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-33-4532 TCGA-33-4533 
         357          573          916         1912         2524         1940 
TCGA-33-4538 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 
        2979         5287         1966         1941          428         1970 
TCGA-33-4589 TCGA-34-2596 TCGA-34-2600 TCGA-34-2605 TCGA-34-2609 TCGA-34-5241 
        1948           80         1874          881          951          428 
TCGA-34-5927 TCGA-34-5928 TCGA-37-3783 TCGA-37-3789 TCGA-37-4133 TCGA-37-4135 
         941          552          120           13          238          207 
TCGA-37-4141 TCGA-37-5819 TCGA-39-5019 TCGA-39-5021 TCGA-39-5027 TCGA-39-5031 
          12          103         1361         1947         1849          833 
TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 
        1107          474         1084         1964         1223          684 
TCGA-43-3394 TCGA-43-3920 TCGA-43-6143 TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 
         822         1007          376          310         1936          212 
TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-A474 TCGA-43-A56U TCGA-43-A56V 
         236         1970          407          353          432          366 
TCGA-46-6026 TCGA-51-4079 TCGA-51-4081 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 
         423           12          911         1948          923         1958 
TCGA-56-1622 TCGA-56-5898 TCGA-56-6545 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 
         881          555           62           30           13           30 
TCGA-56-7582 TCGA-56-7730 TCGA-56-8625 TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4ZJ 
          26            6           63           38           46           25 
TCGA-56-A5DR TCGA-58-8390 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M 
           4          911         1058         2589         1723         1072 
TCGA-60-2695 TCGA-60-2696 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 
         642          109         1958          661         1963         1505 
TCGA-60-2710 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2719 TCGA-60-2720 
        1963          274         1731         1531         1297           97 
TCGA-60-2723 TCGA-60-2724 TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 
        1092          717          358         1973         1957         1955 
TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2753 
        1952         1967         1311           61          641           31 
TCGA-66-2754 TCGA-66-2757 TCGA-66-2758 TCGA-66-2763 TCGA-66-2765 TCGA-66-2771 
          61           30          639           30           61          578 
TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2785 
        1946           61          578         1956          121           60 
TCGA-66-2786 TCGA-66-2787 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2795 
         790         1217         1977          913         1952          122 
TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-A59I TCGA-68-A59J 
        1492           83          202          211          121          104 
TCGA-77-6843 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 
        1941         1968           15         1286         1954         1942 
TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 
        1954          479         1960         1641         1953         1945 
TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8144 TCGA-77-8148 TCGA-77-8150 
        1941         1947         1946          833          293         1961 
TCGA-77-8153 TCGA-77-8154 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA 
        1684         1092         1955         1963         1290         1280 
TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 TCGA-85-6798 TCGA-85-7696 
        1939          839          713          364           34           18 
TCGA-85-7699 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8276 TCGA-85-8277 
           1           26           60           16           13           11 
TCGA-85-8287 TCGA-85-8350 TCGA-85-8352 TCGA-85-8353 TCGA-85-8479 TCGA-85-8580 
          13           60           67           54           22          445 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A510 TCGA-85-A512 
           3          475         1960           25         1967         1987 
TCGA-85-A53L TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q 
          13          358          428          244          331          269 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7943 
          82          106          122          160           70          356 
TCGA-96-A4JK TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-J1-A4AH TCGA-L3-A524 
         273          256          413          224          222          449 
TCGA-MF-A522 TCGA-NC-A5HI 
          83         1135 

$`DEL PEAK 12(4Q22.1) WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3414 TCGA-18-3416 
         370         2464         2417          146          396          862 
TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-5595 TCGA-21-1078 TCGA-21-1081 
         758           50         1331          827          474          284 
TCGA-21-5782 TCGA-21-5784 TCGA-21-A5DI TCGA-22-0940 TCGA-22-1002 TCGA-22-1005 
         962         1268          979          608          131         1952 
TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4596 TCGA-22-4601 
         822         1485          623         1067           17         1057 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5480 TCGA-22-5481 TCGA-22-5491 TCGA-22-5492 
        1346           24         1952         1952         1713          506 
TCGA-22-A5C4 TCGA-33-4547 TCGA-33-6738 TCGA-34-2604 TCGA-34-2608 TCGA-34-5231 
          29         1311          822          958         1000         1528 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-8454 TCGA-37-3792 
        2062         1715          707          365          166           12 
TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-39-5011 TCGA-39-5016 TCGA-39-5022 
         200          247          227         1454         2253         1996 
TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5037 TCGA-39-5039 
        1964           52          740           59         1086          544 
TCGA-43-2581 TCGA-43-5668 TCGA-43-5670 TCGA-43-6647 TCGA-43-8116 TCGA-43-8118 
        1176          349          849          757          358         1971 
TCGA-43-A475 TCGA-46-6025 TCGA-51-4080 TCGA-52-7622 TCGA-52-7812 TCGA-56-5897 
         296          324           12          541         1967            3 
TCGA-56-6546 TCGA-56-7579 TCGA-56-7580 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 
          26           44           40         1961            1           41 
TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 
         178           55           36           17           16           34 
TCGA-56-A4BW TCGA-56-A4BY TCGA-56-A4ZK TCGA-56-A5DS TCGA-58-8388 TCGA-58-8391 
           2           30            4            8          378         2167 
TCGA-58-A46N TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2711 TCGA-60-2715 
         910          311         1950         1943         1260         1075 
TCGA-60-2716 TCGA-60-2721 TCGA-60-2722 TCGA-60-2725 TCGA-63-7022 TCGA-66-2744 
        1475          983          908          816         1947           30 
TCGA-66-2755 TCGA-66-2756 TCGA-66-2759 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 
          28           30          762           31           61           61 
TCGA-66-2769 TCGA-66-2770 TCGA-66-2782 TCGA-66-2783 TCGA-66-2788 TCGA-66-2789 
        1947          700         1954          759          699         1955 
TCGA-66-2790 TCGA-66-2794 TCGA-68-8250 TCGA-68-8251 TCGA-77-6842 TCGA-77-6844 
         699         1645          244           96         1950         1942 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7338 TCGA-77-8008 TCGA-77-8131 TCGA-77-8139 
        1952         1959         1952         1945         1941         1951 
TCGA-77-8140 TCGA-77-8145 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 
        1962         1943           10         1953         1942         1959 
TCGA-85-6561 TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 
         395           10           49         1965           35          911 
TCGA-85-7950 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8288 TCGA-85-8351 
          60          960          428          513           54           55 
TCGA-85-8354 TCGA-85-8355 TCGA-85-8481 TCGA-85-8582 TCGA-85-A4CL TCGA-85-A4PA 
          61           61           21          424           15         1972 
TCGA-85-A50M TCGA-85-A50Z TCGA-85-A511 TCGA-85-A513 TCGA-85-A5B5 TCGA-90-6837 
          19         1973         1972           24          111          758 
TCGA-90-7766 TCGA-90-7767 TCGA-94-7033 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-7545 
         289           89           87          430         1213         1344 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-8023 TCGA-L3-A4E7 TCGA-LA-A446 
         189          211          183          308           35           36 
TCGA-NC-A5HE TCGA-NC-A5HG 
        1722         1548 

  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                            1                             1 
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                         5287                          2464 
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                        641.5                         661.0 
[1] "1.0 - 5287.0 (641.5)" "1.0 - 2464.0 (661.0)"
[1] "hr=" "1.2"
D42V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 12(4Q22.1) MUTATED         0       37       90        1        27
  DEL PEAK 12(4Q22.1) WILD-TYPE       1       35       47        0        25
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 12(4Q22.1) MUTATED          34         36         10        1
  DEL PEAK 12(4Q22.1) WILD-TYPE        37         21         10        5
D42V3, multiclass
            clus
vv           DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  STAGE I                              0                             1
  STAGE IA                            37                            35
  STAGE IB                            90                            47
  STAGE II                             1                             0
  STAGE IIA                           27                            25
  STAGE IIB                           34                            37
  STAGE IIIA                          36                            21
  STAGE IIIB                          10                            10
  STAGE IV                             1                             5
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 12(4Q22.1) MUTATED    48 155  27   8
  DEL PEAK 12(4Q22.1) WILD-TYPE  50  99  21  12
D42V4, multiclass
    clus
vv   DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  T1                          48                            50
  T2                         155                            99
  T3                          27                            21
  T4                           8                            12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 12(4Q22.1) MUTATED   151  62  21   2
  DEL PEAK 12(4Q22.1) WILD-TYPE 110  51  14   3
D42V5, multiclass
    clus
vv   DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  N0                         151                           110
  N1                          62                            51
  N2                          21                            14
  N3                           2                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A  MX
  DEL PEAK 12(4Q22.1) MUTATED   203   1   0  29
  DEL PEAK 12(4Q22.1) WILD-TYPE 155   4   1  21
D42V6, multiclass
     clus
vv    DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  M0                          203                           155
  M1                            1                             4
  M1A                           0                             1
  MX                           29                            21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V7, binary
                               cls
clus                              0   1
  DEL PEAK 12(4Q22.1) MUTATED    66 172
  DEL PEAK 12(4Q22.1) WILD-TYPE  41 141
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4Q22.1) MUTATED     66  172
  DEL PEAK 12(4Q22.1) WILD-TYPE   41  141
        clus
vv       DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  FEMALE                          66                            41
  MALE                           172                           141
[1] 2 2
[1] FALSE
D42V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 12(4Q22.1) MUTATED                                       5
  DEL PEAK 12(4Q22.1) WILD-TYPE                                     7
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 12(4Q22.1) MUTATED                                        2
  DEL PEAK 12(4Q22.1) WILD-TYPE                                      4
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 12(4Q22.1) MUTATED                                         1
  DEL PEAK 12(4Q22.1) WILD-TYPE                                       0
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 12(4Q22.1) MUTATED                                                           230
  DEL PEAK 12(4Q22.1) WILD-TYPE                                                         171
D42V9, multiclass
                                                             clus
vv                                                            DEL PEAK 12(4Q22.1) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         230
                                                             clus
vv                                                            DEL PEAK 12(4Q22.1) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           171
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V10, binary
                               cls
clus                              0   1
  DEL PEAK 12(4Q22.1) MUTATED    11 227
  DEL PEAK 12(4Q22.1) WILD-TYPE   2 180
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4Q22.1) MUTATED     11  227
  DEL PEAK 12(4Q22.1) WILD-TYPE    2  180
     clus
vv    DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  NO                           11                             2
  YES                         227                           180
[1] 2 2
[1] FALSE
D42V11, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 12(4Q22.1) MUTATED   194   2   3  12
  DEL PEAK 12(4Q22.1) WILD-TYPE 148   6   1   6
D42V12, multiclass
    clus
vv   DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  R0                         194                           148
  R1                           2                             6
  R2                           3                             1
  RX                          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                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(4Q22.1) MUTATED       4                        13   164
  DEL PEAK 12(4Q22.1) WILD-TYPE     5                         4   134
D42V13, multiclass
                           clus
vv                          DEL PEAK 12(4Q22.1) MUTATED
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                          13
  WHITE                                             164
                           clus
vv                          DEL PEAK 12(4Q22.1) WILD-TYPE
  ASIAN                                                 5
  BLACK OR AFRICAN AMERICAN                             4
  WHITE                                               134
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V14, binary
                               cls
clus                              0   1
  DEL PEAK 12(4Q22.1) MUTATED     4 149
  DEL PEAK 12(4Q22.1) WILD-TYPE   4 118
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4Q22.1) MUTATED      4  149
  DEL PEAK 12(4Q22.1) WILD-TYPE    4  118
                        clus
vv                       DEL PEAK 12(4Q22.1) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         149
                        clus
vv                       DEL PEAK 12(4Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           118
[1] 2 2
[1] FALSE

Clustering(43) Variable = DEL PEAK 13(4Q32.3) MUTATION ANALYSIS
D43V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 13(4Q32.3) MUTATED   174  78
  DEL PEAK 13(4Q32.3) WILD-TYPE  91  45
  DEL PEAK 13(4Q32.3) MUTATED DEL PEAK 13(4Q32.3) WILD-TYPE 
                          252                           136 
  DEL PEAK 13(4Q32.3) MUTATED DEL PEAK 13(4Q32.3) WILD-TYPE 
                           78                            45 
$`DEL PEAK 13(4Q32.3) MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 TCGA-18-3417 
         370          136         1415          345         1810          758 
TCGA-18-4083 TCGA-18-4086 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 
         187           85           92         3636         1426         3016 
TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1079 TCGA-21-1080 TCGA-21-1082 
        2134         1852         1058          965         3724         3644 
TCGA-21-1083 TCGA-21-5782 TCGA-21-5786 TCGA-21-5787 TCGA-22-0944 TCGA-22-1000 
         267          962         1032          329          223         1945 
TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4594 TCGA-22-4595 TCGA-22-4599 
          53          429          822         1470          734         1161 
TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 TCGA-22-5472 TCGA-22-5473 
         399         1946          587          358         1964         1933 
TCGA-22-5474 TCGA-22-5479 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 
         445         1651          357          573          916         1912 
TCGA-22-5491 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4566 
        1713           29         2524         1940         2979         5287 
TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-34-2596 
        1966         1941          428         1970         1948           80 
TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 
        1874          958          881          428          941          552 
TCGA-37-4129 TCGA-37-4130 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 
         200          247          238          207           12          103 
TCGA-39-5011 TCGA-39-5019 TCGA-39-5021 TCGA-39-5027 TCGA-39-5034 TCGA-39-5035 
        1454         1361         1947         1849         1107          474 
TCGA-39-5036 TCGA-39-5037 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-3394 
        1084         1086         1964         1223          684          822 
TCGA-43-3920 TCGA-43-6143 TCGA-43-6771 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 
        1007          376         1936          236         1970          407 
TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56U TCGA-43-A56V TCGA-46-6025 
         358         1971          353          432          366          324 
TCGA-46-6026 TCGA-51-4079 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 
         423           12          911          541         1948          923 
TCGA-52-7811 TCGA-56-1622 TCGA-56-5898 TCGA-56-6545 TCGA-56-7221 TCGA-56-7222 
        1958          881          555           62           30           13 
TCGA-56-7223 TCGA-56-7582 TCGA-56-7730 TCGA-56-8503 TCGA-56-8625 TCGA-56-8629 
          30           26            6           41           63           34 
TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-58-8390 
          38           46           25            4            4          911 
TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-60-2695 
        2167         1058         2589         1723         1072          642 
TCGA-60-2696 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2707 TCGA-60-2708 
         109          311         1950         1943          661         1963 
TCGA-60-2709 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2719 
        1505         1260          274         1731         1531         1297 
TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-63-7020 
          97          983          908         1092          717         1957 
TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2753 
        1952         1967         1311           61          641           31 
TCGA-66-2754 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2763 TCGA-66-2765 
          61           30           30          639           30           61 
TCGA-66-2766 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 
          31          578         1946           61          578         1956 
TCGA-66-2781 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2791 TCGA-66-2792 
         121           60          790         1217         1977          913 
TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 
        1952         1645          122         1492           83          202 
TCGA-68-7757 TCGA-68-8250 TCGA-68-A59I TCGA-68-A59J TCGA-77-6843 TCGA-77-7139 
         211          244          121          104         1941         1968 
TCGA-77-7141 TCGA-77-7142 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 
          15         1286         1952         1954          479         1960 
TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 
        1945         1641         1953         1945         1941         1947 
TCGA-77-8138 TCGA-77-8140 TCGA-77-8144 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 
        1946         1962          833          293         1961         1684 
TCGA-77-8154 TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 
        1092           10         1959         1955         1963         1290 
TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 TCGA-85-6561 
        1280         1939          839          713          364          395 
TCGA-85-6798 TCGA-85-7696 TCGA-85-7699 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 
          34           18            1           26           60           16 
TCGA-85-8070 TCGA-85-8072 TCGA-85-8277 TCGA-85-8287 TCGA-85-8350 TCGA-85-8352 
         960          513           11           13           60           67 
TCGA-85-8353 TCGA-85-8479 TCGA-85-8580 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL 
          54           22          445            3          475           15 
TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A53L 
        1960           25         1973         1967         1972           13 
TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q 
          89          358          428          244          331          269 
TCGA-92-7340 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 
          82          122          160           70           87          356 
TCGA-94-A4VJ TCGA-96-7544 TCGA-96-7545 TCGA-96-A4JK TCGA-98-7454 TCGA-98-8021 
         430         1213         1344          273          256          413 
TCGA-98-8022 TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HI 
         224          449           36           83         1722         1135 

$`DEL PEAK 13(4Q32.3) WILD-TYPE`
TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3414 TCGA-18-3416 TCGA-18-3419 
        2464         2417          146          396          862           50 
TCGA-18-3421 TCGA-18-4721 TCGA-18-5595 TCGA-21-1078 TCGA-21-1081 TCGA-21-5784 
        1331         2754          827          474          284         1268 
TCGA-21-A5DI TCGA-22-0940 TCGA-22-1002 TCGA-22-1005 TCGA-22-1017 TCGA-22-4591 
         979          608          131         1952         1485          623 
TCGA-22-4593 TCGA-22-4596 TCGA-22-4601 TCGA-22-5471 TCGA-22-5477 TCGA-22-5478 
        1067           17         1057          965         1346           24 
TCGA-22-5480 TCGA-22-5481 TCGA-22-5492 TCGA-33-4547 TCGA-33-6738 TCGA-34-2608 
        1952         1952          506         1311          822         1000 
TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 
         951         1528         2062         1715          707          365 
TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4132 TCGA-39-5016 
         166          120           13           12          227         2253 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 
        1996         1964           52          740           59          833 
TCGA-39-5039 TCGA-43-2581 TCGA-43-5668 TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 
         544         1176          349          849          757          310 
TCGA-43-7656 TCGA-43-A475 TCGA-51-4080 TCGA-52-7812 TCGA-56-5897 TCGA-56-6546 
         212          296           12         1967            3           26 
TCGA-56-7579 TCGA-56-7580 TCGA-56-7731 TCGA-56-7822 TCGA-56-8504 TCGA-56-8622 
          44           40         1961            1          178           55 
TCGA-56-8624 TCGA-56-8626 TCGA-56-8628 TCGA-56-A4BW TCGA-56-A4BY TCGA-56-A5DS 
          36           17           16            2           30            8 
TCGA-58-8388 TCGA-58-A46N TCGA-60-2706 TCGA-60-2710 TCGA-60-2715 TCGA-60-2716 
         378          910         1958         1963         1075         1475 
TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-63-7021 TCGA-63-7022 TCGA-66-2744 
         816          358         1973         1955         1947           30 
TCGA-66-2755 TCGA-66-2759 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 
          28          762           61           61         1947          700 
TCGA-66-2782 TCGA-66-2783 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-68-8251 
        1954          759          699         1955          699           96 
TCGA-77-6842 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7335 TCGA-77-7337 
        1950         1942         1952         1959         1954         1942 
TCGA-77-8131 TCGA-77-8139 TCGA-77-8145 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-85-7697 
        1941         1951         1943         1953         1942           10 
TCGA-85-7698 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8071 
          49         1965           35          911           60          428 
TCGA-85-8276 TCGA-85-8288 TCGA-85-8351 TCGA-85-8354 TCGA-85-8355 TCGA-85-8481 
          13           54           55           61           61           21 
TCGA-85-8582 TCGA-85-A4PA TCGA-85-A50M TCGA-85-A512 TCGA-85-A513 TCGA-85-A5B5 
         424         1972           19         1987           24          111 
TCGA-90-6837 TCGA-90-7766 TCGA-92-7341 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL 
         758          289          106          189          211          183 
TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-NC-A5HG 
         308          222           35         1548 

  DEL PEAK 13(4Q32.3) MUTATED DEL PEAK 13(4Q32.3) WILD-TYPE 
                            1                             1 
  DEL PEAK 13(4Q32.3) MUTATED DEL PEAK 13(4Q32.3) WILD-TYPE 
                         5287                          2754 
  DEL PEAK 13(4Q32.3) MUTATED DEL PEAK 13(4Q32.3) WILD-TYPE 
                        641.5                         661.0 
[1] "1.0 - 5287.0 (641.5)" "1.0 - 2754.0 (661.0)"
[1] "hr=" "1.1"
D43V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 13(4Q32.3) MUTATED         0       45      100        1        25
  DEL PEAK 13(4Q32.3) WILD-TYPE       1       27       37        0        27
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 13(4Q32.3) MUTATED          48         37         11        2
  DEL PEAK 13(4Q32.3) WILD-TYPE        23         20          9        4
D43V3, multiclass
            clus
vv           DEL PEAK 13(4Q32.3) MUTATED DEL PEAK 13(4Q32.3) WILD-TYPE
  STAGE I                              0                             1
  STAGE IA                            45                            27
  STAGE IB                           100                            37
  STAGE II                             1                             0
  STAGE IIA                           25                            27
  STAGE IIB                           48                            23
  STAGE IIIA                          37                            20
  STAGE IIIB                          11                             9
  STAGE IV                             2                             4
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 13(4Q32.3) MUTATED    56 178  28   9
  DEL PEAK 13(4Q32.3) WILD-TYPE  42  76  20  11
D43V4, multiclass
    clus
vv   DEL PEAK 13(4Q32.3) MUTATED DEL PEAK 13(4Q32.3) WILD-TYPE
  T1                          56                            42
  T2                         178                            76
  T3                          28                            20
  T4                           9                            11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 13(4Q32.3) MUTATED   172  72  22   2
  DEL PEAK 13(4Q32.3) WILD-TYPE  89  41  13   3
D43V5, multiclass
    clus
vv   DEL PEAK 13(4Q32.3) MUTATED DEL PEAK 13(4Q32.3) WILD-TYPE
  N0                         172                            89
  N1                          72                            41
  N2                          22                            13
  N3                           2                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A  MX
  DEL PEAK 13(4Q32.3) MUTATED   232   2   0  33
  DEL PEAK 13(4Q32.3) WILD-TYPE 126   3   1  17
D43V6, multiclass
     clus
vv    DEL PEAK 13(4Q32.3) MUTATED DEL PEAK 13(4Q32.3) WILD-TYPE
  M0                          232                           126
  M1                            2                             3
  M1A                           0                             1
  MX                           33                            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"
D43V7, binary
                               cls
clus                              0   1
  DEL PEAK 13(4Q32.3) MUTATED    76 195
  DEL PEAK 13(4Q32.3) WILD-TYPE  31 118
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4Q32.3) MUTATED     76  195
  DEL PEAK 13(4Q32.3) WILD-TYPE   31  118
        clus
vv       DEL PEAK 13(4Q32.3) MUTATED DEL PEAK 13(4Q32.3) WILD-TYPE
  FEMALE                          76                            31
  MALE                           195                           118
[1] 2 2
[1] FALSE
D43V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 13(4Q32.3) MUTATED                                       5
  DEL PEAK 13(4Q32.3) WILD-TYPE                                     7
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 13(4Q32.3) MUTATED                                        2
  DEL PEAK 13(4Q32.3) WILD-TYPE                                      4
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 13(4Q32.3) MUTATED                                         1
  DEL PEAK 13(4Q32.3) WILD-TYPE                                       0
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 13(4Q32.3) MUTATED                                                           263
  DEL PEAK 13(4Q32.3) WILD-TYPE                                                         138
D43V9, multiclass
                                                             clus
vv                                                            DEL PEAK 13(4Q32.3) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         263
                                                             clus
vv                                                            DEL PEAK 13(4Q32.3) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           138
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V10, binary
                               cls
clus                              0   1
  DEL PEAK 13(4Q32.3) MUTATED    11 260
  DEL PEAK 13(4Q32.3) WILD-TYPE   2 147
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4Q32.3) MUTATED     11  260
  DEL PEAK 13(4Q32.3) WILD-TYPE    2  147
     clus
vv    DEL PEAK 13(4Q32.3) MUTATED DEL PEAK 13(4Q32.3) WILD-TYPE
  NO                           11                             2
  YES                         260                           147
[1] 2 2
[1] FALSE
D43V11, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 13(4Q32.3) MUTATED   222   4   2  12
  DEL PEAK 13(4Q32.3) WILD-TYPE 120   4   2   6
D43V12, multiclass
    clus
vv   DEL PEAK 13(4Q32.3) MUTATED DEL PEAK 13(4Q32.3) WILD-TYPE
  R0                         222                           120
  R1                           4                             4
  R2                           2                             2
  RX                          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                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(4Q32.3) MUTATED       4                        12   192
  DEL PEAK 13(4Q32.3) WILD-TYPE     5                         5   106
D43V13, multiclass
                           clus
vv                          DEL PEAK 13(4Q32.3) MUTATED
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                          12
  WHITE                                             192
                           clus
vv                          DEL PEAK 13(4Q32.3) WILD-TYPE
  ASIAN                                                 5
  BLACK OR AFRICAN AMERICAN                             5
  WHITE                                               106
[1] 3 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 13(4Q32.3) MUTATED     5 172
  DEL PEAK 13(4Q32.3) WILD-TYPE   3  95
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4Q32.3) MUTATED      5  172
  DEL PEAK 13(4Q32.3) WILD-TYPE    3   95
                        clus
vv                       DEL PEAK 13(4Q32.3) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         172
                        clus
vv                       DEL PEAK 13(4Q32.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            95
[1] 2 2
[1] FALSE

Clustering(44) Variable = DEL PEAK 14(4Q35.2) MUTATION ANALYSIS
D44V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 14(4Q35.2) MUTATED   176  83
  DEL PEAK 14(4Q35.2) WILD-TYPE  89  40
  DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE 
                          259                           129 
  DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE 
                           83                            40 
$`DEL PEAK 14(4Q35.2) MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3411 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 
         370          136         1415         1810          862          758 
TCGA-18-4083 TCGA-18-4086 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 
         187           85           92         3636         1426         3016 
TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1079 TCGA-21-1080 TCGA-21-1082 
        2134         1852         1058          965         3724         3644 
TCGA-21-1083 TCGA-21-5782 TCGA-21-5786 TCGA-21-5787 TCGA-22-0944 TCGA-22-1000 
         267          962         1032          329          223         1945 
TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4594 TCGA-22-4595 TCGA-22-4599 
          53          429          822         1470          734         1161 
TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 TCGA-22-5472 TCGA-22-5473 
         399         1946          587          358         1964         1933 
TCGA-22-5474 TCGA-22-5479 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 
         445         1651          357          573          916         1912 
TCGA-22-5491 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 
        1713           29         2524         1940         2979         1311 
TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 
        5287         1966         1941          428         1970         1948 
TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-5241 
          80         1874          958          881         1000          428 
TCGA-34-5927 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4133 
         941           13           12          200          247          238 
TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 TCGA-39-5019 TCGA-39-5021 
         207           12          103         1454         1361         1947 
TCGA-39-5027 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5040 
        1849         1107          474         1084         1086         1964 
TCGA-43-2576 TCGA-43-2578 TCGA-43-3394 TCGA-43-3920 TCGA-43-6143 TCGA-43-6647 
        1223          684          822         1007          376          757 
TCGA-43-6770 TCGA-43-6771 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 
         310         1936          236         1970          407          358 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-6025 
        1971          353          296          432          366          324 
TCGA-46-6026 TCGA-51-4079 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 
         423           12          911          541         1948          923 
TCGA-52-7811 TCGA-56-1622 TCGA-56-5898 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 
        1958          881          555           30           13           30 
TCGA-56-7582 TCGA-56-7730 TCGA-56-8503 TCGA-56-8622 TCGA-56-8625 TCGA-56-8629 
          26            6           41           55           63           34 
TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-58-8390 
          38           46           25            4            4          911 
TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-60-2695 
        2167         1058         2589         1723         1072          642 
TCGA-60-2696 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2707 TCGA-60-2708 
         109          311         1950         1943          661         1963 
TCGA-60-2709 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2719 TCGA-60-2720 
        1505          274         1731         1531         1297           97 
TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2726 TCGA-63-7020 TCGA-63-7023 
         908         1092          717          358         1957         1952 
TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2753 TCGA-66-2754 
        1967         1311           61          641           31           61 
TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 
          30           30          639           30           61           31 
TCGA-66-2769 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 
        1947         1946           61          578         1956          121 
TCGA-66-2785 TCGA-66-2787 TCGA-66-2789 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 
          60         1217         1955         1977          913         1952 
TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 
        1645          122         1492           83          202          211 
TCGA-68-8250 TCGA-68-A59I TCGA-68-A59J TCGA-77-6843 TCGA-77-6845 TCGA-77-7138 
         244          121          104         1941         1952         1959 
TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 
        1968           15         1286         1952         1954          479 
TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8133 
        1960         1945         1641         1953         1945         1941 
TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8148 
        1947         1946         1951         1962          833          293 
TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5G6 TCGA-77-A5G7 
        1961         1684         1092           10         1955         1963 
TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-85-6560 TCGA-85-6561 
        1290         1280         1939          839          364          395 
TCGA-85-6798 TCGA-85-7696 TCGA-85-7698 TCGA-85-7699 TCGA-85-8048 TCGA-85-8049 
          34           18           49            1           26           60 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 
          16          960          513           13           11           13 
TCGA-85-8350 TCGA-85-8352 TCGA-85-8353 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 
          60           67           54           22           21          445 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M 
           3          475           15         1960           25           19 
TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A53L TCGA-90-7769 TCGA-90-7964 
        1973         1967         1972           13          358          428 
TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-8063 TCGA-92-8065 TCGA-94-7033 
         244          331          269          122           70           87 
TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-7545 TCGA-96-A4JK TCGA-98-7454 
         356          430         1213         1344          273          256 
TCGA-98-8021 TCGA-98-8022 TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE 
         413          224          449           36           83         1722 
TCGA-NC-A5HI 
        1135 

$`DEL PEAK 14(4Q35.2) WILD-TYPE`
TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3412 TCGA-18-3414 TCGA-18-3419 
        2464         2417          146          345          396           50 
TCGA-18-3421 TCGA-18-4721 TCGA-18-5595 TCGA-21-1078 TCGA-21-1081 TCGA-21-5784 
        1331         2754          827          474          284         1268 
TCGA-21-A5DI TCGA-22-0940 TCGA-22-1002 TCGA-22-1005 TCGA-22-1017 TCGA-22-4591 
         979          608          131         1952         1485          623 
TCGA-22-4593 TCGA-22-4596 TCGA-22-4601 TCGA-22-5471 TCGA-22-5477 TCGA-22-5478 
        1067           17         1057          965         1346           24 
TCGA-22-5480 TCGA-22-5481 TCGA-22-5492 TCGA-33-6738 TCGA-34-2609 TCGA-34-5231 
        1952         1952          506          822          951         1528 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5928 TCGA-34-8454 
        2062         1715          707          365          552          166 
TCGA-37-3783 TCGA-37-4132 TCGA-39-5016 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 
         120          227         2253         1996         1964           52 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5039 TCGA-43-2581 TCGA-43-5668 
         740           59          833          544         1176          349 
TCGA-43-5670 TCGA-43-7656 TCGA-51-4080 TCGA-52-7812 TCGA-56-5897 TCGA-56-6545 
         849          212           12         1967            3           62 
TCGA-56-6546 TCGA-56-7579 TCGA-56-7580 TCGA-56-7731 TCGA-56-7822 TCGA-56-8504 
          26           44           40         1961            1          178 
TCGA-56-8624 TCGA-56-8626 TCGA-56-8628 TCGA-56-A4BW TCGA-56-A4BY TCGA-56-A5DS 
          36           17           16            2           30            8 
TCGA-58-8388 TCGA-58-A46N TCGA-60-2706 TCGA-60-2710 TCGA-60-2711 TCGA-60-2715 
         378          910         1958         1963         1260         1075 
TCGA-60-2716 TCGA-60-2721 TCGA-60-2725 TCGA-63-6202 TCGA-63-7021 TCGA-63-7022 
        1475          983          816         1973         1955         1947 
TCGA-66-2744 TCGA-66-2755 TCGA-66-2759 TCGA-66-2767 TCGA-66-2768 TCGA-66-2770 
          30           28          762           61           61          700 
TCGA-66-2771 TCGA-66-2782 TCGA-66-2783 TCGA-66-2786 TCGA-66-2788 TCGA-66-2790 
         578         1954          759          790          699          699 
TCGA-68-8251 TCGA-77-6842 TCGA-77-6844 TCGA-77-7335 TCGA-77-7337 TCGA-77-8131 
          96         1950         1942         1954         1942         1941 
TCGA-77-8145 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5GH TCGA-85-7697 
        1943         1953         1942         1959          713           10 
TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8071 TCGA-85-8288 
        1965           35          911           60          428           54 
TCGA-85-8351 TCGA-85-8354 TCGA-85-8355 TCGA-85-8582 TCGA-85-A4PA TCGA-85-A512 
          55           61           61          424         1972         1987 
TCGA-85-A513 TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-92-7340 
          24          111          758          289           89           82 
TCGA-92-7341 TCGA-92-8064 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-8023 
         106          160          189          211          183          308 
TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-NC-A5HG 
         222           35         1548 

  DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE 
                            1                             1 
  DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE 
                         5287                          2754 
  DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE 
                          642                           623 
[1] "1.0 - 5287.0 (642.0)" "1.0 - 2754.0 (623.0)"
[1] "hr=" "1"  
D44V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 14(4Q35.2) MUTATED         0       44      102        1        27
  DEL PEAK 14(4Q35.2) WILD-TYPE       1       28       35        0        25
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 14(4Q35.2) MUTATED          50         34         13        2
  DEL PEAK 14(4Q35.2) WILD-TYPE        21         23          7        4
D44V3, multiclass
            clus
vv           DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE
  STAGE I                              0                             1
  STAGE IA                            44                            28
  STAGE IB                           102                            35
  STAGE II                             1                             0
  STAGE IIA                           27                            25
  STAGE IIB                           50                            21
  STAGE IIIA                          34                            23
  STAGE IIIB                          13                             7
  STAGE IV                             2                             4
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 14(4Q35.2) MUTATED    58 177  30  10
  DEL PEAK 14(4Q35.2) WILD-TYPE  40  77  18  10
D44V4, multiclass
    clus
vv   DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE
  T1                          58                            40
  T2                         177                            77
  T3                          30                            18
  T4                          10                            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 14(4Q35.2) MUTATED   179  69  21   3
  DEL PEAK 14(4Q35.2) WILD-TYPE  82  44  14   2
D44V5, multiclass
    clus
vv   DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE
  N0                         179                            82
  N1                          69                            44
  N2                          21                            14
  N3                           3                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A  MX
  DEL PEAK 14(4Q35.2) MUTATED   236   2   0  32
  DEL PEAK 14(4Q35.2) WILD-TYPE 122   3   1  18
D44V6, multiclass
     clus
vv    DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE
  M0                          236                           122
  M1                            2                             3
  M1A                           0                             1
  MX                           32                            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"
D44V7, binary
                               cls
clus                              0   1
  DEL PEAK 14(4Q35.2) MUTATED    73 202
  DEL PEAK 14(4Q35.2) WILD-TYPE  34 111
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(4Q35.2) MUTATED     73  202
  DEL PEAK 14(4Q35.2) WILD-TYPE   34  111
        clus
vv       DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE
  FEMALE                          73                            34
  MALE                           202                           111
[1] 2 2
[1] FALSE
D44V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 14(4Q35.2) MUTATED                                       5
  DEL PEAK 14(4Q35.2) WILD-TYPE                                     7
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 14(4Q35.2) MUTATED                                        3
  DEL PEAK 14(4Q35.2) WILD-TYPE                                      3
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 14(4Q35.2) MUTATED                                         1
  DEL PEAK 14(4Q35.2) WILD-TYPE                                       0
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 14(4Q35.2) MUTATED                                                           266
  DEL PEAK 14(4Q35.2) WILD-TYPE                                                         135
D44V9, multiclass
                                                             clus
vv                                                            DEL PEAK 14(4Q35.2) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         266
                                                             clus
vv                                                            DEL PEAK 14(4Q35.2) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           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"
D44V10, binary
                               cls
clus                              0   1
  DEL PEAK 14(4Q35.2) MUTATED    11 264
  DEL PEAK 14(4Q35.2) WILD-TYPE   2 143
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(4Q35.2) MUTATED     11  264
  DEL PEAK 14(4Q35.2) WILD-TYPE    2  143
     clus
vv    DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE
  NO                           11                             2
  YES                         264                           143
[1] 2 2
[1] FALSE
D44V11, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 14(4Q35.2) MUTATED   226   5   2  12
  DEL PEAK 14(4Q35.2) WILD-TYPE 116   3   2   6
D44V12, multiclass
    clus
vv   DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE
  R0                         226                           116
  R1                           5                             3
  R2                           2                             2
  RX                          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                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(4Q35.2) MUTATED       4                        12   195
  DEL PEAK 14(4Q35.2) WILD-TYPE     5                         5   103
D44V13, multiclass
                           clus
vv                          DEL PEAK 14(4Q35.2) MUTATED
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                          12
  WHITE                                             195
                           clus
vv                          DEL PEAK 14(4Q35.2) WILD-TYPE
  ASIAN                                                 5
  BLACK OR AFRICAN AMERICAN                             5
  WHITE                                               103
[1] 3 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 14(4Q35.2) MUTATED     5 175
  DEL PEAK 14(4Q35.2) WILD-TYPE   3  92
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(4Q35.2) MUTATED      5  175
  DEL PEAK 14(4Q35.2) WILD-TYPE    3   92
                        clus
vv                       DEL PEAK 14(4Q35.2) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         175
                        clus
vv                       DEL PEAK 14(4Q35.2) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            92
[1] 2 2
[1] FALSE

Clustering(45) Variable = DEL PEAK 15(5Q12.1) MUTATION ANALYSIS
D45V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 15(5Q12.1) MUTATED   204  84
  DEL PEAK 15(5Q12.1) WILD-TYPE  61  39
  DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE 
                          288                           100 
  DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE 
                           84                            39 
$`DEL PEAK 15(5Q12.1) MUTATED`
TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 
        2464         2417          146          396         1810          862 
TCGA-18-3417 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 
         758          187           85         2754           92         3636 
TCGA-21-1072 TCGA-21-1075 TCGA-21-1079 TCGA-21-1080 TCGA-21-1082 TCGA-21-1083 
        3016         2134          965         3724         3644          267 
TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 
         962         1268         1032          329          979          608 
TCGA-22-0944 TCGA-22-1002 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 
         223          131           53          429          822          623 
TCGA-22-4593 TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 
        1067          734         1161         1057          399         1946 
TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 
         587          358          965         1964         1933          445 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 
        1346           24         1651          357          573          916 
TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 
        1713          506           29         2524         1940         2979 
TCGA-33-4547 TCGA-33-4582 TCGA-33-4586 TCGA-33-6738 TCGA-34-2596 TCGA-34-2600 
        1311         1966          428          822           80         1874 
TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5239 
         958          881         1000          951         1528          707 
TCGA-34-5241 TCGA-34-5927 TCGA-37-3789 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 
         428          941           13          247          227          238 
TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5016 TCGA-39-5021 TCGA-39-5024 
         207           12          103         2253         1947         1964 
TCGA-39-5027 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5036 TCGA-39-5037 
        1849          740           59          833         1084         1086 
TCGA-39-5039 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 
         544         1223          684         1176          822         1007 
TCGA-43-5668 TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 TCGA-43-7656 TCGA-43-7657 
         349          849          757          310          212          236 
TCGA-43-7658 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56U TCGA-43-A56V 
        1970          358         1971          353          432          366 
TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 
         324          423           12           12          911          541 
TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-56-1622 TCGA-56-5897 TCGA-56-6545 
        1948          923         1958          881            3           62 
TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 
          26           30           13           30           44           40 
TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 TCGA-56-8622 
          26            6         1961            1           41           55 
TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW 
          63           17           16           34           38            2 
TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS 
          46           30           25            4            4            8 
TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M 
         378          911         2167         2589         1723         1072 
TCGA-60-2695 TCGA-60-2696 TCGA-60-2698 TCGA-60-2703 TCGA-60-2706 TCGA-60-2707 
         642          109          311         1950         1958          661 
TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2713 TCGA-60-2714 
        1963         1505         1963         1260         1731         1531 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 
        1297           97          908         1092          717          816 
TCGA-63-7020 TCGA-63-7022 TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 
        1957         1947         1952         1967         1311           61 
TCGA-66-2742 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 
         641           31           61           28           30           30 
TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2766 TCGA-66-2768 TCGA-66-2769 
         639          762           30           31           61         1947 
TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2781 TCGA-66-2785 TCGA-66-2786 
         578         1946           61          121           60          790 
TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 
        1217          699         1955          699         1977          913 
TCGA-66-2793 TCGA-66-2794 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 
        1952         1645         1492           83          202          211 
TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-77-6842 TCGA-77-6844 TCGA-77-6845 
         244           96          121         1950         1942         1952 
TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 
        1968           15         1286         1942         1952         1954 
TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 
         479         1960         1945         1641         1953         1945 
TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8145 
        1941         1947         1946         1951         1962         1943 
TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5G3 
         293         1961         1684         1092           10         1959 
TCGA-77-A5G7 TCGA-77-A5GA TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 TCGA-85-6561 
        1963         1280          839          713          364          395 
TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7843 
          34           18           10           49            1           35 
TCGA-85-7844 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 
         911           16          960          428          513           13 
TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 TCGA-85-8354 
          13           54           60           55           54           61 
TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8666 TCGA-85-A4QQ 
          61           22           21          445          475         1960 
TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 
          25           19         1973         1967         1972         1987 
TCGA-85-A5B5 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-90-A59Q 
         111          289           89          358          428          269 
TCGA-92-7340 TCGA-92-8063 TCGA-92-8064 TCGA-94-7033 TCGA-94-7943 TCGA-96-7544 
          82          122          160           87          356         1213 
TCGA-96-7545 TCGA-96-8169 TCGA-96-A4JK TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 
        1344          189          273          413          224          308 
TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HG TCGA-NC-A5HI 
          35          449           36           83         1548         1135 

$`DEL PEAK 15(5Q12.1) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3411 TCGA-18-3412 TCGA-18-3419 TCGA-18-3421 
         370          136         1415          345           50         1331 
TCGA-18-5595 TCGA-21-1071 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1081 
         827         1426         1852         1058          474          284 
TCGA-22-1000 TCGA-22-1005 TCGA-22-1017 TCGA-22-4594 TCGA-22-4596 TCGA-22-5480 
        1945         1952         1485         1470           17         1952 
TCGA-22-5481 TCGA-22-5489 TCGA-33-4566 TCGA-33-4583 TCGA-33-4587 TCGA-33-4589 
        1952         1912         5287         1941         1970         1948 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5240 TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 
        2062         1715          365          552          166          120 
TCGA-37-3792 TCGA-37-4129 TCGA-39-5011 TCGA-39-5019 TCGA-39-5022 TCGA-39-5028 
          12          200         1454         1361         1996           52 
TCGA-39-5034 TCGA-39-5035 TCGA-39-5040 TCGA-43-6143 TCGA-43-6771 TCGA-43-8115 
        1107          474         1964          376         1936          407 
TCGA-43-A475 TCGA-52-7812 TCGA-56-5898 TCGA-56-8504 TCGA-56-8624 TCGA-58-8393 
         296         1967          555          178           36         1058 
TCGA-58-A46N TCGA-60-2704 TCGA-60-2712 TCGA-60-2715 TCGA-60-2716 TCGA-60-2721 
         910         1943          274         1075         1475          983 
TCGA-60-2726 TCGA-63-6202 TCGA-63-7021 TCGA-66-2744 TCGA-66-2765 TCGA-66-2767 
         358         1973         1955           30           61           61 
TCGA-66-2770 TCGA-66-2778 TCGA-66-2780 TCGA-66-2782 TCGA-66-2783 TCGA-66-2795 
         700          578         1956         1954          759          122 
TCGA-68-A59J TCGA-77-6843 TCGA-77-7138 TCGA-77-7335 TCGA-77-8131 TCGA-77-8144 
         104         1941         1959         1954         1941          833 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G8 TCGA-77-A5GB TCGA-85-7710 
        1953         1942         1955         1290         1939         1965 
TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8277 TCGA-85-8352 TCGA-85-8582 
          60           26           60           11           67          424 
TCGA-85-8664 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 
           3           15         1972           24           13          758 
TCGA-90-A4ED TCGA-90-A4EE TCGA-92-7341 TCGA-92-8065 TCGA-94-A4VJ TCGA-96-8170 
         244          331          106           70          430          211 
TCGA-96-A4JL TCGA-98-7454 TCGA-J1-A4AH TCGA-NC-A5HE 
         183          256          222         1722 

  DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE 
                            1                             3 
  DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE 
                         3724                          5287 
  DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE 
                        631.0                         758.5 
[1] "1.0 - 3724.0 (631.0)" "3.0 - 5287.0 (758.5)"
[1] "hr=" "1.2"
D45V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 15(5Q12.1) MUTATED         1       54      101        1        39
  DEL PEAK 15(5Q12.1) WILD-TYPE       0       18       36        0        13
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 15(5Q12.1) MUTATED          50         44         14        6
  DEL PEAK 15(5Q12.1) WILD-TYPE        21         13          6        0
D45V3, multiclass
            clus
vv           DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE
  STAGE I                              1                             0
  STAGE IA                            54                            18
  STAGE IB                           101                            36
  STAGE II                             1                             0
  STAGE IIA                           39                            13
  STAGE IIB                           50                            21
  STAGE IIIA                          44                            13
  STAGE IIIB                          14                             6
  STAGE IV                             6                             0
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 15(5Q12.1) MUTATED    75 190  32  16
  DEL PEAK 15(5Q12.1) WILD-TYPE  23  64  16   4
D45V4, multiclass
    clus
vv   DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE
  T1                          75                            23
  T2                         190                            64
  T3                          32                            16
  T4                          16                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 15(5Q12.1) MUTATED   198  84  26   2
  DEL PEAK 15(5Q12.1) WILD-TYPE  63  29   9   3
D45V5, multiclass
    clus
vv   DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE
  N0                         198                            63
  N1                          84                            29
  N2                          26                             9
  N3                           2                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A  MX
  DEL PEAK 15(5Q12.1) MUTATED   263   5   1  38
  DEL PEAK 15(5Q12.1) WILD-TYPE  95   0   0  12
D45V6, multiclass
     clus
vv    DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE
  M0                          263                            95
  M1                            5                             0
  M1A                           1                             0
  MX                           38                            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"
D45V7, binary
                               cls
clus                              0   1
  DEL PEAK 15(5Q12.1) MUTATED    76 237
  DEL PEAK 15(5Q12.1) WILD-TYPE  31  76
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(5Q12.1) MUTATED     76  237
  DEL PEAK 15(5Q12.1) WILD-TYPE   31   76
        clus
vv       DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE
  FEMALE                          76                            31
  MALE                           237                            76
[1] 2 2
[1] FALSE
D45V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 15(5Q12.1) MUTATED                                       9
  DEL PEAK 15(5Q12.1) WILD-TYPE                                     3
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 15(5Q12.1) MUTATED                                        3
  DEL PEAK 15(5Q12.1) WILD-TYPE                                      3
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 15(5Q12.1) MUTATED                                         0
  DEL PEAK 15(5Q12.1) WILD-TYPE                                       1
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 15(5Q12.1) MUTATED                                                           301
  DEL PEAK 15(5Q12.1) WILD-TYPE                                                         100
D45V9, multiclass
                                                             clus
vv                                                            DEL PEAK 15(5Q12.1) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         301
                                                             clus
vv                                                            DEL PEAK 15(5Q12.1) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           100
[1] 4 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 15(5Q12.1) MUTATED    12 301
  DEL PEAK 15(5Q12.1) WILD-TYPE   1 106
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(5Q12.1) MUTATED     12  301
  DEL PEAK 15(5Q12.1) WILD-TYPE    1  106
     clus
vv    DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE
  NO                           12                             1
  YES                         301                           106
[1] 2 2
[1] FALSE
D45V11, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 15(5Q12.1) MUTATED   255   7   2  11
  DEL PEAK 15(5Q12.1) WILD-TYPE  87   1   2   7
D45V12, multiclass
    clus
vv   DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE
  R0                         255                            87
  R1                           7                             1
  R2                           2                             2
  RX                          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                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(5Q12.1) MUTATED       4                        16   222
  DEL PEAK 15(5Q12.1) WILD-TYPE     5                         1    76
D45V13, multiclass
                           clus
vv                          DEL PEAK 15(5Q12.1) MUTATED
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                          16
  WHITE                                             222
                           clus
vv                          DEL PEAK 15(5Q12.1) WILD-TYPE
  ASIAN                                                 5
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                76
[1] 3 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 15(5Q12.1) MUTATED     6 195
  DEL PEAK 15(5Q12.1) WILD-TYPE   2  72
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(5Q12.1) MUTATED      6  195
  DEL PEAK 15(5Q12.1) WILD-TYPE    2   72
                        clus
vv                       DEL PEAK 15(5Q12.1) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                         195
                        clus
vv                       DEL PEAK 15(5Q12.1) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            72
[1] 2 2
[1] FALSE

Clustering(46) Variable = DEL PEAK 16(5Q31.1) MUTATION ANALYSIS
D46V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 16(5Q31.1) MUTATED   212  88
  DEL PEAK 16(5Q31.1) WILD-TYPE  53  35
  DEL PEAK 16(5Q31.1) MUTATED DEL PEAK 16(5Q31.1) WILD-TYPE 
                          300                            88 
  DEL PEAK 16(5Q31.1) MUTATED DEL PEAK 16(5Q31.1) WILD-TYPE 
                           88                            35 
$`DEL PEAK 16(5Q31.1) MUTATED`
TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
        2464         2417          146         1415          345          396 
TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 
        1810          862          758          187           85         2754 
TCGA-18-5592 TCGA-21-1070 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1079 
          92         3636         3016         2134         1852          965 
TCGA-21-1082 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI 
        3644          962         1268         1032          329          979 
TCGA-22-0940 TCGA-22-0944 TCGA-22-1002 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 
         608          223          131           53          429          822 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 
         623         1067         1470          734         1161         1057 
TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 
         399         1946          587          358          965         1964 
TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5482 
        1933          445         1346           24         1651          357 
TCGA-22-5483 TCGA-22-5485 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 
         573          916         1713          506           29         2524 
TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4582 TCGA-33-4586 TCGA-33-4587 
        1940         2979         1311         1966          428         1970 
TCGA-33-6738 TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 
         822           80         1874          958          881         1000 
TCGA-34-2609 TCGA-34-5231 TCGA-34-5234 TCGA-34-5239 TCGA-34-5241 TCGA-34-5927 
         951         1528         1715          707          428          941 
TCGA-34-8454 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 
         166          247          227          238          207           12 
TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5021 TCGA-39-5024 TCGA-39-5027 
         103         1454         2253         1947         1964         1849 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 
         740           59          833         1084         1086          544 
TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 
        1223          684         1176          822         1007          349 
TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 
         849          757          310          212          236         1970 
TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56U TCGA-43-A56V TCGA-46-6025 
         358         1971          353          432          366          324 
TCGA-46-6026 TCGA-51-4079 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 
         423           12          911          541         1948          923 
TCGA-52-7811 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6546 TCGA-56-7221 
        1958          881            3          555           26           30 
TCGA-56-7222 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 
          13           44           40           26            6         1961 
TCGA-56-7822 TCGA-56-8503 TCGA-56-8622 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 
           1           41           55           63           17           16 
TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ 
          34           38            2           46           30           25 
TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 
           4            4            8          378          911         2167 
TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-60-2695 TCGA-60-2696 TCGA-60-2703 
        2589         1723         1072          642          109         1950 
TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 
        1958          661         1963         1505         1963         1260 
TCGA-60-2713 TCGA-60-2714 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 
        1731         1531         1297           97          983          908 
TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-63-6202 TCGA-63-7020 TCGA-63-7022 
        1092          717          816         1973         1957         1947 
TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2753 
        1952         1967         1311           61          641           31 
TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 
          28           30           30          762           30           61 
TCGA-66-2766 TCGA-66-2768 TCGA-66-2769 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 
          31           61         1947          578         1946           61 
TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2785 TCGA-66-2786 
         578         1956          121         1954           60          790 
TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 
        1217          699         1955          699         1977          913 
TCGA-66-2793 TCGA-66-2794 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 
        1952         1645         1492           83          202          211 
TCGA-68-8250 TCGA-68-8251 TCGA-77-6842 TCGA-77-6844 TCGA-77-6845 TCGA-77-7139 
         244           96         1950         1942         1952         1968 
TCGA-77-7141 TCGA-77-7142 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 
          15         1286         1942         1952         1954          479 
TCGA-77-8007 TCGA-77-8008 TCGA-77-8128 TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 
        1960         1945         1953         1945         1941         1947 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 
        1946         1951         1962         1943          293         1961 
TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 
        1684         1092           10         1959         1955         1963 
TCGA-77-A5G8 TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 
        1290          839          713          364          395           34 
TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 
          18           10           49            1         1965           35 
TCGA-85-7950 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 
          60           16          960          428          513           13 
TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 
          11           13           54           60           55           67 
TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 
          54           61           61           22           21          445 
TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M 
         424            3          475         1960           25           19 
TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A5B5 TCGA-90-7766 TCGA-90-7767 
        1967         1972         1987          111          289           89 
TCGA-90-7769 TCGA-90-7964 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 
         358          428          331          269           82          106 
TCGA-92-8063 TCGA-92-8064 TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-7545 
         122          160          356          430         1213         1344 
TCGA-96-8169 TCGA-96-A4JK TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-J1-A4AH 
         189          273          413          224          308          222 
TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HG TCGA-NC-A5HI 
          35          449           36           83         1548         1135 

$`DEL PEAK 16(5Q31.1) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3419 TCGA-18-3421 TCGA-18-5595 TCGA-21-1071 
         370          136           50         1331          827         1426 
TCGA-21-1077 TCGA-21-1078 TCGA-21-1080 TCGA-21-1081 TCGA-21-1083 TCGA-22-1000 
        1058          474         3724          284          267         1945 
TCGA-22-1005 TCGA-22-1017 TCGA-22-4596 TCGA-22-5480 TCGA-22-5481 TCGA-22-5489 
        1952         1485           17         1952         1952         1912 
TCGA-33-4566 TCGA-33-4583 TCGA-33-4589 TCGA-34-5232 TCGA-34-5240 TCGA-34-5928 
        5287         1941         1948         2062          365          552 
TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-39-5019 TCGA-39-5022 
         120           13           12          200         1361         1996 
TCGA-39-5028 TCGA-39-5034 TCGA-39-5035 TCGA-39-5040 TCGA-43-6143 TCGA-43-6771 
          52         1107          474         1964          376         1936 
TCGA-43-8115 TCGA-43-A475 TCGA-51-4080 TCGA-52-7812 TCGA-56-6545 TCGA-56-7223 
         407          296           12         1967           62           30 
TCGA-56-8504 TCGA-56-8624 TCGA-58-8393 TCGA-58-A46N TCGA-60-2698 TCGA-60-2704 
         178           36         1058          910          311         1943 
TCGA-60-2712 TCGA-60-2715 TCGA-60-2716 TCGA-60-2726 TCGA-63-7021 TCGA-66-2744 
         274         1075         1475          358         1955           30 
TCGA-66-2754 TCGA-66-2758 TCGA-66-2767 TCGA-66-2770 TCGA-66-2783 TCGA-66-2795 
          61          639           61          700          759          122 
TCGA-68-A59I TCGA-68-A59J TCGA-77-6843 TCGA-77-7138 TCGA-77-7335 TCGA-77-8009 
         121          104         1941         1959         1954         1641 
TCGA-77-8131 TCGA-77-8144 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5GA TCGA-77-A5GB 
        1941          833         1953         1942         1280         1939 
TCGA-85-7844 TCGA-85-8048 TCGA-85-8049 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A50Z 
         911           26           60           15         1972         1973 
TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 TCGA-90-A4ED TCGA-92-8065 TCGA-94-7033 
          24           13          758          244           70           87 
TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-NC-A5HE 
         211          183          256         1722 

  DEL PEAK 16(5Q31.1) MUTATED DEL PEAK 16(5Q31.1) WILD-TYPE 
                            1                            12 
  DEL PEAK 16(5Q31.1) MUTATED DEL PEAK 16(5Q31.1) WILD-TYPE 
                         3644                          5287 
  DEL PEAK 16(5Q31.1) MUTATED DEL PEAK 16(5Q31.1) WILD-TYPE 
                        641.5                         669.5 
[1] "1.0 - 3644.0 (641.5)"  "12.0 - 5287.0 (669.5)"
[1] "hr=" "1.3"
D46V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 16(5Q31.1) MUTATED         1       58      102        1        41
  DEL PEAK 16(5Q31.1) WILD-TYPE       0       14       35        0        11
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 16(5Q31.1) MUTATED          51         49         14        6
  DEL PEAK 16(5Q31.1) WILD-TYPE        20          8          6        0
D46V3, multiclass
            clus
vv           DEL PEAK 16(5Q31.1) MUTATED DEL PEAK 16(5Q31.1) WILD-TYPE
  STAGE I                              1                             0
  STAGE IA                            58                            14
  STAGE IB                           102                            35
  STAGE II                             1                             0
  STAGE IIA                           41                            11
  STAGE IIB                           51                            20
  STAGE IIIA                          49                             8
  STAGE IIIB                          14                             6
  STAGE IV                             6                             0
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 16(5Q31.1) MUTATED    79 195  37  15
  DEL PEAK 16(5Q31.1) WILD-TYPE  19  59  11   5
D46V4, multiclass
    clus
vv   DEL PEAK 16(5Q31.1) MUTATED DEL PEAK 16(5Q31.1) WILD-TYPE
  T1                          79                            19
  T2                         195                            59
  T3                          37                            11
  T4                          15                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 16(5Q31.1) MUTATED   206  85  29   3
  DEL PEAK 16(5Q31.1) WILD-TYPE  55  28   6   2
D46V5, multiclass
    clus
vv   DEL PEAK 16(5Q31.1) MUTATED DEL PEAK 16(5Q31.1) WILD-TYPE
  N0                         206                            55
  N1                          85                            28
  N2                          29                             6
  N3                           3                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A  MX
  DEL PEAK 16(5Q31.1) MUTATED   276   5   1  40
  DEL PEAK 16(5Q31.1) WILD-TYPE  82   0   0  10
D46V6, multiclass
     clus
vv    DEL PEAK 16(5Q31.1) MUTATED DEL PEAK 16(5Q31.1) WILD-TYPE
  M0                          276                            82
  M1                            5                             0
  M1A                           1                             0
  MX                           40                            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"
D46V7, binary
                               cls
clus                              0   1
  DEL PEAK 16(5Q31.1) MUTATED    84 242
  DEL PEAK 16(5Q31.1) WILD-TYPE  23  71
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(5Q31.1) MUTATED     84  242
  DEL PEAK 16(5Q31.1) WILD-TYPE   23   71
        clus
vv       DEL PEAK 16(5Q31.1) MUTATED DEL PEAK 16(5Q31.1) WILD-TYPE
  FEMALE                          84                            23
  MALE                           242                            71
[1] 2 2
[1] FALSE
D46V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 16(5Q31.1) MUTATED                                       8
  DEL PEAK 16(5Q31.1) WILD-TYPE                                     4
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 16(5Q31.1) MUTATED                                        3
  DEL PEAK 16(5Q31.1) WILD-TYPE                                      3
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 16(5Q31.1) MUTATED                                         1
  DEL PEAK 16(5Q31.1) WILD-TYPE                                       0
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 16(5Q31.1) MUTATED                                                           314
  DEL PEAK 16(5Q31.1) WILD-TYPE                                                          87
D46V9, multiclass
                                                             clus
vv                                                            DEL PEAK 16(5Q31.1) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         314
                                                             clus
vv                                                            DEL PEAK 16(5Q31.1) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            87
[1] 4 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 16(5Q31.1) MUTATED    12 314
  DEL PEAK 16(5Q31.1) WILD-TYPE   1  93
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(5Q31.1) MUTATED     12  314
  DEL PEAK 16(5Q31.1) WILD-TYPE    1   93
     clus
vv    DEL PEAK 16(5Q31.1) MUTATED DEL PEAK 16(5Q31.1) WILD-TYPE
  NO                           12                             1
  YES                         314                            93
[1] 2 2
[1] FALSE
D46V11, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 16(5Q31.1) MUTATED   264   7   3  11
  DEL PEAK 16(5Q31.1) WILD-TYPE  78   1   1   7
D46V12, multiclass
    clus
vv   DEL PEAK 16(5Q31.1) MUTATED DEL PEAK 16(5Q31.1) WILD-TYPE
  R0                         264                            78
  R1                           7                             1
  R2                           3                             1
  RX                          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                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(5Q31.1) MUTATED       4                        14   231
  DEL PEAK 16(5Q31.1) WILD-TYPE     5                         3    67
D46V13, multiclass
                           clus
vv                          DEL PEAK 16(5Q31.1) MUTATED
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                          14
  WHITE                                             231
                           clus
vv                          DEL PEAK 16(5Q31.1) WILD-TYPE
  ASIAN                                                 5
  BLACK OR AFRICAN AMERICAN                             3
  WHITE                                                67
[1] 3 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 16(5Q31.1) MUTATED     6 203
  DEL PEAK 16(5Q31.1) WILD-TYPE   2  64
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(5Q31.1) MUTATED      6  203
  DEL PEAK 16(5Q31.1) WILD-TYPE    2   64
                        clus
vv                       DEL PEAK 16(5Q31.1) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                         203
                        clus
vv                       DEL PEAK 16(5Q31.1) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            64
[1] 2 2
[1] FALSE

Clustering(47) Variable = DEL PEAK 17(6P25.3) MUTATION ANALYSIS
D47V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 17(6P25.3) MUTATED    65  35
  DEL PEAK 17(6P25.3) WILD-TYPE 200  88
  DEL PEAK 17(6P25.3) MUTATED DEL PEAK 17(6P25.3) WILD-TYPE 
                          100                           288 
  DEL PEAK 17(6P25.3) MUTATED DEL PEAK 17(6P25.3) WILD-TYPE 
                           35                            88 
$`DEL PEAK 17(6P25.3) MUTATED`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3416 TCGA-18-4083 
         370         2464         1415          345          862          187 
TCGA-18-4086 TCGA-18-4721 TCGA-21-1076 TCGA-22-0940 TCGA-22-1012 TCGA-22-4593 
          85         2754         1852          608          429         1067 
TCGA-22-4596 TCGA-22-4599 TCGA-22-4604 TCGA-22-5473 TCGA-22-5477 TCGA-22-5478 
          17         1161          399         1933         1346           24 
TCGA-22-5479 TCGA-22-5482 TCGA-22-5483 TCGA-22-5491 TCGA-33-4547 TCGA-33-4582 
        1651          357          573         1713         1311         1966 
TCGA-33-4583 TCGA-33-4589 TCGA-34-2596 TCGA-34-2604 TCGA-34-5232 TCGA-37-3789 
        1941         1948           80          958         2062           13 
TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5027 TCGA-39-5029 TCGA-39-5035 
         103         1454         2253         1849          740          474 
TCGA-39-5037 TCGA-39-5039 TCGA-43-6143 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 
        1086          544          376         1971          353          296 
TCGA-43-A56V TCGA-51-4081 TCGA-52-7622 TCGA-56-7579 TCGA-56-7582 TCGA-56-7822 
         366          911          541           44           26            1 
TCGA-56-8624 TCGA-56-8626 TCGA-56-A4ZK TCGA-58-8391 TCGA-58-A46M TCGA-60-2698 
          36           17            4         2167         1072          311 
TCGA-60-2707 TCGA-60-2725 TCGA-60-2726 TCGA-63-7020 TCGA-63-7021 TCGA-66-2782 
         661          816          358         1957         1955         1954 
TCGA-66-2786 TCGA-66-2788 TCGA-66-2789 TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 
         790          699         1955         1977          913         1645 
TCGA-68-7755 TCGA-68-7756 TCGA-68-A59I TCGA-77-7141 TCGA-77-7337 TCGA-77-7338 
          83          202          121           15         1942         1952 
TCGA-77-8128 TCGA-77-8131 TCGA-77-8138 TCGA-77-8150 TCGA-77-A5G3 TCGA-77-A5G8 
        1953         1941         1946         1961         1959         1290 
TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7843 TCGA-85-7950 TCGA-85-8049 
          18           10           49           35           60           60 
TCGA-85-8070 TCGA-85-8277 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4QQ TCGA-85-A512 
         960           11          475           15         1960         1987 
TCGA-85-A5B5 TCGA-90-7767 TCGA-90-A59Q TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 
         111           89          269          106          122          160 
TCGA-92-8065 TCGA-96-7544 TCGA-96-A4JK TCGA-J1-A4AH 
          70         1213          273          222 

$`DEL PEAK 17(6P25.3) WILD-TYPE`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 
         136         2417          146          396         1810          758 
TCGA-18-3419 TCGA-18-3421 TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 
          50         1331           92          827         3636         1426 
TCGA-21-1072 TCGA-21-1075 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 
        3016         2134         1058          474          965         3724 
TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 
         284         3644          267          962         1268         1032 
TCGA-21-5787 TCGA-21-A5DI TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 
         329          979          223         1945          131         1952 
TCGA-22-1011 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4594 TCGA-22-4595 
          53          822         1485          623         1470          734 
TCGA-22-4601 TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 
        1057         1946          587          358          965         1964 
TCGA-22-5474 TCGA-22-5480 TCGA-22-5481 TCGA-22-5485 TCGA-22-5489 TCGA-22-5492 
         445         1952         1952          916         1912          506 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4566 TCGA-33-4586 
          29         2524         1940         2979         5287          428 
TCGA-33-4587 TCGA-33-6738 TCGA-34-2600 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 
        1970          822         1874          881         1000          951 
TCGA-34-5231 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 
        1528         1715          707          365          428          941 
TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 
         552          166          120           12          200          247 
TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-39-5019 TCGA-39-5021 
         227          238          207           12         1361         1947 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 
        1996         1964           52           59          833         1107 
TCGA-39-5036 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 
        1084         1964         1223          684         1176          822 
TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 
        1007          349          849          757          310         1936 
TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-A56U 
         212          236         1970          407          358          432 
TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-52-7809 TCGA-52-7810 
         324          423           12           12         1948          923 
TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 
        1958         1967          881            3          555           62 
TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7580 TCGA-56-7730 
          26           30           13           30           40            6 
TCGA-56-7731 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8625 TCGA-56-8628 
        1961           41          178           55           63           16 
TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ 
          34           38            2           46           30           25 
TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 TCGA-58-8393 TCGA-58-A46J 
           4            8          378          911         1058         2589 
TCGA-58-A46L TCGA-58-A46N TCGA-60-2695 TCGA-60-2696 TCGA-60-2703 TCGA-60-2704 
        1723          910          642          109         1950         1943 
TCGA-60-2706 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 
        1958         1963         1505         1963         1260          274 
TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 
        1731         1531         1075         1475         1297           97 
TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-63-6202 TCGA-63-7022 
         983          908         1092          717         1973         1947 
TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 
        1952         1967         1311           61          641           30 
TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 
          31           61           28           30           30          639 
TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 
         762           30           61           31           61           61 
TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 
        1947          700          578         1946           61          578 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2783 TCGA-66-2785 TCGA-66-2787 TCGA-66-2790 
        1956          121          759           60         1217          699 
TCGA-66-2793 TCGA-66-2795 TCGA-66-2800 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 
        1952          122         1492          211          244           96 
TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 
         104         1950         1941         1942         1952         1959 
TCGA-77-7139 TCGA-77-7142 TCGA-77-7335 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 
        1968         1286         1954         1954          479         1960 
TCGA-77-8008 TCGA-77-8009 TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 TCGA-77-8139 
        1945         1641         1945         1941         1947         1951 
TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8153 TCGA-77-8154 
        1962          833         1943          293         1684         1092 
TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5GA 
          10         1953         1942         1955         1963         1280 
TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 
        1939          839          713          364          395           34 
TCGA-85-7699 TCGA-85-7710 TCGA-85-7844 TCGA-85-8048 TCGA-85-8052 TCGA-85-8071 
           1         1965          911           26           16          428 
TCGA-85-8072 TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 
         513           13           13           54           60           55 
TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 
          67           54           61           61           22           21 
TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 TCGA-85-A4PA TCGA-85-A4QR TCGA-85-A50M 
         445          424            3         1972           25           19 
TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 
        1973         1967         1972           24           13          758 
TCGA-90-7766 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-92-7340 
         289          358          428          244          331           82 
TCGA-94-7033 TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 
          87          356          430         1344          189          211 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-L3-A4E7 
         183          256          413          224          308           35 
TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HI 
         449           36           83         1722         1548         1135 

  DEL PEAK 17(6P25.3) MUTATED DEL PEAK 17(6P25.3) WILD-TYPE 
                            1                             1 
  DEL PEAK 17(6P25.3) MUTATED DEL PEAK 17(6P25.3) WILD-TYPE 
                         2754                          5287 
  DEL PEAK 17(6P25.3) MUTATED DEL PEAK 17(6P25.3) WILD-TYPE 
                        590.5                         663.0 
[1] "1.0 - 2754.0 (590.5)" "1.0 - 5287.0 (663.0)"
[1] "hr=" "1.1"
D47V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 17(6P25.3) MUTATED         0       17       35        1        19
  DEL PEAK 17(6P25.3) WILD-TYPE       1       55      102        0        33
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 17(6P25.3) MUTATED          21         15          3        2
  DEL PEAK 17(6P25.3) WILD-TYPE        50         42         17        4
D47V3, multiclass
            clus
vv           DEL PEAK 17(6P25.3) MUTATED DEL PEAK 17(6P25.3) WILD-TYPE
  STAGE I                              0                             1
  STAGE IA                            17                            55
  STAGE IB                            35                           102
  STAGE II                             1                             0
  STAGE IIA                           19                            33
  STAGE IIB                           21                            50
  STAGE IIIA                          15                            42
  STAGE IIIB                           3                            17
  STAGE IV                             2                             4
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 17(6P25.3) MUTATED    28  66  15   4
  DEL PEAK 17(6P25.3) WILD-TYPE  70 188  33  16
D47V4, multiclass
    clus
vv   DEL PEAK 17(6P25.3) MUTATED DEL PEAK 17(6P25.3) WILD-TYPE
  T1                          28                            70
  T2                          66                           188
  T3                          15                            33
  T4                           4                            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 17(6P25.3) MUTATED    66  34   9   2
  DEL PEAK 17(6P25.3) WILD-TYPE 195  79  26   3
D47V5, multiclass
    clus
vv   DEL PEAK 17(6P25.3) MUTATED DEL PEAK 17(6P25.3) WILD-TYPE
  N0                          66                           195
  N1                          34                            79
  N2                           9                            26
  N3                           2                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A  MX
  DEL PEAK 17(6P25.3) MUTATED    99   1   1  11
  DEL PEAK 17(6P25.3) WILD-TYPE 259   4   0  39
D47V6, multiclass
     clus
vv    DEL PEAK 17(6P25.3) MUTATED DEL PEAK 17(6P25.3) WILD-TYPE
  M0                           99                           259
  M1                            1                             4
  M1A                           1                             0
  MX                           11                            39
[1] 4 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 17(6P25.3) MUTATED    24  89
  DEL PEAK 17(6P25.3) WILD-TYPE  83 224
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(6P25.3) MUTATED     24   89
  DEL PEAK 17(6P25.3) WILD-TYPE   83  224
        clus
vv       DEL PEAK 17(6P25.3) MUTATED DEL PEAK 17(6P25.3) WILD-TYPE
  FEMALE                          24                            83
  MALE                            89                           224
[1] 2 2
[1] FALSE
D47V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 17(6P25.3) MUTATED                                       2
  DEL PEAK 17(6P25.3) WILD-TYPE                                    10
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 17(6P25.3) MUTATED                                        1
  DEL PEAK 17(6P25.3) WILD-TYPE                                      5
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 17(6P25.3) MUTATED                                         0
  DEL PEAK 17(6P25.3) WILD-TYPE                                       1
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 17(6P25.3) MUTATED                                                           110
  DEL PEAK 17(6P25.3) WILD-TYPE                                                         291
D47V9, multiclass
                                                             clus
vv                                                            DEL PEAK 17(6P25.3) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         110
                                                             clus
vv                                                            DEL PEAK 17(6P25.3) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  10
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           291
[1] 4 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 17(6P25.3) MUTATED     2 111
  DEL PEAK 17(6P25.3) WILD-TYPE  11 296
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(6P25.3) MUTATED      2  111
  DEL PEAK 17(6P25.3) WILD-TYPE   11  296
     clus
vv    DEL PEAK 17(6P25.3) MUTATED DEL PEAK 17(6P25.3) WILD-TYPE
  NO                            2                            11
  YES                         111                           296
[1] 2 2
[1] FALSE
D47V11, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 17(6P25.3) MUTATED    91   5   0   8
  DEL PEAK 17(6P25.3) WILD-TYPE 251   3   4  10
D47V12, multiclass
    clus
vv   DEL PEAK 17(6P25.3) MUTATED DEL PEAK 17(6P25.3) WILD-TYPE
  R0                          91                           251
  R1                           5                             3
  R2                           0                             4
  RX                           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                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(6P25.3) MUTATED       1                         5    85
  DEL PEAK 17(6P25.3) WILD-TYPE     8                        12   213
D47V13, multiclass
                           clus
vv                          DEL PEAK 17(6P25.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           5
  WHITE                                              85
                           clus
vv                          DEL PEAK 17(6P25.3) WILD-TYPE
  ASIAN                                                 8
  BLACK OR AFRICAN AMERICAN                            12
  WHITE                                               213
[1] 3 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 17(6P25.3) MUTATED     4  71
  DEL PEAK 17(6P25.3) WILD-TYPE   4 196
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(6P25.3) MUTATED      4   71
  DEL PEAK 17(6P25.3) WILD-TYPE    4  196
                        clus
vv                       DEL PEAK 17(6P25.3) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          71
                        clus
vv                       DEL PEAK 17(6P25.3) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           196
[1] 2 2
[1] FALSE

Clustering(48) Variable = DEL PEAK 18(6Q22.31) MUTATION ANALYSIS
D48V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 18(6Q22.31) MUTATED    70  27
  DEL PEAK 18(6Q22.31) WILD-TYPE 195  96
  DEL PEAK 18(6Q22.31) MUTATED DEL PEAK 18(6Q22.31) WILD-TYPE 
                            97                            291 
  DEL PEAK 18(6Q22.31) MUTATED DEL PEAK 18(6Q22.31) WILD-TYPE 
                            27                             96 
$`DEL PEAK 18(6Q22.31) MUTATED`
TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 TCGA-18-3421 TCGA-18-4083 
        2464         1415          345         1810         1331          187 
TCGA-18-5592 TCGA-21-1072 TCGA-21-1083 TCGA-21-5786 TCGA-21-5787 TCGA-22-0940 
          92         3016          267         1032          329          608 
TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4607 TCGA-22-5471 
         734           17         1161         1057          587          965 
TCGA-22-5478 TCGA-22-5479 TCGA-22-5492 TCGA-33-4582 TCGA-33-4583 TCGA-34-2596 
          24         1651          506         1966         1941           80 
TCGA-34-2604 TCGA-34-5231 TCGA-34-5928 TCGA-37-4133 TCGA-39-5016 TCGA-39-5021 
         958         1528          552          238         2253         1947 
TCGA-39-5027 TCGA-39-5034 TCGA-39-5037 TCGA-39-5039 TCGA-43-2581 TCGA-43-6143 
        1849         1107         1086          544         1176          376 
TCGA-43-6770 TCGA-43-8115 TCGA-46-6025 TCGA-51-4081 TCGA-52-7812 TCGA-56-6545 
         310          407          324          911         1967           62 
TCGA-56-7582 TCGA-56-7730 TCGA-56-8624 TCGA-56-8625 TCGA-56-A49D TCGA-56-A4BY 
          26            6           36           63           38           30 
TCGA-56-A4ZK TCGA-58-8393 TCGA-58-A46M TCGA-60-2707 TCGA-60-2711 TCGA-60-2722 
           4         1058         1072          661         1260          908 
TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-66-2758 TCGA-66-2763 TCGA-66-2773 
         358         1973         1957          639           30         1946 
TCGA-66-2780 TCGA-66-2782 TCGA-66-2783 TCGA-66-2788 TCGA-66-2792 TCGA-66-2795 
        1956         1954          759          699          913          122 
TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-A59I TCGA-77-7141 TCGA-77-8007 
          83          202          211          121           15         1960 
TCGA-77-8009 TCGA-77-8150 TCGA-77-A5G8 TCGA-85-7696 TCGA-85-7698 TCGA-85-7710 
        1641         1961         1290           18           49         1965 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8072 TCGA-85-8277 TCGA-85-8354 TCGA-85-8479 
          16          960          513           11           61           22 
TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A5B5 
        1960           25           19         1973         1967          111 
TCGA-90-7767 TCGA-92-7341 TCGA-94-7033 TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A524 
          89          106           87          308          222          449 
TCGA-NC-A5HG 
        1548 

$`DEL PEAK 18(6Q22.31) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3414 TCGA-18-3416 
         370          136         2417          146          396          862 
TCGA-18-3417 TCGA-18-3419 TCGA-18-4086 TCGA-18-4721 TCGA-18-5595 TCGA-21-1070 
         758           50           85         2754          827         3636 
TCGA-21-1071 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 
        1426         2134         1852         1058          474          965 
TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-5782 TCGA-21-5784 TCGA-21-A5DI 
        3724          284         3644          962         1268          979 
TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 
         223         1945          131         1952           53          429 
TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4604 
         822         1485          623         1067         1470          399 
TCGA-22-4605 TCGA-22-4613 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 
        1946          358         1964         1933          445         1346 
TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 
        1952         1952          357          573          916         1912 
TCGA-22-5491 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 
        1713           29         2524         1940         2979         1311 
TCGA-33-4566 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-33-6738 TCGA-34-2600 
        5287          428         1970         1948          822         1874 
TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 
         881         1000          951         2062         1715          707 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 
         365          428          941          166          120           13 
TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4135 TCGA-37-4141 
          12          200          247          227          207           12 
TCGA-37-5819 TCGA-39-5011 TCGA-39-5019 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 
         103         1454         1361         1996         1964           52 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 TCGA-39-5040 
         740           59          833          474         1084         1964 
TCGA-43-2576 TCGA-43-2578 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 
        1223          684          822         1007          349          849 
TCGA-43-6647 TCGA-43-6771 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8116 
         757         1936          212          236         1970          358 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-6026 
        1971          353          296          432          366          423 
TCGA-51-4079 TCGA-51-4080 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 
          12           12          541         1948          923         1958 
TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 
         881            3          555           26           30           13 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 
          30           44           40         1961            1           41 
TCGA-56-8504 TCGA-56-8622 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW 
         178           55           17           16           34            2 
TCGA-56-A4BX TCGA-56-A4ZJ TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 
          46           25            4            8          378          911 
TCGA-58-8391 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46N TCGA-60-2695 TCGA-60-2696 
        2167         2589         1723          910          642          109 
TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2708 TCGA-60-2709 
         311         1950         1943         1958         1963         1505 
TCGA-60-2710 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 
        1963          274         1731         1531         1075         1475 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 
        1297           97          983         1092          717          816 
TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 
        1955         1947         1952         1967         1311           61 
TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 
         641           30           31           61           28           30 
TCGA-66-2757 TCGA-66-2759 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 
          30          762           61           31           61           61 
TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2777 TCGA-66-2778 TCGA-66-2781 
        1947          700          578           61          578          121 
TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 
          60          790         1217         1955          699         1977 
TCGA-66-2793 TCGA-66-2794 TCGA-66-2800 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59J 
        1952         1645         1492          244           96          104 
TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 
        1950         1941         1942         1952         1959         1968 
TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 
        1286         1954         1942         1952         1954          479 
TCGA-77-8008 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 
        1945         1953         1945         1941         1941         1947 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 
        1946         1951         1962          833         1943          293 
TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 
        1684         1092           10         1953         1942         1959 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH 
        1955         1963         1280         1939          839          713 
TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7697 TCGA-85-7699 TCGA-85-7843 
         364          395           34           10            1           35 
TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8071 TCGA-85-8276 
         911           60           26           60          428           13 
TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 
          13           54           60           55           67           54 
TCGA-85-8355 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 
          61           21          445          424            3          475 
TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L 
          15         1972         1972         1987           24           13 
TCGA-90-6837 TCGA-90-7766 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE 
         758          289          358          428          244          331 
TCGA-90-A59Q TCGA-92-7340 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7943 
         269           82          122          160           70          356 
TCGA-94-A4VJ TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK 
         430         1213         1344          189          211          273 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-L3-A4E7 TCGA-LA-A446 
         183          256          413          224           35           36 
TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HI 
          83         1722         1135 

  DEL PEAK 18(6Q22.31) MUTATED DEL PEAK 18(6Q22.31) WILD-TYPE 
                             4                              1 
  DEL PEAK 18(6Q22.31) MUTATED DEL PEAK 18(6Q22.31) WILD-TYPE 
                          3016                           5287 
  DEL PEAK 18(6Q22.31) MUTATED DEL PEAK 18(6Q22.31) WILD-TYPE 
                           587                            699 
[1] "4.0 - 3016.0 (587.0)" "1.0 - 5287.0 (699.0)"
[1] "hr=" "1.1"
D48V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 18(6Q22.31) MUTATED         0       10       40        0        16
  DEL PEAK 18(6Q22.31) WILD-TYPE       1       62       97        1        36
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 18(6Q22.31) MUTATED          18         15          3        1
  DEL PEAK 18(6Q22.31) WILD-TYPE        53         42         17        5
D48V3, multiclass
            clus
vv           DEL PEAK 18(6Q22.31) MUTATED DEL PEAK 18(6Q22.31) WILD-TYPE
  STAGE I                               0                              1
  STAGE IA                             10                             62
  STAGE IB                             40                             97
  STAGE II                              0                              1
  STAGE IIA                            16                             36
  STAGE IIB                            18                             53
  STAGE IIIA                           15                             42
  STAGE IIIB                            3                             17
  STAGE IV                              1                              5
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 18(6Q22.31) MUTATED    16  67  15   5
  DEL PEAK 18(6Q22.31) WILD-TYPE  82 187  33  15
D48V4, multiclass
    clus
vv   DEL PEAK 18(6Q22.31) MUTATED DEL PEAK 18(6Q22.31) WILD-TYPE
  T1                           16                             82
  T2                           67                            187
  T3                           15                             33
  T4                            5                             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 18(6Q22.31) MUTATED    68  27   7   1
  DEL PEAK 18(6Q22.31) WILD-TYPE 193  86  28   4
D48V5, multiclass
    clus
vv   DEL PEAK 18(6Q22.31) MUTATED DEL PEAK 18(6Q22.31) WILD-TYPE
  N0                           68                            193
  N1                           27                             86
  N2                            7                             28
  N3                            1                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A  MX
  DEL PEAK 18(6Q22.31) MUTATED    89   0   1  12
  DEL PEAK 18(6Q22.31) WILD-TYPE 269   5   0  38
D48V6, multiclass
     clus
vv    DEL PEAK 18(6Q22.31) MUTATED DEL PEAK 18(6Q22.31) WILD-TYPE
  M0                            89                            269
  M1                             0                              5
  M1A                            1                              0
  MX                            12                             38
[1] 4 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 18(6Q22.31) MUTATED    23  80
  DEL PEAK 18(6Q22.31) WILD-TYPE  84 233
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(6Q22.31) MUTATED     23   80
  DEL PEAK 18(6Q22.31) WILD-TYPE   84  233
        clus
vv       DEL PEAK 18(6Q22.31) MUTATED DEL PEAK 18(6Q22.31) WILD-TYPE
  FEMALE                           23                             84
  MALE                             80                            233
[1] 2 2
[1] FALSE
D48V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 18(6Q22.31) MUTATED                                       3
  DEL PEAK 18(6Q22.31) WILD-TYPE                                     9
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 18(6Q22.31) MUTATED                                        3
  DEL PEAK 18(6Q22.31) WILD-TYPE                                      3
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 18(6Q22.31) MUTATED                                         0
  DEL PEAK 18(6Q22.31) WILD-TYPE                                       1
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 18(6Q22.31) MUTATED                                                            97
  DEL PEAK 18(6Q22.31) WILD-TYPE                                                         304
D48V9, multiclass
                                                             clus
vv                                                            DEL PEAK 18(6Q22.31) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           97
                                                             clus
vv                                                            DEL PEAK 18(6Q22.31) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            304
[1] 4 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 18(6Q22.31) MUTATED     4  99
  DEL PEAK 18(6Q22.31) WILD-TYPE   9 308
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(6Q22.31) MUTATED      4   99
  DEL PEAK 18(6Q22.31) WILD-TYPE    9  308
     clus
vv    DEL PEAK 18(6Q22.31) MUTATED DEL PEAK 18(6Q22.31) WILD-TYPE
  NO                             4                              9
  YES                           99                            308
[1] 2 2
[1] FALSE
D48V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 18(6Q22.31) MUTATED    86   1   2   6
  DEL PEAK 18(6Q22.31) WILD-TYPE 256   7   2  12
D48V12, multiclass
    clus
vv   DEL PEAK 18(6Q22.31) MUTATED DEL PEAK 18(6Q22.31) WILD-TYPE
  R0                           86                            256
  R1                            1                              7
  R2                            2                              2
  RX                            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                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(6Q22.31) MUTATED       2                         3    76
  DEL PEAK 18(6Q22.31) WILD-TYPE     7                        14   222
D48V13, multiclass
                           clus
vv                          DEL PEAK 18(6Q22.31) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               76
                           clus
vv                          DEL PEAK 18(6Q22.31) WILD-TYPE
  ASIAN                                                  7
  BLACK OR AFRICAN AMERICAN                             14
  WHITE                                                222
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V14, binary
                                cls
clus                               0   1
  DEL PEAK 18(6Q22.31) MUTATED     2  67
  DEL PEAK 18(6Q22.31) WILD-TYPE   6 200
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(6Q22.31) MUTATED      2   67
  DEL PEAK 18(6Q22.31) WILD-TYPE    6  200
                        clus
vv                       DEL PEAK 18(6Q22.31) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           67
                        clus
vv                       DEL PEAK 18(6Q22.31) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            200
[1] 2 2
[1] FALSE

Clustering(49) Variable = DEL PEAK 19(6Q26) MUTATION ANALYSIS
D49V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 19(6Q26) MUTATED    68  35
  DEL PEAK 19(6Q26) WILD-TYPE 197  88
  DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE 
                        103                         285 
  DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE 
                         35                          88 
$`DEL PEAK 19(6Q26) MUTATED`
TCGA-18-3408 TCGA-18-3411 TCGA-18-3415 TCGA-18-3419 TCGA-18-4083 TCGA-18-5592 
        2464         1415         1810           50          187           92 
TCGA-21-1072 TCGA-21-1083 TCGA-21-5786 TCGA-21-5787 TCGA-22-0940 TCGA-22-1011 
        3016          267         1032          329          608           53 
TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4607 TCGA-22-5471 
         734           17         1161         1057          587          965 
TCGA-22-5478 TCGA-22-5479 TCGA-22-5481 TCGA-22-5489 TCGA-22-5492 TCGA-33-4582 
          24         1651         1952         1912          506         1966 
TCGA-33-4583 TCGA-34-2596 TCGA-34-2604 TCGA-34-2608 TCGA-34-5231 TCGA-34-5927 
        1941           80          958         1000         1528          941 
TCGA-34-5928 TCGA-37-4133 TCGA-39-5016 TCGA-39-5021 TCGA-39-5027 TCGA-39-5028 
         552          238         2253         1947         1849           52 
TCGA-39-5034 TCGA-39-5037 TCGA-39-5039 TCGA-43-2581 TCGA-43-5668 TCGA-43-6143 
        1107         1086          544         1176          349          376 
TCGA-43-6770 TCGA-43-8118 TCGA-46-6025 TCGA-51-4081 TCGA-52-7812 TCGA-56-6545 
         310         1971          324          911         1967           62 
TCGA-56-7222 TCGA-56-7223 TCGA-56-7582 TCGA-56-7730 TCGA-56-8624 TCGA-56-8625 
          13           30           26            6           36           63 
TCGA-56-A4BY TCGA-56-A4ZK TCGA-58-8393 TCGA-58-A46M TCGA-60-2707 TCGA-60-2722 
          30            4         1058         1072          661          908 
TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-66-2727 TCGA-66-2758 TCGA-66-2759 
         358         1973         1957         1967          639          762 
TCGA-66-2763 TCGA-66-2773 TCGA-66-2780 TCGA-66-2782 TCGA-66-2783 TCGA-66-2791 
          30         1946         1956         1954          759         1977 
TCGA-66-2795 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-77-7141 TCGA-77-8007 
         122           83          202          211           15         1960 
TCGA-77-8009 TCGA-77-8144 TCGA-77-8150 TCGA-77-A5G3 TCGA-77-A5G8 TCGA-85-7696 
        1641          833         1961         1959         1290           18 
TCGA-85-7698 TCGA-85-7710 TCGA-85-8052 TCGA-85-8070 TCGA-85-8072 TCGA-85-8277 
          49         1965           16          960          513           11 
TCGA-85-8354 TCGA-85-8479 TCGA-85-A4CL TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M 
          61           22           15         1960           25           19 
TCGA-85-A50Z TCGA-85-A510 TCGA-85-A5B5 TCGA-92-7341 TCGA-J1-A4AH TCGA-L3-A524 
        1973         1967          111          106          222          449 
TCGA-LA-A446 
          36 

$`DEL PEAK 19(6Q26) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3412 TCGA-18-3414 
         370          136         2417          146          345          396 
TCGA-18-3416 TCGA-18-3417 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 TCGA-18-5595 
         862          758         1331           85         2754          827 
TCGA-21-1070 TCGA-21-1071 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 
        3636         1426         2134         1852         1058          474 
TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-5782 TCGA-21-5784 
         965         3724          284         3644          962         1268 
TCGA-21-A5DI TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1012 
         979          223         1945          131         1952          429 
TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4604 
         822         1485          623         1067         1470          399 
TCGA-22-4605 TCGA-22-4613 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 
        1946          358         1964         1933          445         1346 
TCGA-22-5480 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5491 TCGA-22-A5C4 
        1952          357          573          916         1713           29 
TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4586 
        2524         1940         2979         1311         5287          428 
TCGA-33-4587 TCGA-33-4589 TCGA-33-6738 TCGA-34-2600 TCGA-34-2605 TCGA-34-2609 
        1970         1948          822         1874          881          951 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-8454 
        2062         1715          707          365          428          166 
TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 
         120           13           12          200          247          227 
TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 TCGA-39-5019 TCGA-39-5022 
         207           12          103         1454         1361         1996 
TCGA-39-5024 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 
        1964          740           59          833          474         1084 
TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 
        1964         1223          684          822         1007          849 
TCGA-43-6647 TCGA-43-6771 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 
         757         1936          212          236         1970          407 
TCGA-43-8116 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-6026 
         358          353          296          432          366          423 
TCGA-51-4079 TCGA-51-4080 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 
          12           12          541         1948          923         1958 
TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6546 TCGA-56-7221 TCGA-56-7579 
         881            3          555           26           30           44 
TCGA-56-7580 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 
          40         1961            1           41          178           55 
TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX 
          17           16           34           38            2           46 
TCGA-56-A4ZJ TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 
          25            4            8          378          911         2167 
TCGA-58-A46J TCGA-58-A46L TCGA-58-A46N TCGA-60-2695 TCGA-60-2696 TCGA-60-2698 
        2589         1723          910          642          109          311 
TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 
        1950         1943         1958         1963         1505         1963 
TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 
        1260          274         1731         1531         1075         1475 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 
        1297           97          983         1092          717          816 
TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 
        1955         1947         1952         1311           61          641 
TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 
          30           31           61           28           30           30 
TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 
          61           31           61           61         1947          700 
TCGA-66-2771 TCGA-66-2777 TCGA-66-2778 TCGA-66-2781 TCGA-66-2785 TCGA-66-2786 
         578           61          578          121           60          790 
TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2792 TCGA-66-2793 
        1217          699         1955          699          913         1952 
TCGA-66-2794 TCGA-66-2800 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J 
        1645         1492          244           96          121          104 
TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 
        1950         1941         1942         1952         1959         1968 
TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 
        1286         1954         1942         1952         1954          479 
TCGA-77-8008 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 
        1945         1953         1945         1941         1941         1947 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8145 TCGA-77-8148 TCGA-77-8153 
        1946         1951         1962         1943          293         1684 
TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 
        1092           10         1953         1942         1955         1963 
TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 TCGA-85-6561 
        1280         1939          839          713          364          395 
TCGA-85-6798 TCGA-85-7697 TCGA-85-7699 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 
          34           10            1           35          911           60 
TCGA-85-8048 TCGA-85-8049 TCGA-85-8071 TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 
          26           60          428           13           13           54 
TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8355 TCGA-85-8481 
          60           55           67           54           61           21 
TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4PA TCGA-85-A511 
         445          424            3          475         1972         1972 
TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 
        1987           24           13          758          289           89 
TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 
         358          428          244          331          269           82 
TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 TCGA-94-A4VJ 
         122          160           70           87          356          430 
TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL 
        1213         1344          189          211          273          183 
TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-L3-A4E7 TCGA-MF-A522 
         256          413          224          308           35           83 
TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HI 
        1722         1548         1135 

  DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE 
                          4                           1 
  DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE 
                       3016                        5287 
  DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE 
                        639                         642 
[1] "4.0 - 3016.0 (639.0)" "1.0 - 5287.0 (642.0)"
[1] "hr=" "1"  
D49V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 19(6Q26) MUTATED         0       16       41        0        15
  DEL PEAK 19(6Q26) WILD-TYPE       1       56       96        1        37
                             vv
clus                          STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 19(6Q26) MUTATED          19         16          4        1
  DEL PEAK 19(6Q26) WILD-TYPE        52         41         16        5
D49V3, multiclass
            clus
vv           DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE
  STAGE I                            0                           1
  STAGE IA                          16                          56
  STAGE IB                          41                          96
  STAGE II                           0                           1
  STAGE IIA                         15                          37
  STAGE IIB                         19                          52
  STAGE IIIA                        16                          41
  STAGE IIIB                         4                          16
  STAGE IV                           1                           5
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2  T3  T4
  DEL PEAK 19(6Q26) MUTATED    23  70  14   6
  DEL PEAK 19(6Q26) WILD-TYPE  75 184  34  14
D49V4, multiclass
    clus
vv   DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE
  T1                        23                          75
  T2                        70                         184
  T3                        14                          34
  T4                         6                          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 19(6Q26) MUTATED    76  27   8   2
  DEL PEAK 19(6Q26) WILD-TYPE 185  86  27   3
D49V5, multiclass
    clus
vv   DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE
  N0                        76                         185
  N1                        27                          86
  N2                         8                          27
  N3                         2                           3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           M0  M1 M1A  MX
  DEL PEAK 19(6Q26) MUTATED   100   0   1  10
  DEL PEAK 19(6Q26) WILD-TYPE 258   5   0  40
D49V6, multiclass
     clus
vv    DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE
  M0                        100                         258
  M1                          0                           5
  M1A                         1                           0
  MX                         10                          40
[1] 4 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 19(6Q26) MUTATED    26  87
  DEL PEAK 19(6Q26) WILD-TYPE  81 226
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 19(6Q26) MUTATED     26   87
  DEL PEAK 19(6Q26) WILD-TYPE   81  226
        clus
vv       DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE
  FEMALE                        26                          81
  MALE                          87                         226
[1] 2 2
[1] FALSE
D49V8, continuous
                             vv
clus                          LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 19(6Q26) MUTATED                                       3
  DEL PEAK 19(6Q26) WILD-TYPE                                     9
                             vv
clus                          LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 19(6Q26) MUTATED                                        2
  DEL PEAK 19(6Q26) WILD-TYPE                                      4
                             vv
clus                          LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 19(6Q26) MUTATED                                         0
  DEL PEAK 19(6Q26) WILD-TYPE                                       1
                             vv
clus                          LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 19(6Q26) MUTATED                                                           108
  DEL PEAK 19(6Q26) WILD-TYPE                                                         293
D49V9, multiclass
                                                             clus
vv                                                            DEL PEAK 19(6Q26) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                               3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                              2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                             0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                       108
                                                             clus
vv                                                            DEL PEAK 19(6Q26) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         293
[1] 4 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 19(6Q26) MUTATED     4 109
  DEL PEAK 19(6Q26) WILD-TYPE   9 298
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 19(6Q26) MUTATED      4  109
  DEL PEAK 19(6Q26) WILD-TYPE    9  298
     clus
vv    DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE
  NO                          4                           9
  YES                       109                         298
[1] 2 2
[1] FALSE
D49V11, continuous
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 19(6Q26) MUTATED    89   2   2   6
  DEL PEAK 19(6Q26) WILD-TYPE 253   6   2  12
D49V12, multiclass
    clus
vv   DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE
  R0                        89                         253
  R1                         2                           6
  R2                         2                           2
  RX                         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                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 19(6Q26) MUTATED       2                         3    82
  DEL PEAK 19(6Q26) WILD-TYPE     7                        14   216
D49V13, multiclass
                           clus
vv                          DEL PEAK 19(6Q26) MUTATED
  ASIAN                                             2
  BLACK OR AFRICAN AMERICAN                         3
  WHITE                                            82
                           clus
vv                          DEL PEAK 19(6Q26) WILD-TYPE
  ASIAN                                               7
  BLACK OR AFRICAN AMERICAN                          14
  WHITE                                             216
[1] 3 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 19(6Q26) MUTATED     2  71
  DEL PEAK 19(6Q26) WILD-TYPE   6 196
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 19(6Q26) MUTATED      2   71
  DEL PEAK 19(6Q26) WILD-TYPE    6  196
                        clus
vv                       DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE
  HISPANIC OR LATINO                             2                           6
  NOT HISPANIC OR LATINO                        71                         196
[1] 2 2
[1] FALSE

Clustering(50) Variable = DEL PEAK 20(7Q11.22) MUTATION ANALYSIS
D50V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 20(7Q11.22) MUTATED    27  10
  DEL PEAK 20(7Q11.22) WILD-TYPE 238 113
  DEL PEAK 20(7Q11.22) MUTATED DEL PEAK 20(7Q11.22) WILD-TYPE 
                            37                            351 
  DEL PEAK 20(7Q11.22) MUTATED DEL PEAK 20(7Q11.22) WILD-TYPE 
                            10                            113 
$`DEL PEAK 20(7Q11.22) MUTATED`
TCGA-18-3421 TCGA-21-1082 TCGA-21-5787 TCGA-22-1016 TCGA-22-5477 TCGA-22-5481 
        1331         3644          329          822         1346         1952 
TCGA-37-5819 TCGA-43-2578 TCGA-43-2581 TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 
         103          684         1176          310         1936          212 
TCGA-46-6026 TCGA-56-6545 TCGA-56-6546 TCGA-56-7580 TCGA-56-8629 TCGA-56-A4BW 
         423           62           26           40           34            2 
TCGA-60-2695 TCGA-60-2703 TCGA-60-2719 TCGA-66-2727 TCGA-66-2754 TCGA-66-2773 
         642         1950         1297         1967           61         1946 
TCGA-66-2788 TCGA-77-7465 TCGA-77-8139 TCGA-77-8144 TCGA-77-A5GH TCGA-85-6560 
         699          479         1951          833          713          364 
TCGA-85-7699 TCGA-85-7843 TCGA-85-8048 TCGA-85-8072 TCGA-85-8350 TCGA-85-8353 
           1           35           26          513           60           54 
TCGA-85-A510 
        1967 

$`DEL PEAK 20(7Q11.22) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
         370          136         2464         2417          146         1415 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 
         345          396         1810          862          758           50 
TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 
         187           85         2754           92          827         3636 
TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 
        1426         3016         2134         1852         1058          474 
TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 
         965         3724          284          267          962         1268 
TCGA-21-5786 TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 
        1032          979          608          223         1945          131 
TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 
        1952           53          429         1485          623         1067 
TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 
        1470          734           17         1161         1057          399 
TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 
        1946          587          358          965         1964         1933 
TCGA-22-5474 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5482 TCGA-22-5483 
         445           24         1651         1952          357          573 
TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 
         916         1912         1713          506           29         2524 
TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 
        1940         2979         1311         5287         1966         1941 
TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-33-6738 TCGA-34-2596 TCGA-34-2600 
         428         1970         1948          822           80         1874 
TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 
         958          881         1000          951         1528         2062 
TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 
        1715          707          365          428          941          552 
TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 
         166          120           13           12          200          247 
TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-39-5011 TCGA-39-5016 
         227          238          207           12         1454         2253 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 
        1361         1947         1996         1964         1849           52 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 
         740           59          833         1107          474         1084 
TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-3394 TCGA-43-3920 
        1086          544         1964         1223          822         1007 
TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-7657 TCGA-43-7658 
         349          849          376          757          236         1970 
TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U 
         407          358         1971          353          296          432 
TCGA-43-A56V TCGA-46-6025 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 
         366          324           12           12          911          541 
TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 
        1948          923         1958         1967          881            3 
TCGA-56-5898 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7582 
         555           30           13           30           44           26 
TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 
           6         1961            1           41          178           55 
TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-A49D TCGA-56-A4BX 
          36           63           17           16           38           46 
TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8388 
          30           25            4            4            8          378 
TCGA-58-8390 TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M 
         911         2167         1058         2589         1723         1072 
TCGA-58-A46N TCGA-60-2696 TCGA-60-2698 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 
         910          109          311         1943         1958          661 
TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 
        1963         1505         1963         1260          274         1731 
TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 
        1531         1075         1475           97          983          908 
TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 
        1092          717          816          358         1973         1957 
TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 
        1955         1947         1952         1311           61          641 
TCGA-66-2744 TCGA-66-2753 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 
          30           31           28           30           30          639 
TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 
         762           30           61           31           61           61 
TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 
        1947          700          578           61          578         1956 
TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 
         121         1954          759           60          790         1217 
TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 
        1955          699         1977          913         1952         1645 
TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 
         122         1492           83          202          211          244 
TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 
          96          121          104         1950         1941         1942 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 
        1952         1959         1968           15         1286         1954 
TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 
        1942         1952         1954         1960         1945         1641 
TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 
        1953         1945         1941         1941         1947         1946 
TCGA-77-8140 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 
        1962         1943          293         1961         1684         1092 
TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 
          10         1953         1942         1959         1955         1963 
TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-85-6561 TCGA-85-6798 
        1290         1280         1939          839          395           34 
TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 
          18           10           49         1965          911           60 
TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8276 TCGA-85-8277 
          60           16          960          428           13           11 
TCGA-85-8287 TCGA-85-8288 TCGA-85-8351 TCGA-85-8352 TCGA-85-8354 TCGA-85-8355 
          13           54           55           67           61           61 
TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 
          22           21          445          424            3          475 
TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z 
          15         1972         1960           25           19         1973 
TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 
        1972         1987           24           13          111          758 
TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE 
         289           89          358          428          244          331 
TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 
         269           82          106          122          160           70 
TCGA-94-7033 TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 
          87          356          430         1213         1344          189 
TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 
         211          273          183          256          413          224 
TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 
         308          222           35          449           36           83 
TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HI 
        1722         1548         1135 

  DEL PEAK 20(7Q11.22) MUTATED DEL PEAK 20(7Q11.22) WILD-TYPE 
                             1                              1 
  DEL PEAK 20(7Q11.22) MUTATED DEL PEAK 20(7Q11.22) WILD-TYPE 
                          3644                           5287 
  DEL PEAK 20(7Q11.22) MUTATED DEL PEAK 20(7Q11.22) WILD-TYPE 
                           513                            661 
[1] "1.0 - 3644.0 (513.0)" "1.0 - 5287.0 (661.0)"
[1] "hr=" "1"  
D50V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 20(7Q11.22) MUTATED         0        7       14        0         6
  DEL PEAK 20(7Q11.22) WILD-TYPE       1       65      123        1        46
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 20(7Q11.22) MUTATED           5          6          0        0
  DEL PEAK 20(7Q11.22) WILD-TYPE        66         51         20        6
D50V3, multiclass
            clus
vv           DEL PEAK 20(7Q11.22) MUTATED DEL PEAK 20(7Q11.22) WILD-TYPE
  STAGE I                               0                              1
  STAGE IA                              7                             65
  STAGE IB                             14                            123
  STAGE II                              0                              1
  STAGE IIA                             6                             46
  STAGE IIB                             5                             66
  STAGE IIIA                            6                             51
  STAGE IIIB                            0                             20
  STAGE IV                              0                              6
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 20(7Q11.22) MUTATED     9  25   3   1
  DEL PEAK 20(7Q11.22) WILD-TYPE  89 229  45  19
D50V4, multiclass
    clus
vv   DEL PEAK 20(7Q11.22) MUTATED DEL PEAK 20(7Q11.22) WILD-TYPE
  T1                            9                             89
  T2                           25                            229
  T3                            3                             45
  T4                            1                             19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 20(7Q11.22) MUTATED    25  10   3   0
  DEL PEAK 20(7Q11.22) WILD-TYPE 236 103  32   5
D50V5, multiclass
    clus
vv   DEL PEAK 20(7Q11.22) MUTATED DEL PEAK 20(7Q11.22) WILD-TYPE
  N0                           25                            236
  N1                           10                            103
  N2                            3                             32
  N3                            0                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A  MX
  DEL PEAK 20(7Q11.22) MUTATED    33   0   0   5
  DEL PEAK 20(7Q11.22) WILD-TYPE 325   5   1  45
D50V6, multiclass
     clus
vv    DEL PEAK 20(7Q11.22) MUTATED DEL PEAK 20(7Q11.22) WILD-TYPE
  M0                            33                            325
  M1                             0                              5
  M1A                            0                              1
  MX                             5                             45
[1] 4 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 20(7Q11.22) MUTATED    10  28
  DEL PEAK 20(7Q11.22) WILD-TYPE  97 285
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(7Q11.22) MUTATED     10   28
  DEL PEAK 20(7Q11.22) WILD-TYPE   97  285
        clus
vv       DEL PEAK 20(7Q11.22) MUTATED DEL PEAK 20(7Q11.22) WILD-TYPE
  FEMALE                           10                             97
  MALE                             28                            285
[1] 2 2
[1] FALSE
D50V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 20(7Q11.22) MUTATED                                       1
  DEL PEAK 20(7Q11.22) WILD-TYPE                                    11
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 20(7Q11.22) MUTATED                                        0
  DEL PEAK 20(7Q11.22) WILD-TYPE                                      6
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 20(7Q11.22) MUTATED                                         0
  DEL PEAK 20(7Q11.22) WILD-TYPE                                       1
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 20(7Q11.22) MUTATED                                                            37
  DEL PEAK 20(7Q11.22) WILD-TYPE                                                         364
D50V9, multiclass
                                                             clus
vv                                                            DEL PEAK 20(7Q11.22) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           37
                                                             clus
vv                                                            DEL PEAK 20(7Q11.22) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   11
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            364
[1] 4 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 20(7Q11.22) MUTATED     2  36
  DEL PEAK 20(7Q11.22) WILD-TYPE  11 371
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(7Q11.22) MUTATED      2   36
  DEL PEAK 20(7Q11.22) WILD-TYPE   11  371
     clus
vv    DEL PEAK 20(7Q11.22) MUTATED DEL PEAK 20(7Q11.22) WILD-TYPE
  NO                             2                             11
  YES                           36                            371
[1] 2 2
[1] FALSE
D50V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 20(7Q11.22) MUTATED    33   0   1   2
  DEL PEAK 20(7Q11.22) WILD-TYPE 309   8   3  16
D50V12, multiclass
    clus
vv   DEL PEAK 20(7Q11.22) MUTATED DEL PEAK 20(7Q11.22) WILD-TYPE
  R0                           33                            309
  R1                            0                              8
  R2                            1                              3
  RX                            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                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(7Q11.22) MUTATED       0                         2    29
  DEL PEAK 20(7Q11.22) WILD-TYPE     9                        15   269
D50V13, multiclass
                           clus
vv                          DEL PEAK 20(7Q11.22) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               29
                           clus
vv                          DEL PEAK 20(7Q11.22) WILD-TYPE
  ASIAN                                                  9
  BLACK OR AFRICAN AMERICAN                             15
  WHITE                                                269
[1] 3 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 20(7Q11.22) MUTATED     0  26
  DEL PEAK 20(7Q11.22) WILD-TYPE   8 241
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(7Q11.22) MUTATED      0   26
  DEL PEAK 20(7Q11.22) WILD-TYPE    8  241
                        clus
vv                       DEL PEAK 20(7Q11.22) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           26
                        clus
vv                       DEL PEAK 20(7Q11.22) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                            241
[1] 2 2
[1] FALSE

Clustering(51) Variable = DEL PEAK 21(7Q36.3) MUTATION ANALYSIS
D51V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 21(7Q36.3) MUTATED    54  30
  DEL PEAK 21(7Q36.3) WILD-TYPE 211  93
  DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE 
                           84                           304 
  DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE 
                           30                            93 
$`DEL PEAK 21(7Q36.3) MUTATED`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3415 TCGA-18-4721 TCGA-18-5595 TCGA-21-1072 
         370         2464         1810         2754          827         3016 
TCGA-21-1082 TCGA-21-5786 TCGA-22-1002 TCGA-22-1011 TCGA-22-1016 TCGA-22-1017 
        3644         1032          131           53          822         1485 
TCGA-22-4595 TCGA-22-4601 TCGA-22-5481 TCGA-22-5482 TCGA-33-4589 TCGA-34-5241 
         734         1057         1952          357         1948          428 
TCGA-37-3789 TCGA-37-3792 TCGA-37-4135 TCGA-37-5819 TCGA-39-5024 TCGA-39-5031 
          13           12          207          103         1964          833 
TCGA-39-5034 TCGA-43-2578 TCGA-43-2581 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 
        1107          684         1176         1007          349          849 
TCGA-43-6771 TCGA-43-7658 TCGA-43-A475 TCGA-46-6026 TCGA-52-7809 TCGA-56-1622 
        1936         1970          296          423         1948          881 
TCGA-56-6545 TCGA-56-7580 TCGA-56-8503 TCGA-56-8626 TCGA-56-8629 TCGA-56-A49D 
          62           40           41           17           34           38 
TCGA-56-A4BW TCGA-56-A4BY TCGA-58-A46L TCGA-60-2695 TCGA-60-2696 TCGA-60-2703 
           2           30         1723          642          109         1950 
TCGA-60-2707 TCGA-60-2712 TCGA-60-2726 TCGA-63-7022 TCGA-66-2753 TCGA-66-2773 
         661          274          358         1947           31         1946 
TCGA-66-2788 TCGA-68-7755 TCGA-68-7757 TCGA-68-8250 TCGA-77-6843 TCGA-77-6844 
         699           83          211          244         1941         1942 
TCGA-77-7138 TCGA-77-7337 TCGA-77-7465 TCGA-77-8131 TCGA-77-8136 TCGA-77-8139 
        1959         1942          479         1941         1947         1951 
TCGA-77-8144 TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6560 TCGA-85-7699 TCGA-85-8048 
         833         1939          713          364            1           26 
TCGA-85-8070 TCGA-85-8287 TCGA-85-8353 TCGA-85-A4QQ TCGA-85-A510 TCGA-85-A512 
         960           13           54         1960         1967         1987 
TCGA-85-A513 TCGA-85-A53L TCGA-90-7767 TCGA-92-8065 TCGA-94-A4VJ TCGA-98-8022 
          24           13           89           70          430          224 

$`DEL PEAK 21(7Q36.3) WILD-TYPE`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
         136         2417          146         1415          345          396 
TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 
         862          758           50         1331          187           85 
TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 
          92         3636         1426         2134         1852         1058 
TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1083 TCGA-21-5782 
         474          965         3724          284          267          962 
TCGA-21-5784 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 
        1268          329          979          608          223         1945 
TCGA-22-1005 TCGA-22-1012 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4596 
        1952          429          623         1067         1470           17 
TCGA-22-4599 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 
        1161          399         1946          587          358          965 
TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 
        1964         1933          445         1346           24         1651 
TCGA-22-5480 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 
        1952          573          916         1912         1713          506 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 
          29         2524         1940         2979         1311         5287 
TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-6738 TCGA-34-2596 
        1966         1941          428         1970          822           80 
TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 
        1874          958          881         1000          951         1528 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5927 TCGA-34-5928 
        2062         1715          707          365          941          552 
TCGA-34-8454 TCGA-37-3783 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 
         166          120          200          247          227          238 
TCGA-37-4141 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 
          12         1454         2253         1361         1947         1996 
TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5035 TCGA-39-5036 
        1849           52          740           59          474         1084 
TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-3394 TCGA-43-6143 
        1086          544         1964         1223          822          376 
TCGA-43-6647 TCGA-43-6770 TCGA-43-7656 TCGA-43-7657 TCGA-43-8115 TCGA-43-8116 
         757          310          212          236          407          358 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A56U TCGA-43-A56V TCGA-46-6025 TCGA-51-4079 
        1971          353          432          366          324           12 
TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 
          12          911          541          923         1958         1967 
TCGA-56-5897 TCGA-56-5898 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 
           3          555           26           30           13           30 
TCGA-56-7579 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8504 
          44           26            6         1961            1          178 
TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8628 TCGA-56-A4BX TCGA-56-A4ZJ 
          55           36           63           16           46           25 
TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 
           4            4            8          378          911         2167 
TCGA-58-8393 TCGA-58-A46J TCGA-58-A46M TCGA-58-A46N TCGA-60-2698 TCGA-60-2704 
        1058         2589         1072          910          311         1943 
TCGA-60-2706 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2713 
        1958         1963         1505         1963         1260         1731 
TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 
        1531         1075         1475         1297           97          983 
TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-63-6202 TCGA-63-7020 
         908         1092          717          816         1973         1957 
TCGA-63-7021 TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 
        1955         1952         1967         1311           61          641 
TCGA-66-2744 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 
          30           61           28           30           30          639 
TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 
         762           30           61           31           61           61 
TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 
        1947          700          578           61          578         1956 
TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 
         121         1954          759           60          790         1217 
TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 
        1955          699         1977          913         1952         1645 
TCGA-66-2795 TCGA-66-2800 TCGA-68-7756 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J 
         122         1492          202           96          121          104 
TCGA-77-6842 TCGA-77-6845 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 
        1950         1952         1968           15         1286         1954 
TCGA-77-7338 TCGA-77-7463 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 
        1952         1954         1960         1945         1641         1953 
TCGA-77-8130 TCGA-77-8133 TCGA-77-8138 TCGA-77-8140 TCGA-77-8145 TCGA-77-8148 
        1945         1941         1946         1962         1943          293 
TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 
        1961         1684         1092           10         1953         1942 
TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GF 
        1959         1955         1963         1290         1280          839 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 
         395           34           18           10           49         1965 
TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8049 TCGA-85-8052 TCGA-85-8071 
          35          911           60           60           16          428 
TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 
         513           13           11           54           60           55 
TCGA-85-8352 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 
          67           61           61           22           21          445 
TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QR 
         424            3          475           15         1972           25 
TCGA-85-A50M TCGA-85-A50Z TCGA-85-A511 TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 
          19         1973         1972          111          758          289 
TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 
         358          428          244          331          269           82 
TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-94-7033 TCGA-94-7943 TCGA-96-7544 
         106          122          160           87          356         1213 
TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 
        1344          189          211          273          183          256 
TCGA-98-8021 TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 
         413          308          222           35          449           36 
TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HI 
          83         1722         1548         1135 

  DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE 
                            1                             1 
  DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE 
                         3644                          5287 
  DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE 
                        691.5                         615.5 
[1] "1.0 - 3644.0 (691.5)" "1.0 - 5287.0 (615.5)"
[1] "hr=" "1.2"
D51V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 21(7Q36.3) MUTATED         0       17       31        0        12
  DEL PEAK 21(7Q36.3) WILD-TYPE       1       55      106        1        40
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 21(7Q36.3) MUTATED          16         10          1        0
  DEL PEAK 21(7Q36.3) WILD-TYPE        55         47         19        6
D51V3, multiclass
            clus
vv           DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE
  STAGE I                              0                             1
  STAGE IA                            17                            55
  STAGE IB                            31                           106
  STAGE II                             0                             1
  STAGE IIA                           12                            40
  STAGE IIB                           16                            55
  STAGE IIIA                          10                            47
  STAGE IIIB                           1                            19
  STAGE IV                             0                             6
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 21(7Q36.3) MUTATED    22  53  10   2
  DEL PEAK 21(7Q36.3) WILD-TYPE  76 201  38  18
D51V4, multiclass
    clus
vv   DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE
  T1                          22                            76
  T2                          53                           201
  T3                          10                            38
  T4                           2                            18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 21(7Q36.3) MUTATED    58  21   5   0
  DEL PEAK 21(7Q36.3) WILD-TYPE 203  92  30   5
D51V5, multiclass
    clus
vv   DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE
  N0                          58                           203
  N1                          21                            92
  N2                           5                            30
  N3                           0                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A  MX
  DEL PEAK 21(7Q36.3) MUTATED    76   0   0   9
  DEL PEAK 21(7Q36.3) WILD-TYPE 282   5   1  41
D51V6, multiclass
     clus
vv    DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE
  M0                           76                           282
  M1                            0                             5
  M1A                           0                             1
  MX                            9                            41
[1] 4 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 21(7Q36.3) MUTATED    24  63
  DEL PEAK 21(7Q36.3) WILD-TYPE  83 250
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(7Q36.3) MUTATED     24   63
  DEL PEAK 21(7Q36.3) WILD-TYPE   83  250
        clus
vv       DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE
  FEMALE                          24                            83
  MALE                            63                           250
[1] 2 2
[1] FALSE
D51V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 21(7Q36.3) MUTATED                                       3
  DEL PEAK 21(7Q36.3) WILD-TYPE                                     9
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 21(7Q36.3) MUTATED                                        0
  DEL PEAK 21(7Q36.3) WILD-TYPE                                      6
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 21(7Q36.3) MUTATED                                         0
  DEL PEAK 21(7Q36.3) WILD-TYPE                                       1
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 21(7Q36.3) MUTATED                                                            84
  DEL PEAK 21(7Q36.3) WILD-TYPE                                                         317
D51V9, multiclass
                                                             clus
vv                                                            DEL PEAK 21(7Q36.3) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          84
                                                             clus
vv                                                            DEL PEAK 21(7Q36.3) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           317
[1] 4 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 21(7Q36.3) MUTATED     3  84
  DEL PEAK 21(7Q36.3) WILD-TYPE  10 323
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(7Q36.3) MUTATED      3   84
  DEL PEAK 21(7Q36.3) WILD-TYPE   10  323
     clus
vv    DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE
  NO                            3                            10
  YES                          84                           323
[1] 2 2
[1] FALSE
D51V11, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 21(7Q36.3) MUTATED    71   1   1   5
  DEL PEAK 21(7Q36.3) WILD-TYPE 271   7   3  13
D51V12, multiclass
    clus
vv   DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE
  R0                          71                           271
  R1                           1                             7
  R2                           1                             3
  RX                           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                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(7Q36.3) MUTATED       2                         2    67
  DEL PEAK 21(7Q36.3) WILD-TYPE     7                        15   231
D51V13, multiclass
                           clus
vv                          DEL PEAK 21(7Q36.3) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              67
                           clus
vv                          DEL PEAK 21(7Q36.3) WILD-TYPE
  ASIAN                                                 7
  BLACK OR AFRICAN AMERICAN                            15
  WHITE                                               231
[1] 3 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 21(7Q36.3) MUTATED     2  58
  DEL PEAK 21(7Q36.3) WILD-TYPE   6 209
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(7Q36.3) MUTATED      2   58
  DEL PEAK 21(7Q36.3) WILD-TYPE    6  209
                        clus
vv                       DEL PEAK 21(7Q36.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          58
                        clus
vv                       DEL PEAK 21(7Q36.3) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           209
[1] 2 2
[1] FALSE

Clustering(52) Variable = DEL PEAK 22(8P23.2) MUTATION ANALYSIS
D52V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 22(8P23.2) MUTATED   180  86
  DEL PEAK 22(8P23.2) WILD-TYPE  85  37
  DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE 
                          266                           122 
  DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE 
                           86                            37 
$`DEL PEAK 22(8P23.2) MUTATED`
TCGA-18-3406 TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 TCGA-18-3416 TCGA-18-3419 
         370         1415          345         1810          862           50 
TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 
         187           85         2754           92          827         3636 
TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1080 TCGA-21-1081 
        3016         2134         1852         1058         3724          284 
TCGA-21-1083 TCGA-21-5782 TCGA-21-5786 TCGA-21-5787 TCGA-22-1000 TCGA-22-1002 
         267          962         1032          329         1945          131 
TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4594 TCGA-22-4596 
         429          822         1485          623         1470           17 
TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4613 TCGA-22-5471 
        1161         1057          399         1946          358          965 
TCGA-22-5473 TCGA-22-5477 TCGA-22-5478 TCGA-22-5480 TCGA-22-5481 TCGA-22-5483 
        1933         1346           24         1952         1952          573 
TCGA-22-5485 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4547 
         916         1713          506           29         2524         1311 
TCGA-33-4566 TCGA-33-4582 TCGA-33-4586 TCGA-33-4589 TCGA-33-6738 TCGA-34-2596 
        5287         1966          428         1948          822           80 
TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2609 TCGA-34-5231 TCGA-34-5241 
        1874          958          881          951         1528          428 
TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4132 
         552          166          120           13           12          227 
TCGA-37-4135 TCGA-37-4141 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 
         207           12         1454         2253         1361         1947 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5031 TCGA-39-5037 
        1964         1849           52          740          833         1086 
TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 
         544         1964         1223          684         1176          822 
TCGA-43-3920 TCGA-43-5668 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 
        1007          349          376          757          310         1936 
TCGA-43-7657 TCGA-43-7658 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V 
         236         1970          358         1971          353          366 
TCGA-46-6025 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 
         324           12          911          541         1948          923 
TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-7222 TCGA-56-7223 
        1967          881            3          555           13           30 
TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-8504 TCGA-56-8626 TCGA-56-8628 
          44           40           26          178           17           16 
TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZK 
          34           38            2           46           30            4 
TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8390 TCGA-58-8393 TCGA-58-A46L TCGA-58-A46M 
           4            8          911         1058         1723         1072 
TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2708 TCGA-60-2710 
         311         1950         1943         1958         1963         1963 
TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2719 TCGA-60-2720 
        1260          274         1731         1531         1297           97 
TCGA-60-2721 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 
         983         1092          717          816          358         1973 
TCGA-63-7020 TCGA-63-7021 TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 
        1957         1955         1952         1967         1311           61 
TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 
          30           31           61           28           30           30 
TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2766 TCGA-66-2768 TCGA-66-2769 
         639          762           30           31           61         1947 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2787 
        1956          121         1954          759           60         1217 
TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2795 
        1955          699         1977          913         1952          122 
TCGA-66-2800 TCGA-68-7755 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J 
        1492           83          244           96          121          104 
TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 
        1950         1941         1942         1952         1959         1968 
TCGA-77-7141 TCGA-77-7142 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 
          15         1286         1942         1952         1954          479 
TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8136 
        1960         1945         1641         1953         1945         1947 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 
        1946         1951         1962          833         1943          293 
TCGA-77-8154 TCGA-77-8156 TCGA-77-A5G6 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GF 
        1092           10         1955         1290         1280          839 
TCGA-77-A5GH TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 
         713          364          395           34           18           10 
TCGA-85-7698 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 
          49         1965           35          911           60           26 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 
          16          960          428          513           13           11 
TCGA-85-8350 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8481 
          60           67           54           61           61           21 
TCGA-85-8582 TCGA-85-8664 TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z 
         424            3         1960           25           19         1973 
TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7766 TCGA-90-7767 
        1972           24           13          111          289           89 
TCGA-90-A4ED TCGA-92-7341 TCGA-92-8063 TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7544 
         244          106          122          356          430         1213 
TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-98-8021 TCGA-98-8022 
        1344          189          211          273          413          224 
TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE 
         308          222          449           36           83         1722 
TCGA-NC-A5HG TCGA-NC-A5HI 
        1548         1135 

$`DEL PEAK 22(8P23.2) WILD-TYPE`
TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3414 TCGA-18-3417 
         136         2464         2417          146          396          758 
TCGA-18-3421 TCGA-21-1071 TCGA-21-1078 TCGA-21-1079 TCGA-21-1082 TCGA-21-5784 
        1331         1426          474          965         3644         1268 
TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1005 TCGA-22-1011 TCGA-22-4593 
         979          608          223         1952           53         1067 
TCGA-22-4595 TCGA-22-4607 TCGA-22-5472 TCGA-22-5474 TCGA-22-5479 TCGA-22-5482 
         734          587         1964          445         1651          357 
TCGA-22-5489 TCGA-33-4533 TCGA-33-4538 TCGA-33-4583 TCGA-33-4587 TCGA-34-2608 
        1912         1940         2979         1941         1970         1000 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5927 TCGA-37-4129 
        2062         1715          707          365          941          200 
TCGA-37-4130 TCGA-37-4133 TCGA-37-5819 TCGA-39-5022 TCGA-39-5030 TCGA-39-5034 
         247          238          103         1996           59         1107 
TCGA-39-5035 TCGA-39-5036 TCGA-43-5670 TCGA-43-7656 TCGA-43-8115 TCGA-43-A475 
         474         1084          849          212          407          296 
TCGA-43-A56U TCGA-46-6026 TCGA-51-4079 TCGA-52-7811 TCGA-56-6545 TCGA-56-6546 
         432          423           12         1958           62           26 
TCGA-56-7221 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 TCGA-56-8622 
          30            6         1961            1           41           55 
TCGA-56-8624 TCGA-56-8625 TCGA-56-A4ZJ TCGA-58-8388 TCGA-58-8391 TCGA-58-A46J 
          36           63           25          378         2167         2589 
TCGA-58-A46N TCGA-60-2695 TCGA-60-2696 TCGA-60-2707 TCGA-60-2709 TCGA-60-2715 
         910          642          109          661         1505         1075 
TCGA-60-2716 TCGA-60-2722 TCGA-63-7022 TCGA-66-2742 TCGA-66-2765 TCGA-66-2767 
        1475          908         1947          641           61           61 
TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2786 
         700          578         1946           61          578          790 
TCGA-66-2788 TCGA-66-2794 TCGA-68-7756 TCGA-68-7757 TCGA-77-7335 TCGA-77-8131 
         699         1645          202          211         1954         1941 
TCGA-77-8133 TCGA-77-8150 TCGA-77-8153 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 
        1941         1961         1684         1953         1942         1959 
TCGA-77-A5G7 TCGA-77-A5GB TCGA-85-7699 TCGA-85-8049 TCGA-85-8287 TCGA-85-8288 
        1963         1939            1           60           13           54 
TCGA-85-8351 TCGA-85-8479 TCGA-85-8580 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4PA 
          55           22          445          475           15         1972 
TCGA-85-A510 TCGA-85-A512 TCGA-90-6837 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4EE 
        1967         1987          758          358          428          331 
TCGA-90-A59Q TCGA-92-7340 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-96-A4JL 
         269           82          160           70           87          183 
TCGA-98-7454 TCGA-L3-A4E7 
         256           35 

  DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE 
                            2                             1 
  DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE 
                         5287                          3644 
  DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE 
                        706.0                         597.5 
[1] "2.0 - 5287.0 (706.0)" "1.0 - 3644.0 (597.5)"
[1] "hr=" "1.1"
D52V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 22(8P23.2) MUTATED         0       54       87        0        35
  DEL PEAK 22(8P23.2) WILD-TYPE       1       18       50        1        17
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 22(8P23.2) MUTATED          54         45         13        2
  DEL PEAK 22(8P23.2) WILD-TYPE        17         12          7        4
D52V3, multiclass
            clus
vv           DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE
  STAGE I                              0                             1
  STAGE IA                            54                            18
  STAGE IB                            87                            50
  STAGE II                             0                             1
  STAGE IIA                           35                            17
  STAGE IIB                           54                            17
  STAGE IIIA                          45                            12
  STAGE IIIB                          13                             7
  STAGE IV                             2                             4
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 22(8P23.2) MUTATED    71 173  35  12
  DEL PEAK 22(8P23.2) WILD-TYPE  27  81  13   8
D52V4, multiclass
    clus
vv   DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE
  T1                          71                            27
  T2                         173                            81
  T3                          35                            13
  T4                          12                             8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 22(8P23.2) MUTATED   174  84  27   3
  DEL PEAK 22(8P23.2) WILD-TYPE  87  29   8   2
D52V5, multiclass
    clus
vv   DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE
  N0                         174                            87
  N1                          84                            29
  N2                          27                             8
  N3                           3                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A  MX
  DEL PEAK 22(8P23.2) MUTATED   257   1   1  29
  DEL PEAK 22(8P23.2) WILD-TYPE 101   4   0  21
D52V6, multiclass
     clus
vv    DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE
  M0                          257                           101
  M1                            1                             4
  M1A                           1                             0
  MX                           29                            21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V7, binary
                               cls
clus                              0   1
  DEL PEAK 22(8P23.2) MUTATED    71 220
  DEL PEAK 22(8P23.2) WILD-TYPE  36  93
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(8P23.2) MUTATED     71  220
  DEL PEAK 22(8P23.2) WILD-TYPE   36   93
        clus
vv       DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE
  FEMALE                          71                            36
  MALE                           220                            93
[1] 2 2
[1] FALSE
D52V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 22(8P23.2) MUTATED                                       7
  DEL PEAK 22(8P23.2) WILD-TYPE                                     5
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 22(8P23.2) MUTATED                                        3
  DEL PEAK 22(8P23.2) WILD-TYPE                                      3
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 22(8P23.2) MUTATED                                         0
  DEL PEAK 22(8P23.2) WILD-TYPE                                       1
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 22(8P23.2) MUTATED                                                           281
  DEL PEAK 22(8P23.2) WILD-TYPE                                                         120
D52V9, multiclass
                                                             clus
vv                                                            DEL PEAK 22(8P23.2) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         281
                                                             clus
vv                                                            DEL PEAK 22(8P23.2) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           120
[1] 4 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 22(8P23.2) MUTATED    10 281
  DEL PEAK 22(8P23.2) WILD-TYPE   3 126
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(8P23.2) MUTATED     10  281
  DEL PEAK 22(8P23.2) WILD-TYPE    3  126
     clus
vv    DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE
  NO                           10                             3
  YES                         281                           126
[1] 2 2
[1] FALSE
D52V11, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 22(8P23.2) MUTATED   241   6   2  10
  DEL PEAK 22(8P23.2) WILD-TYPE 101   2   2   8
D52V12, multiclass
    clus
vv   DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE
  R0                         241                           101
  R1                           6                             2
  R2                           2                             2
  RX                          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                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 22(8P23.2) MUTATED       5                        11   208
  DEL PEAK 22(8P23.2) WILD-TYPE     4                         6    90
D52V13, multiclass
                           clus
vv                          DEL PEAK 22(8P23.2) MUTATED
  ASIAN                                               5
  BLACK OR AFRICAN AMERICAN                          11
  WHITE                                             208
                           clus
vv                          DEL PEAK 22(8P23.2) WILD-TYPE
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                                90
[1] 3 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 22(8P23.2) MUTATED     5 182
  DEL PEAK 22(8P23.2) WILD-TYPE   3  85
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(8P23.2) MUTATED      5  182
  DEL PEAK 22(8P23.2) WILD-TYPE    3   85
                        clus
vv                       DEL PEAK 22(8P23.2) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         182
                        clus
vv                       DEL PEAK 22(8P23.2) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            85
[1] 2 2
[1] FALSE

Clustering(53) Variable = DEL PEAK 23(9P23) MUTATION ANALYSIS
D53V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 23(9P23) MUTATED   175  78
  DEL PEAK 23(9P23) WILD-TYPE  90  45
  DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE 
                        253                         135 
  DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE 
                         78                          45 
$`DEL PEAK 23(9P23) MUTATED`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 
         370         2417         1415          345          396         1810 
TCGA-18-3417 TCGA-18-3419 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1071 
         758           50           85         2754           92         1426 
TCGA-21-1072 TCGA-21-1075 TCGA-21-1077 TCGA-21-1079 TCGA-21-1080 TCGA-21-1082 
        3016         2134         1058          965         3724         3644 
TCGA-21-1083 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 TCGA-22-1000 
         267         1032          329          979          608         1945 
TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 
        1952           53          429          822          623         1067 
TCGA-22-4594 TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 TCGA-22-4607 TCGA-22-4613 
        1470          734         1161         1057          587          358 
TCGA-22-5471 TCGA-22-5472 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5482 
         965         1964         1346           24         1651          357 
TCGA-22-5483 TCGA-22-5485 TCGA-22-5491 TCGA-22-A5C4 TCGA-33-4538 TCGA-33-4547 
         573          916         1713           29         2979         1311 
TCGA-33-4582 TCGA-33-6738 TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 
        1966          822           80         1874          958          881 
TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5241 TCGA-34-5927 
        1000          951         1528         2062          428          941 
TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-4130 TCGA-37-4135 TCGA-37-4141 
         166          120           13          247          207           12 
TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 
         103         1454         2253         1849           52          740 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5036 TCGA-39-5040 TCGA-43-2578 TCGA-43-3394 
          59          833         1084         1964          684          822 
TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 
        1007          349          849          310         1936          212 
TCGA-43-7657 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V 
         236          407          358         1971          353          366 
TCGA-46-6026 TCGA-51-4079 TCGA-51-4081 TCGA-52-7809 TCGA-52-7810 TCGA-56-1622 
         423           12          911         1948          923          881 
TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 
           3          555           62           26           30           13 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 
          30           44           40           26            6         1961 
TCGA-56-7822 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 
           1           41          178           55           36           63 
TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX 
          17           16           34           38            2           46 
TCGA-56-A4ZJ TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8390 TCGA-58-8393 TCGA-58-A46J 
          25            4            8          911         1058         2589 
TCGA-58-A46L TCGA-60-2696 TCGA-60-2698 TCGA-60-2703 TCGA-60-2706 TCGA-60-2707 
        1723          109          311         1950         1958          661 
TCGA-60-2708 TCGA-60-2710 TCGA-60-2711 TCGA-60-2713 TCGA-60-2719 TCGA-60-2720 
        1963         1963         1260         1731         1297           97 
TCGA-60-2721 TCGA-60-2724 TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7022 
         983          717          358         1973         1957         1947 
TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 
        1952         1967         1311           61          641           30 
TCGA-66-2753 TCGA-66-2754 TCGA-66-2756 TCGA-66-2759 TCGA-66-2765 TCGA-66-2768 
          31           61           30          762           61           61 
TCGA-66-2769 TCGA-66-2771 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 
        1947          578           61          578         1956          121 
TCGA-66-2782 TCGA-66-2785 TCGA-66-2786 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 
        1954           60          790          699         1955          699 
TCGA-66-2793 TCGA-66-2800 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I TCGA-77-6843 
        1952         1492          211           96          121         1941 
TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 
        1942         1952         1959         1286         1954         1942 
TCGA-77-7338 TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 
        1952          479         1945         1641         1953         1945 
TCGA-77-8133 TCGA-77-8138 TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 
        1941         1946         1962          833         1943          293 
TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 
        1684         1092           10         1942         1955         1963 
TCGA-77-A5G8 TCGA-77-A5GH TCGA-85-6560 TCGA-85-7696 TCGA-85-7697 TCGA-85-7699 
        1290          713          364           18           10            1 
TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8071 
        1965           35          911           60           26          428 
TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 
          13           13           54           60           55           67 
TCGA-85-8354 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8664 TCGA-85-8666 
          61           22           21          445            3          475 
TCGA-85-A4CL TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 
          15         1960           25           19         1973         1967 
TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7766 TCGA-90-7767 
        1972           24           13          111          289           89 
TCGA-90-7964 TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8065 
         428          269           82          106          122           70 
TCGA-94-7033 TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7545 TCGA-96-8169 TCGA-96-A4JK 
          87          356          430         1344          189          273 
TCGA-96-A4JL TCGA-98-8021 TCGA-98-8023 TCGA-L3-A524 TCGA-MF-A522 TCGA-NC-A5HG 
         183          413          308          449           83         1548 
TCGA-NC-A5HI 
        1135 

$`DEL PEAK 23(9P23) WILD-TYPE`
TCGA-18-3407 TCGA-18-3408 TCGA-18-3410 TCGA-18-3416 TCGA-18-3421 TCGA-18-4083 
         136         2464          146          862         1331          187 
TCGA-18-5595 TCGA-21-1070 TCGA-21-1076 TCGA-21-1078 TCGA-21-1081 TCGA-21-5782 
         827         3636         1852          474          284          962 
TCGA-21-5784 TCGA-22-0944 TCGA-22-1002 TCGA-22-1017 TCGA-22-4596 TCGA-22-4604 
        1268          223          131         1485           17          399 
TCGA-22-4605 TCGA-22-5473 TCGA-22-5474 TCGA-22-5480 TCGA-22-5481 TCGA-22-5489 
        1946         1933          445         1952         1952         1912 
TCGA-22-5492 TCGA-33-4532 TCGA-33-4533 TCGA-33-4566 TCGA-33-4583 TCGA-33-4586 
         506         2524         1940         5287         1941          428 
TCGA-33-4587 TCGA-33-4589 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5928 
        1970         1948         1715          707          365          552 
TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 TCGA-37-4133 TCGA-39-5019 TCGA-39-5021 
          12          200          227          238         1361         1947 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5034 TCGA-39-5035 TCGA-39-5037 TCGA-39-5039 
        1996         1964         1107          474         1086          544 
TCGA-43-2576 TCGA-43-2581 TCGA-43-6143 TCGA-43-6647 TCGA-43-7658 TCGA-43-A475 
        1223         1176          376          757         1970          296 
TCGA-43-A56U TCGA-46-6025 TCGA-51-4080 TCGA-52-7622 TCGA-52-7811 TCGA-52-7812 
         432          324           12          541         1958         1967 
TCGA-56-A4BY TCGA-56-A4ZK TCGA-58-8388 TCGA-58-8391 TCGA-58-A46M TCGA-58-A46N 
          30            4          378         2167         1072          910 
TCGA-60-2695 TCGA-60-2704 TCGA-60-2709 TCGA-60-2712 TCGA-60-2714 TCGA-60-2715 
         642         1943         1505          274         1531         1075 
TCGA-60-2716 TCGA-60-2722 TCGA-60-2723 TCGA-60-2725 TCGA-63-7021 TCGA-66-2755 
        1475          908         1092          816         1955           28 
TCGA-66-2757 TCGA-66-2758 TCGA-66-2763 TCGA-66-2766 TCGA-66-2767 TCGA-66-2770 
          30          639           30           31           61          700 
TCGA-66-2773 TCGA-66-2783 TCGA-66-2787 TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 
        1946          759         1217         1977          913         1645 
TCGA-66-2795 TCGA-68-7755 TCGA-68-7756 TCGA-68-8250 TCGA-68-A59J TCGA-77-6842 
         122           83          202          244          104         1950 
TCGA-77-7139 TCGA-77-7141 TCGA-77-7463 TCGA-77-8007 TCGA-77-8131 TCGA-77-8136 
        1968           15         1954         1960         1941         1947 
TCGA-77-8139 TCGA-77-8150 TCGA-77-A5FZ TCGA-77-A5G3 TCGA-77-A5GA TCGA-77-A5GB 
        1951         1961         1953         1959         1280         1939 
TCGA-77-A5GF TCGA-85-6561 TCGA-85-6798 TCGA-85-7698 TCGA-85-8049 TCGA-85-8052 
         839          395           34           49           60           16 
TCGA-85-8070 TCGA-85-8072 TCGA-85-8277 TCGA-85-8353 TCGA-85-8355 TCGA-85-8582 
         960          513           11           54           61          424 
TCGA-85-A4PA TCGA-85-A512 TCGA-90-6837 TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE 
        1972         1987          758          358          244          331 
TCGA-92-8064 TCGA-96-7544 TCGA-96-8170 TCGA-98-7454 TCGA-98-8022 TCGA-J1-A4AH 
         160         1213          211          256          224          222 
TCGA-L3-A4E7 TCGA-LA-A446 TCGA-NC-A5HE 
          35           36         1722 

  DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE 
                          1                           4 
  DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE 
                       3724                        5287 
  DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE 
                        578                         759 
[1] "1.0 - 3724.0 (578.0)" "4.0 - 5287.0 (759.0)"
[1] "hr=" "1.1"
D53V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 23(9P23) MUTATED         1       52       85        0        40
  DEL PEAK 23(9P23) WILD-TYPE       0       20       52        1        12
                             vv
clus                          STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 23(9P23) MUTATED          40         41         10        5
  DEL PEAK 23(9P23) WILD-TYPE        31         16         10        1
D53V3, multiclass
            clus
vv           DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE
  STAGE I                            1                           0
  STAGE IA                          52                          20
  STAGE IB                          85                          52
  STAGE II                           0                           1
  STAGE IIA                         40                          12
  STAGE IIB                         40                          31
  STAGE IIIA                        41                          16
  STAGE IIIB                        10                          10
  STAGE IV                           5                           1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2  T3  T4
  DEL PEAK 23(9P23) MUTATED    71 160  33  13
  DEL PEAK 23(9P23) WILD-TYPE  27  94  15   7
D53V4, multiclass
    clus
vv   DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE
  T1                        71                          27
  T2                       160                          94
  T3                        33                          15
  T4                        13                           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 23(9P23) MUTATED   177  70  25   2
  DEL PEAK 23(9P23) WILD-TYPE  84  43  10   3
D53V5, multiclass
    clus
vv   DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE
  N0                       177                          84
  N1                        70                          43
  N2                        25                          10
  N3                         2                           3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           M0  M1 M1A  MX
  DEL PEAK 23(9P23) MUTATED   234   4   1  33
  DEL PEAK 23(9P23) WILD-TYPE 124   1   0  17
D53V6, multiclass
     clus
vv    DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE
  M0                        234                         124
  M1                          4                           1
  M1A                         1                           0
  MX                         33                          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"
D53V7, binary
                             cls
clus                            0   1
  DEL PEAK 23(9P23) MUTATED    66 211
  DEL PEAK 23(9P23) WILD-TYPE  41 102
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 23(9P23) MUTATED     66  211
  DEL PEAK 23(9P23) WILD-TYPE   41  102
        clus
vv       DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE
  FEMALE                        66                          41
  MALE                         211                         102
[1] 2 2
[1] FALSE
D53V8, continuous
                             vv
clus                          LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 23(9P23) MUTATED                                       5
  DEL PEAK 23(9P23) WILD-TYPE                                     7
                             vv
clus                          LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 23(9P23) MUTATED                                        3
  DEL PEAK 23(9P23) WILD-TYPE                                      3
                             vv
clus                          LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 23(9P23) MUTATED                                         0
  DEL PEAK 23(9P23) WILD-TYPE                                       1
                             vv
clus                          LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 23(9P23) MUTATED                                                           269
  DEL PEAK 23(9P23) WILD-TYPE                                                         132
D53V9, multiclass
                                                             clus
vv                                                            DEL PEAK 23(9P23) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                               5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                              3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                             0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                       269
                                                             clus
vv                                                            DEL PEAK 23(9P23) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         132
[1] 4 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 23(9P23) MUTATED     8 269
  DEL PEAK 23(9P23) WILD-TYPE   5 138
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 23(9P23) MUTATED      8  269
  DEL PEAK 23(9P23) WILD-TYPE    5  138
     clus
vv    DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE
  NO                          8                           5
  YES                       269                         138
[1] 2 2
[1] FALSE
D53V11, continuous
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 23(9P23) MUTATED   226   5   3  11
  DEL PEAK 23(9P23) WILD-TYPE 116   3   1   7
D53V12, multiclass
    clus
vv   DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE
  R0                       226                         116
  R1                         5                           3
  R2                         3                           1
  RX                        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                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 23(9P23) MUTATED       7                        12   193
  DEL PEAK 23(9P23) WILD-TYPE     2                         5   105
D53V13, multiclass
                           clus
vv                          DEL PEAK 23(9P23) MUTATED
  ASIAN                                             7
  BLACK OR AFRICAN AMERICAN                        12
  WHITE                                           193
                           clus
vv                          DEL PEAK 23(9P23) WILD-TYPE
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           5
  WHITE                                             105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V14, binary
                             cls
clus                            0   1
  DEL PEAK 23(9P23) MUTATED     4 173
  DEL PEAK 23(9P23) WILD-TYPE   4  94
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 23(9P23) MUTATED      4  173
  DEL PEAK 23(9P23) WILD-TYPE    4   94
                        clus
vv                       DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE
  HISPANIC OR LATINO                             4                           4
  NOT HISPANIC OR LATINO                       173                          94
[1] 2 2
[1] FALSE

Clustering(54) Variable = DEL PEAK 24(9P21.3) MUTATION ANALYSIS
D54V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 24(9P21.3) MUTATED   203  93
  DEL PEAK 24(9P21.3) WILD-TYPE  62  30
  DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE 
                          296                            92 
  DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE 
                           93                            30 
$`DEL PEAK 24(9P21.3) MUTATED`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
         370         2417          146         1415          345          396 
TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 
        1810          758           50          187           85         2754 
TCGA-18-5592 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1077 TCGA-21-1080 
          92         1426         3016         2134         1058         3724 
TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI 
        3644          267          962         1032          329          979 
TCGA-22-0944 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 
         223         1952           53          429          822          623 
TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 
        1067         1470          734         1161         1057          399 
TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 
         587          358          965         1964         1933          445 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 
        1346           24         1651          357          573          916 
TCGA-22-5489 TCGA-22-5491 TCGA-22-A5C4 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 
        1912         1713           29         2979         1311         5287 
TCGA-33-4582 TCGA-33-4586 TCGA-33-6738 TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 
        1966          428          822           80         1874          958 
TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5241 
         881         1000          951         1528         2062          428 
TCGA-34-5927 TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-4130 TCGA-37-4135 
         941          166          120           13          247          207 
TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 
          12          103         1454         2253         1361         1947 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 
        1964         1849           52          740           59          833 
TCGA-39-5036 TCGA-39-5037 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-3394 
        1084         1086         1964         1223          684          822 
TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 
        1007          349          849          757          310         1936 
TCGA-43-7656 TCGA-43-7657 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 
         212          236          407          358         1971          353 
TCGA-43-A56V TCGA-46-6026 TCGA-51-4079 TCGA-51-4081 TCGA-52-7809 TCGA-52-7810 
         366          423           12          911         1948          923 
TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 
        1967          881            3          555           62           26 
TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 
          30           13           30           44           40           26 
TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 
           6         1961            1           41          178           55 
TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D 
          36           63           17           16           34           38 
TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZJ TCGA-56-A5DS TCGA-58-8390 TCGA-58-8391 
           2           46           25            8          911         2167 
TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-60-2696 TCGA-60-2698 
        1058         2589         1723         1072          109          311 
TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2710 
        1950         1943         1958          661         1963         1963 
TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2719 TCGA-60-2720 
        1260          274         1731         1531         1297           97 
TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 
         983          908         1092          717          816          358 
TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-66-2727 
        1973         1957         1955         1947         1952         1967 
TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 
        1311           61          641           31           61           28 
TCGA-66-2756 TCGA-66-2758 TCGA-66-2759 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 
          30          639          762           61           31           61 
TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 
          61         1947          700          578         1946           61 
TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2785 TCGA-66-2786 
         578         1956          121         1954           60          790 
TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2793 TCGA-66-2794 TCGA-66-2800 
         699         1955          699         1952         1645         1492 
TCGA-68-7755 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I TCGA-77-6842 TCGA-77-6843 
          83          211           96          121         1950         1941 
TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 
        1942         1952         1959           15         1286         1954 
TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 
        1942         1952         1954          479         1945         1641 
TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8138 TCGA-77-8140 
        1953         1945         1941         1941         1946         1962 
TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 
         833         1943          293         1684         1092           10 
TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA 
        1942         1959         1955         1963         1290         1280 
TCGA-77-A5GH TCGA-85-6560 TCGA-85-7696 TCGA-85-7697 TCGA-85-7699 TCGA-85-7710 
         713          364           18           10            1         1965 
TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8071 TCGA-85-8072 
          35          911           60           26          428          513 
TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 
          13           13           54           60           55           67 
TCGA-85-8354 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 
          61           22           21          445          424            3 
TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z 
         475           15         1960           25           19         1973 
TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 
        1967         1972         1987           24           13          111 
TCGA-90-7766 TCGA-90-7767 TCGA-90-7964 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 
         289           89          428          331          269           82 
TCGA-92-7341 TCGA-92-8063 TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 TCGA-94-A4VJ 
         106          122           70           87          356          430 
TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL 
        1213         1344          189          211          273          183 
TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 
         413          224          308          449           36           83 
TCGA-NC-A5HG TCGA-NC-A5HI 
        1548         1135 

$`DEL PEAK 24(9P21.3) WILD-TYPE`
TCGA-18-3407 TCGA-18-3408 TCGA-18-3416 TCGA-18-3421 TCGA-18-5595 TCGA-21-1070 
         136         2464          862         1331          827         3636 
TCGA-21-1076 TCGA-21-1078 TCGA-21-1079 TCGA-21-1081 TCGA-21-5784 TCGA-22-0940 
        1852          474          965          284         1268          608 
TCGA-22-1000 TCGA-22-1002 TCGA-22-1017 TCGA-22-4596 TCGA-22-4605 TCGA-22-5480 
        1945          131         1485           17         1946         1952 
TCGA-22-5481 TCGA-22-5492 TCGA-33-4532 TCGA-33-4533 TCGA-33-4583 TCGA-33-4587 
        1952          506         2524         1940         1941         1970 
TCGA-33-4589 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5928 TCGA-37-3792 
        1948         1715          707          365          552           12 
TCGA-37-4129 TCGA-37-4132 TCGA-37-4133 TCGA-39-5022 TCGA-39-5034 TCGA-39-5035 
         200          227          238         1996         1107          474 
TCGA-39-5039 TCGA-43-2581 TCGA-43-6143 TCGA-43-7658 TCGA-43-A475 TCGA-43-A56U 
         544         1176          376         1970          296          432 
TCGA-46-6025 TCGA-51-4080 TCGA-52-7622 TCGA-52-7811 TCGA-56-A4BY TCGA-56-A4ZK 
         324           12          541         1958           30            4 
TCGA-56-A5DR TCGA-58-8388 TCGA-58-A46N TCGA-60-2695 TCGA-60-2709 TCGA-60-2715 
           4          378          910          642         1505         1075 
TCGA-60-2716 TCGA-66-2744 TCGA-66-2757 TCGA-66-2763 TCGA-66-2783 TCGA-66-2787 
        1475           30           30           30          759         1217 
TCGA-66-2791 TCGA-66-2792 TCGA-66-2795 TCGA-68-7756 TCGA-68-8250 TCGA-68-A59J 
        1977          913          122          202          244          104 
TCGA-77-7139 TCGA-77-8007 TCGA-77-8136 TCGA-77-8139 TCGA-77-8150 TCGA-77-A5FZ 
        1968         1960         1947         1951         1961         1953 
TCGA-77-A5GB TCGA-77-A5GF TCGA-85-6561 TCGA-85-6798 TCGA-85-7698 TCGA-85-8049 
        1939          839          395           34           49           60 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8277 TCGA-85-8353 TCGA-85-8355 TCGA-85-A4PA 
          16          960           11           54           61         1972 
TCGA-90-6837 TCGA-90-7769 TCGA-90-A4ED TCGA-92-8064 TCGA-98-7454 TCGA-J1-A4AH 
         758          358          244          160          256          222 
TCGA-L3-A4E7 TCGA-NC-A5HE 
          35         1722 

  DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE 
                            1                             4 
  DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE 
                         5287                          3636 
  DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE 
                          651                           625 
[1] "1.0 - 5287.0 (651.0)" "4.0 - 3636.0 (625.0)"
[1] "hr=" "1"  
D54V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 24(9P21.3) MUTATED         1       57      101        0        47
  DEL PEAK 24(9P21.3) WILD-TYPE       0       15       36        1         5
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 24(9P21.3) MUTATED          49         48         12        5
  DEL PEAK 24(9P21.3) WILD-TYPE        22          9          8        1
D54V3, multiclass
            clus
vv           DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE
  STAGE I                              1                             0
  STAGE IA                            57                            15
  STAGE IB                           101                            36
  STAGE II                             0                             1
  STAGE IIA                           47                             5
  STAGE IIB                           49                            22
  STAGE IIIA                          48                             9
  STAGE IIIB                          12                             8
  STAGE IV                             5                             1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 24(9P21.3) MUTATED    79 195  35  14
  DEL PEAK 24(9P21.3) WILD-TYPE  19  59  13   6
D54V4, multiclass
    clus
vv   DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE
  T1                          79                            19
  T2                         195                            59
  T3                          35                            13
  T4                          14                             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 24(9P21.3) MUTATED   197  86  33   3
  DEL PEAK 24(9P21.3) WILD-TYPE  64  27   2   2
D54V5, multiclass
    clus
vv   DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE
  N0                         197                            64
  N1                          86                            27
  N2                          33                             2
  N3                           3                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A  MX
  DEL PEAK 24(9P21.3) MUTATED   277   4   1  36
  DEL PEAK 24(9P21.3) WILD-TYPE  81   1   0  14
D54V6, multiclass
     clus
vv    DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE
  M0                          277                            81
  M1                            4                             1
  M1A                           1                             0
  MX                           36                            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"
D54V7, binary
                               cls
clus                              0   1
  DEL PEAK 24(9P21.3) MUTATED    76 247
  DEL PEAK 24(9P21.3) WILD-TYPE  31  66
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 24(9P21.3) MUTATED     76  247
  DEL PEAK 24(9P21.3) WILD-TYPE   31   66
        clus
vv       DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE
  FEMALE                          76                            31
  MALE                           247                            66
[1] 2 2
[1] FALSE
D54V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 24(9P21.3) MUTATED                                       6
  DEL PEAK 24(9P21.3) WILD-TYPE                                     6
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 24(9P21.3) MUTATED                                        4
  DEL PEAK 24(9P21.3) WILD-TYPE                                      2
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 24(9P21.3) MUTATED                                         0
  DEL PEAK 24(9P21.3) WILD-TYPE                                       1
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 24(9P21.3) MUTATED                                                           313
  DEL PEAK 24(9P21.3) WILD-TYPE                                                          88
D54V9, multiclass
                                                             clus
vv                                                            DEL PEAK 24(9P21.3) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         313
                                                             clus
vv                                                            DEL PEAK 24(9P21.3) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            88
[1] 4 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 24(9P21.3) MUTATED     9 314
  DEL PEAK 24(9P21.3) WILD-TYPE   4  93
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 24(9P21.3) MUTATED      9  314
  DEL PEAK 24(9P21.3) WILD-TYPE    4   93
     clus
vv    DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE
  NO                            9                             4
  YES                         314                            93
[1] 2 2
[1] FALSE
D54V11, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 24(9P21.3) MUTATED   265   5   3  13
  DEL PEAK 24(9P21.3) WILD-TYPE  77   3   1   5
D54V12, multiclass
    clus
vv   DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE
  R0                         265                            77
  R1                           5                             3
  R2                           3                             1
  RX                          13                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 24(9P21.3) MUTATED       8                        12   227
  DEL PEAK 24(9P21.3) WILD-TYPE     1                         5    71
D54V13, multiclass
                           clus
vv                          DEL PEAK 24(9P21.3) MUTATED
  ASIAN                                               8
  BLACK OR AFRICAN AMERICAN                          12
  WHITE                                             227
                           clus
vv                          DEL PEAK 24(9P21.3) WILD-TYPE
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             5
  WHITE                                                71
[1] 3 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 24(9P21.3) MUTATED     5 201
  DEL PEAK 24(9P21.3) WILD-TYPE   3  66
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 24(9P21.3) MUTATED      5  201
  DEL PEAK 24(9P21.3) WILD-TYPE    3   66
                        clus
vv                       DEL PEAK 24(9P21.3) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         201
                        clus
vv                       DEL PEAK 24(9P21.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            66
[1] 2 2
[1] FALSE

Clustering(55) Variable = DEL PEAK 25(9P21.1) MUTATION ANALYSIS
D55V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 25(9P21.1) MUTATED   172  79
  DEL PEAK 25(9P21.1) WILD-TYPE  93  44
  DEL PEAK 25(9P21.1) MUTATED DEL PEAK 25(9P21.1) WILD-TYPE 
                          251                           137 
  DEL PEAK 25(9P21.1) MUTATED DEL PEAK 25(9P21.1) WILD-TYPE 
                           79                            44 
$`DEL PEAK 25(9P21.1) MUTATED`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
         370         2417          146         1415          345          396 
TCGA-18-3415 TCGA-18-3419 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 
        1810           50          187           85         2754           92 
TCGA-21-1071 TCGA-21-1072 TCGA-21-1080 TCGA-21-1082 TCGA-21-1083 TCGA-21-5786 
        1426         3016         3724         3644          267         1032 
TCGA-21-5787 TCGA-21-A5DI TCGA-22-0944 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 
         329          979          223          131         1952           53 
TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4599 
         429          822          623         1067         1470         1161 
TCGA-22-4601 TCGA-22-4604 TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 
        1057          399          587          358          965         1964 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 
        1346           24          357          573          916         1912 
TCGA-22-5491 TCGA-22-A5C4 TCGA-33-4538 TCGA-33-4547 TCGA-33-4582 TCGA-33-6738 
        1713           29         2979         1311         1966          822 
TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 
          80         1874          958          881         1000          951 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5241 TCGA-34-5927 TCGA-34-8454 TCGA-37-3789 
        1528         2062          428          941          166           13 
TCGA-37-4130 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 
         247          207           12          103         1454         2253 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 
        1361         1947         1964         1849           52          740 
TCGA-39-5030 TCGA-39-5036 TCGA-39-5040 TCGA-43-2576 TCGA-43-3394 TCGA-43-3920 
          59         1084         1964         1223          822         1007 
TCGA-43-5668 TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 
         349          849          757          310         1936          212 
TCGA-43-7657 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V 
         236          407          358         1971          353          366 
TCGA-46-6026 TCGA-51-4079 TCGA-51-4081 TCGA-52-7809 TCGA-52-7810 TCGA-56-1622 
         423           12          911         1948          923          881 
TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7222 TCGA-56-7223 
           3          555           62           26           13           30 
TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 
          44           40           26            6         1961            1 
TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 
          41          178           55           36           63           17 
TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZJ 
          16           34           38            2           46           25 
TCGA-56-A5DS TCGA-58-8390 TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L 
           8          911         2167         1058         2589         1723 
TCGA-60-2696 TCGA-60-2698 TCGA-60-2703 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 
         109          311         1950         1958          661         1963 
TCGA-60-2711 TCGA-60-2713 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 
        1260         1731           97          983          908         1092 
TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-7020 TCGA-63-7022 TCGA-66-2727 
         717          816          358         1957         1947         1967 
TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2753 TCGA-66-2755 TCGA-66-2765 
        1311           61          641           31           28           61 
TCGA-66-2766 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 
          31           61         1947          700          578         1946 
TCGA-66-2778 TCGA-66-2781 TCGA-66-2782 TCGA-66-2785 TCGA-66-2786 TCGA-66-2788 
         578          121         1954           60          790          699 
TCGA-66-2789 TCGA-66-2790 TCGA-66-2793 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I 
        1955          699         1952          211           96          121 
TCGA-68-A59J TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7141 
         104         1941         1942         1952         1959           15 
TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 
        1286         1954         1942         1952         1954          479 
TCGA-77-8008 TCGA-77-8009 TCGA-77-8130 TCGA-77-8133 TCGA-77-8138 TCGA-77-8140 
        1945         1641         1945         1941         1946         1962 
TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8153 TCGA-77-8154 TCGA-77-A5G1 
         833         1943          293         1684         1092         1942 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GH TCGA-85-6560 TCGA-85-7696 
        1955         1963         1290          713          364           18 
TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 
          10           49            1         1965           35          911 
TCGA-85-7950 TCGA-85-8048 TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 
          60           26           13           13           54           60 
TCGA-85-8351 TCGA-85-8352 TCGA-85-8479 TCGA-85-8580 TCGA-85-8664 TCGA-85-8666 
          55           67           22          445            3          475 
TCGA-85-A4CL TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 
          15           25           19         1973         1967         1972 
TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7766 TCGA-90-7767 
        1987           24           13          111          289           89 
TCGA-90-7964 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 
         428          331          269           82          106          122 
TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-7545 
          70           87          356          430         1213         1344 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-8021 TCGA-98-8022 
         189          211          273          183          413          224 
TCGA-98-8023 TCGA-L3-A524 TCGA-MF-A522 TCGA-NC-A5HG TCGA-NC-A5HI 
         308          449           83         1548         1135 

$`DEL PEAK 25(9P21.1) WILD-TYPE`
TCGA-18-3407 TCGA-18-3408 TCGA-18-3416 TCGA-18-3417 TCGA-18-3421 TCGA-18-5595 
         136         2464          862          758         1331          827 
TCGA-21-1070 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 
        3636         2134         1852         1058          474          965 
TCGA-21-1081 TCGA-21-5782 TCGA-21-5784 TCGA-22-0940 TCGA-22-1000 TCGA-22-1017 
         284          962         1268          608         1945         1485 
TCGA-22-4595 TCGA-22-4596 TCGA-22-4605 TCGA-22-5473 TCGA-22-5474 TCGA-22-5479 
         734           17         1946         1933          445         1651 
TCGA-22-5480 TCGA-22-5481 TCGA-22-5492 TCGA-33-4532 TCGA-33-4533 TCGA-33-4566 
        1952         1952          506         2524         1940         5287 
TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-34-5234 TCGA-34-5239 
        1941          428         1970         1948         1715          707 
TCGA-34-5240 TCGA-34-5928 TCGA-37-3783 TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 
         365          552          120           12          200          227 
TCGA-37-4133 TCGA-39-5022 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5037 
         238         1996          833         1107          474         1086 
TCGA-39-5039 TCGA-43-2578 TCGA-43-2581 TCGA-43-6143 TCGA-43-7658 TCGA-43-A475 
         544          684         1176          376         1970          296 
TCGA-43-A56U TCGA-46-6025 TCGA-51-4080 TCGA-52-7622 TCGA-52-7811 TCGA-52-7812 
         432          324           12          541         1958         1967 
TCGA-56-7221 TCGA-56-A4BY TCGA-56-A4ZK TCGA-56-A5DR TCGA-58-8388 TCGA-58-A46M 
          30           30            4            4          378         1072 
TCGA-58-A46N TCGA-60-2695 TCGA-60-2704 TCGA-60-2709 TCGA-60-2710 TCGA-60-2712 
         910          642         1943         1505         1963          274 
TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-63-6202 TCGA-63-7021 
        1531         1075         1475         1297         1973         1955 
TCGA-63-7023 TCGA-66-2744 TCGA-66-2754 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 
        1952           30           61           30           30          639 
TCGA-66-2759 TCGA-66-2763 TCGA-66-2767 TCGA-66-2777 TCGA-66-2780 TCGA-66-2783 
         762           30           61           61         1956          759 
TCGA-66-2787 TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 
        1217         1977          913         1645          122         1492 
TCGA-68-7755 TCGA-68-7756 TCGA-68-8250 TCGA-77-6842 TCGA-77-7139 TCGA-77-8007 
          83          202          244         1950         1968         1960 
TCGA-77-8128 TCGA-77-8131 TCGA-77-8136 TCGA-77-8139 TCGA-77-8150 TCGA-77-8156 
        1953         1941         1947         1951         1961           10 
TCGA-77-A5FZ TCGA-77-A5G3 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-85-6561 
        1953         1959         1280         1939          839          395 
TCGA-85-6798 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 
          34           60           16          960          428          513 
TCGA-85-8277 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8481 TCGA-85-8582 
          11           54           61           61           21          424 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-90-6837 TCGA-90-7769 TCGA-90-A4ED TCGA-92-8064 
        1972         1960          758          358          244          160 
TCGA-98-7454 TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-LA-A446 TCGA-NC-A5HE 
         256          222           35           36         1722 

  DEL PEAK 25(9P21.1) MUTATED DEL PEAK 25(9P21.1) WILD-TYPE 
                            1                             4 
  DEL PEAK 25(9P21.1) MUTATED DEL PEAK 25(9P21.1) WILD-TYPE 
                         3724                          5287 
  DEL PEAK 25(9P21.1) MUTATED DEL PEAK 25(9P21.1) WILD-TYPE 
                          479                           762 
[1] "1.0 - 3724.0 (479.0)" "4.0 - 5287.0 (762.0)"
[1] "hr=" "1.2"
D55V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 25(9P21.1) MUTATED         1       51       89        0        40
  DEL PEAK 25(9P21.1) WILD-TYPE       0       21       48        1        12
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 25(9P21.1) MUTATED          40         41          8        3
  DEL PEAK 25(9P21.1) WILD-TYPE        31         16         12        3
D55V3, multiclass
            clus
vv           DEL PEAK 25(9P21.1) MUTATED DEL PEAK 25(9P21.1) WILD-TYPE
  STAGE I                              1                             0
  STAGE IA                            51                            21
  STAGE IB                            89                            48
  STAGE II                             0                             1
  STAGE IIA                           40                            12
  STAGE IIB                           40                            31
  STAGE IIIA                          41                            16
  STAGE IIIB                           8                            12
  STAGE IV                             3                             3
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 25(9P21.1) MUTATED    69 165  30  11
  DEL PEAK 25(9P21.1) WILD-TYPE  29  89  18   9
D55V4, multiclass
    clus
vv   DEL PEAK 25(9P21.1) MUTATED DEL PEAK 25(9P21.1) WILD-TYPE
  T1                          69                            29
  T2                         165                            89
  T3                          30                            18
  T4                          11                             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 25(9P21.1) MUTATED   176  71  24   2
  DEL PEAK 25(9P21.1) WILD-TYPE  85  42  11   3
D55V5, multiclass
    clus
vv   DEL PEAK 25(9P21.1) MUTATED DEL PEAK 25(9P21.1) WILD-TYPE
  N0                         176                            85
  N1                          71                            42
  N2                          24                            11
  N3                           2                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A  MX
  DEL PEAK 25(9P21.1) MUTATED   233   2   1  36
  DEL PEAK 25(9P21.1) WILD-TYPE 125   3   0  14
D55V6, multiclass
     clus
vv    DEL PEAK 25(9P21.1) MUTATED DEL PEAK 25(9P21.1) WILD-TYPE
  M0                          233                           125
  M1                            2                             3
  M1A                           1                             0
  MX                           36                            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"
D55V7, binary
                               cls
clus                              0   1
  DEL PEAK 25(9P21.1) MUTATED    69 206
  DEL PEAK 25(9P21.1) WILD-TYPE  38 107
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 25(9P21.1) MUTATED     69  206
  DEL PEAK 25(9P21.1) WILD-TYPE   38  107
        clus
vv       DEL PEAK 25(9P21.1) MUTATED DEL PEAK 25(9P21.1) WILD-TYPE
  FEMALE                          69                            38
  MALE                           206                           107
[1] 2 2
[1] FALSE
D55V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 25(9P21.1) MUTATED                                       5
  DEL PEAK 25(9P21.1) WILD-TYPE                                     7
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 25(9P21.1) MUTATED                                        2
  DEL PEAK 25(9P21.1) WILD-TYPE                                      4
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 25(9P21.1) MUTATED                                         0
  DEL PEAK 25(9P21.1) WILD-TYPE                                       1
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 25(9P21.1) MUTATED                                                           268
  DEL PEAK 25(9P21.1) WILD-TYPE                                                         133
D55V9, multiclass
                                                             clus
vv                                                            DEL PEAK 25(9P21.1) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         268
                                                             clus
vv                                                            DEL PEAK 25(9P21.1) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           133
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V10, binary
                               cls
clus                              0   1
  DEL PEAK 25(9P21.1) MUTATED     7 268
  DEL PEAK 25(9P21.1) WILD-TYPE   6 139
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 25(9P21.1) MUTATED      7  268
  DEL PEAK 25(9P21.1) WILD-TYPE    6  139
     clus
vv    DEL PEAK 25(9P21.1) MUTATED DEL PEAK 25(9P21.1) WILD-TYPE
  NO                            7                             6
  YES                         268                           139
[1] 2 2
[1] FALSE
D55V11, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 25(9P21.1) MUTATED   221   5   3  13
  DEL PEAK 25(9P21.1) WILD-TYPE 121   3   1   5
D55V12, multiclass
    clus
vv   DEL PEAK 25(9P21.1) MUTATED DEL PEAK 25(9P21.1) WILD-TYPE
  R0                         221                           121
  R1                           5                             3
  R2                           3                             1
  RX                          13                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 25(9P21.1) MUTATED       8                        12   199
  DEL PEAK 25(9P21.1) WILD-TYPE     1                         5    99
D55V13, multiclass
                           clus
vv                          DEL PEAK 25(9P21.1) MUTATED
  ASIAN                                               8
  BLACK OR AFRICAN AMERICAN                          12
  WHITE                                             199
                           clus
vv                          DEL PEAK 25(9P21.1) WILD-TYPE
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             5
  WHITE                                                99
[1] 3 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 25(9P21.1) MUTATED     4 179
  DEL PEAK 25(9P21.1) WILD-TYPE   4  88
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 25(9P21.1) MUTATED      4  179
  DEL PEAK 25(9P21.1) WILD-TYPE    4   88
                        clus
vv                       DEL PEAK 25(9P21.1) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         179
                        clus
vv                       DEL PEAK 25(9P21.1) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                            88
[1] 2 2
[1] FALSE

Clustering(56) Variable = DEL PEAK 26(9Q21.11) MUTATION ANALYSIS
D56V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 26(9Q21.11) MUTATED   136  61
  DEL PEAK 26(9Q21.11) WILD-TYPE 129  62
  DEL PEAK 26(9Q21.11) MUTATED DEL PEAK 26(9Q21.11) WILD-TYPE 
                           197                            191 
  DEL PEAK 26(9Q21.11) MUTATED DEL PEAK 26(9Q21.11) WILD-TYPE 
                            61                             62 
$`DEL PEAK 26(9Q21.11) MUTATED`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3411 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 
         370         2417         1415          758           50         1331 
TCGA-18-4083 TCGA-21-1070 TCGA-21-1075 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 
         187         3636         2134         3644          267          962 
TCGA-21-5786 TCGA-21-A5DI TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1016 
        1032          979          131         1952           53          822 
TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4601 TCGA-22-4604 
        1485          623         1067         1470         1057          399 
TCGA-22-4607 TCGA-22-5473 TCGA-22-5474 TCGA-22-5478 TCGA-22-5481 TCGA-22-5483 
         587         1933          445           24         1952          573 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4547 TCGA-33-4582 TCGA-33-4587 TCGA-33-6738 
          29         2524         1311         1966         1970          822 
TCGA-34-2600 TCGA-34-2604 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 
        1874          958         1000          951         1528         2062 
TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-37-4130 TCGA-37-4135 TCGA-37-4141 
         428          941          552          247          207           12 
TCGA-37-5819 TCGA-39-5011 TCGA-39-5019 TCGA-39-5024 TCGA-39-5028 TCGA-39-5034 
         103         1454         1361         1964           52         1107 
TCGA-39-5035 TCGA-39-5040 TCGA-43-2576 TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 
         474         1964         1223         1007          849          376 
TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 TCGA-43-7657 TCGA-43-8115 
         757          310         1936          212          236          407 
TCGA-43-8116 TCGA-43-8118 TCGA-43-A56V TCGA-46-6026 TCGA-52-7809 TCGA-52-7810 
         358         1971          366          423         1948          923 
TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 
         881            3          555           62           26           30 
TCGA-56-7222 TCGA-56-7579 TCGA-56-7580 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 
          13           44           40         1961            1           41 
TCGA-56-8622 TCGA-56-8624 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D 
          55           36           17           16           34           38 
TCGA-56-A4BW TCGA-56-A4ZJ TCGA-56-A5DS TCGA-58-8390 TCGA-58-8393 TCGA-58-A46J 
           2           25            8          911         1058         2589 
TCGA-60-2696 TCGA-60-2698 TCGA-60-2703 TCGA-60-2706 TCGA-60-2708 TCGA-60-2712 
         109          311         1950         1958         1963          274 
TCGA-60-2714 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2723 TCGA-60-2724 
        1531         1297           97          983         1092          717 
TCGA-60-2726 TCGA-63-7020 TCGA-63-7022 TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 
         358         1957         1947         1967         1311           61 
TCGA-66-2742 TCGA-66-2753 TCGA-66-2756 TCGA-66-2758 TCGA-66-2763 TCGA-66-2766 
         641           31           30          639           30           31 
TCGA-66-2769 TCGA-66-2771 TCGA-66-2773 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 
        1947          578         1946          578         1956          121 
TCGA-66-2782 TCGA-66-2785 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2793 
        1954           60          699         1955          699         1952 
TCGA-66-2800 TCGA-68-7755 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I 
        1492           83          211          244           96          121 
TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7463 
         104         1950         1941         1942         1952         1954 
TCGA-77-8007 TCGA-77-8008 TCGA-77-8130 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 
        1960         1945         1945         1947         1946         1951 
TCGA-77-8140 TCGA-77-8150 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5G1 TCGA-77-A5G6 
        1962         1961         1092           10         1942         1955 
TCGA-77-A5G7 TCGA-77-A5GH TCGA-85-6560 TCGA-85-7697 TCGA-85-7843 TCGA-85-8048 
        1963          713          364           10           35           26 
TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8479 
          13           54           60           55           67           22 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 
           3          475           25           19         1973         1967 
TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7766 TCGA-90-7767 TCGA-90-7964 
          24           13          111          289           89          428 
TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 
         331          269           82           70           87          356 
TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-98-8021 TCGA-98-8022 
         430         1213          189          211          413          224 
TCGA-98-8023 TCGA-L3-A4E7 TCGA-MF-A522 TCGA-NC-A5HG TCGA-NC-A5HI 
         308           35           83         1548         1135 

$`DEL PEAK 26(9Q21.11) WILD-TYPE`
TCGA-18-3407 TCGA-18-3408 TCGA-18-3410 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 
         136         2464          146          345          396         1810 
TCGA-18-3416 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1071 
         862           85         2754           92          827         1426 
TCGA-21-1072 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 
        3016         1852         1058          474          965         3724 
TCGA-21-1081 TCGA-21-5784 TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 
         284         1268          329          608          223         1945 
TCGA-22-1012 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4605 TCGA-22-4613 
         429          734           17         1161         1946          358 
TCGA-22-5471 TCGA-22-5472 TCGA-22-5477 TCGA-22-5479 TCGA-22-5480 TCGA-22-5482 
         965         1964         1346         1651         1952          357 
TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4533 TCGA-33-4538 
         916         1912         1713          506         1940         2979 
TCGA-33-4566 TCGA-33-4583 TCGA-33-4586 TCGA-33-4589 TCGA-34-2596 TCGA-34-2605 
        5287         1941          428         1948           80          881 
TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 
        1715          707          365          166          120           13 
TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 TCGA-37-4133 TCGA-39-5016 TCGA-39-5021 
          12          200          227          238         2253         1947 
TCGA-39-5022 TCGA-39-5027 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5036 
        1996         1849          740           59          833         1084 
TCGA-39-5037 TCGA-39-5039 TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 TCGA-43-5668 
        1086          544          684         1176          822          349 
TCGA-43-7658 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-46-6025 TCGA-51-4079 
        1970          353          296          432          324           12 
TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7811 TCGA-52-7812 TCGA-56-7223 
          12          911          541         1958         1967           30 
TCGA-56-7582 TCGA-56-7730 TCGA-56-8504 TCGA-56-8625 TCGA-56-A4BX TCGA-56-A4BY 
          26            6          178           63           46           30 
TCGA-56-A4ZK TCGA-56-A5DR TCGA-58-8388 TCGA-58-8391 TCGA-58-A46L TCGA-58-A46M 
           4            4          378         2167         1723         1072 
TCGA-58-A46N TCGA-60-2695 TCGA-60-2704 TCGA-60-2707 TCGA-60-2709 TCGA-60-2710 
         910          642         1943          661         1505         1963 
TCGA-60-2711 TCGA-60-2713 TCGA-60-2715 TCGA-60-2716 TCGA-60-2722 TCGA-60-2725 
        1260         1731         1075         1475          908          816 
TCGA-63-6202 TCGA-63-7021 TCGA-63-7023 TCGA-66-2744 TCGA-66-2754 TCGA-66-2755 
        1973         1955         1952           30           61           28 
TCGA-66-2757 TCGA-66-2759 TCGA-66-2765 TCGA-66-2767 TCGA-66-2768 TCGA-66-2770 
          30          762           61           61           61          700 
TCGA-66-2777 TCGA-66-2783 TCGA-66-2786 TCGA-66-2787 TCGA-66-2791 TCGA-66-2792 
          61          759          790         1217         1977          913 
TCGA-66-2794 TCGA-66-2795 TCGA-68-7756 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 
        1645          122          202         1959         1968           15 
TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7465 TCGA-77-8009 
        1286         1954         1942         1952          479         1641 
TCGA-77-8128 TCGA-77-8131 TCGA-77-8133 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 
        1953         1941         1941          833         1943          293 
TCGA-77-8153 TCGA-77-A5FZ TCGA-77-A5G3 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB 
        1684         1953         1959         1290         1280         1939 
TCGA-77-A5GF TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7698 TCGA-85-7699 
         839          395           34           18           49            1 
TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 
        1965          911           60           60           16          960 
TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8353 TCGA-85-8354 
         428          513           13           11           54           61 
TCGA-85-8355 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-A4CL TCGA-85-A4PA 
          61           21          445          424           15         1972 
TCGA-85-A4QQ TCGA-85-A511 TCGA-85-A512 TCGA-90-6837 TCGA-90-7769 TCGA-90-A4ED 
        1960         1972         1987          758          358          244 
TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-96-7545 TCGA-96-A4JK TCGA-96-A4JL 
         106          122          160         1344          273          183 
TCGA-98-7454 TCGA-J1-A4AH TCGA-L3-A524 TCGA-LA-A446 TCGA-NC-A5HE 
         256          222          449           36         1722 

  DEL PEAK 26(9Q21.11) MUTATED DEL PEAK 26(9Q21.11) WILD-TYPE 
                             1                              1 
  DEL PEAK 26(9Q21.11) MUTATED DEL PEAK 26(9Q21.11) WILD-TYPE 
                          3644                           5287 
  DEL PEAK 26(9Q21.11) MUTATED DEL PEAK 26(9Q21.11) WILD-TYPE 
                           573                            740 
[1] "1.0 - 3644.0 (573.0)" "1.0 - 5287.0 (740.0)"
[1] "hr=" "1"  
D56V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 26(9Q21.11) MUTATED         1       42       62        0        28
  DEL PEAK 26(9Q21.11) WILD-TYPE       0       30       75        1        24
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 26(9Q21.11) MUTATED          37         27          7        3
  DEL PEAK 26(9Q21.11) WILD-TYPE        34         30         13        3
D56V3, multiclass
            clus
vv           DEL PEAK 26(9Q21.11) MUTATED DEL PEAK 26(9Q21.11) WILD-TYPE
  STAGE I                               1                              0
  STAGE IA                             42                             30
  STAGE IB                             62                             75
  STAGE II                              0                              1
  STAGE IIA                            28                             24
  STAGE IIB                            37                             34
  STAGE IIIA                           27                             30
  STAGE IIIB                            7                             13
  STAGE IV                              3                              3
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 26(9Q21.11) MUTATED    55 126  22   7
  DEL PEAK 26(9Q21.11) WILD-TYPE  43 128  26  13
D56V4, multiclass
    clus
vv   DEL PEAK 26(9Q21.11) MUTATED DEL PEAK 26(9Q21.11) WILD-TYPE
  T1                           55                             43
  T2                          126                            128
  T3                           22                             26
  T4                            7                             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 26(9Q21.11) MUTATED   134  56  16   2
  DEL PEAK 26(9Q21.11) WILD-TYPE 127  57  19   3
D56V5, multiclass
    clus
vv   DEL PEAK 26(9Q21.11) MUTATED DEL PEAK 26(9Q21.11) WILD-TYPE
  N0                          134                            127
  N1                           56                             57
  N2                           16                             19
  N3                            2                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A  MX
  DEL PEAK 26(9Q21.11) MUTATED   174   2   1  31
  DEL PEAK 26(9Q21.11) WILD-TYPE 184   3   0  19
D56V6, multiclass
     clus
vv    DEL PEAK 26(9Q21.11) MUTATED DEL PEAK 26(9Q21.11) WILD-TYPE
  M0                           174                            184
  M1                             2                              3
  M1A                            1                              0
  MX                            31                             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"
D56V7, binary
                                cls
clus                               0   1
  DEL PEAK 26(9Q21.11) MUTATED    62 148
  DEL PEAK 26(9Q21.11) WILD-TYPE  45 165
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(9Q21.11) MUTATED     62  148
  DEL PEAK 26(9Q21.11) WILD-TYPE   45  165
        clus
vv       DEL PEAK 26(9Q21.11) MUTATED DEL PEAK 26(9Q21.11) WILD-TYPE
  FEMALE                           62                             45
  MALE                            148                            165
[1] 2 2
[1] FALSE
D56V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 26(9Q21.11) MUTATED                                       4
  DEL PEAK 26(9Q21.11) WILD-TYPE                                     8
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 26(9Q21.11) MUTATED                                        1
  DEL PEAK 26(9Q21.11) WILD-TYPE                                      5
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 26(9Q21.11) MUTATED                                         1
  DEL PEAK 26(9Q21.11) WILD-TYPE                                       0
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 26(9Q21.11) MUTATED                                                           204
  DEL PEAK 26(9Q21.11) WILD-TYPE                                                         197
D56V9, multiclass
                                                             clus
vv                                                            DEL PEAK 26(9Q21.11) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          204
                                                             clus
vv                                                            DEL PEAK 26(9Q21.11) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            197
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V10, binary
                                cls
clus                               0   1
  DEL PEAK 26(9Q21.11) MUTATED     4 206
  DEL PEAK 26(9Q21.11) WILD-TYPE   9 201
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(9Q21.11) MUTATED      4  206
  DEL PEAK 26(9Q21.11) WILD-TYPE    9  201
     clus
vv    DEL PEAK 26(9Q21.11) MUTATED DEL PEAK 26(9Q21.11) WILD-TYPE
  NO                             4                              9
  YES                          206                            201
[1] 2 2
[1] FALSE
D56V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 26(9Q21.11) MUTATED   166   2   2   7
  DEL PEAK 26(9Q21.11) WILD-TYPE 176   6   2  11
D56V12, multiclass
    clus
vv   DEL PEAK 26(9Q21.11) MUTATED DEL PEAK 26(9Q21.11) WILD-TYPE
  R0                          166                            176
  R1                            2                              6
  R2                            2                              2
  RX                            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                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 26(9Q21.11) MUTATED       3                        11   150
  DEL PEAK 26(9Q21.11) WILD-TYPE     6                         6   148
D56V13, multiclass
                           clus
vv                          DEL PEAK 26(9Q21.11) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                           11
  WHITE                                              150
                           clus
vv                          DEL PEAK 26(9Q21.11) WILD-TYPE
  ASIAN                                                  6
  BLACK OR AFRICAN AMERICAN                              6
  WHITE                                                148
[1] 3 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 26(9Q21.11) MUTATED     1 139
  DEL PEAK 26(9Q21.11) WILD-TYPE   7 128
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(9Q21.11) MUTATED      1  139
  DEL PEAK 26(9Q21.11) WILD-TYPE    7  128
                        clus
vv                       DEL PEAK 26(9Q21.11) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                          139
                        clus
vv                       DEL PEAK 26(9Q21.11) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            128
[1] 2 2
[1] FALSE

Clustering(57) Variable = DEL PEAK 27(10P15.2) MUTATION ANALYSIS
D57V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 27(10P15.2) MUTATED   124  51
  DEL PEAK 27(10P15.2) WILD-TYPE 141  72
  DEL PEAK 27(10P15.2) MUTATED DEL PEAK 27(10P15.2) WILD-TYPE 
                           175                            213 
  DEL PEAK 27(10P15.2) MUTATED DEL PEAK 27(10P15.2) WILD-TYPE 
                            51                             72 
$`DEL PEAK 27(10P15.2) MUTATED`
TCGA-18-3406 TCGA-18-3411 TCGA-18-3421 TCGA-18-4083 TCGA-18-5595 TCGA-21-1072 
         370         1415         1331          187          827         3016 
TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1079 TCGA-21-1080 TCGA-21-1082 
        2134         1852         1058          965         3724         3644 
TCGA-21-5782 TCGA-21-5786 TCGA-21-A5DI TCGA-22-0940 TCGA-22-1000 TCGA-22-1011 
         962         1032          979          608         1945           53 
TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 
         822          623         1067          734           17         1161 
TCGA-22-4613 TCGA-22-5471 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 
         358          965          445         1346           24         1651 
TCGA-22-5482 TCGA-22-5483 TCGA-22-5491 TCGA-33-4533 TCGA-33-4582 TCGA-33-4583 
         357          573         1713         1940         1966         1941 
TCGA-33-4586 TCGA-34-2596 TCGA-34-2605 TCGA-34-5240 TCGA-34-5927 TCGA-34-8454 
         428           80          881          365          941          166 
TCGA-37-3789 TCGA-37-3792 TCGA-37-4135 TCGA-39-5011 TCGA-39-5019 TCGA-39-5021 
          13           12          207         1454         1361         1947 
TCGA-39-5027 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5036 
        1849          740           59          833         1107         1084 
TCGA-39-5037 TCGA-39-5039 TCGA-43-2576 TCGA-43-2578 TCGA-43-6143 TCGA-43-6647 
        1086          544         1223          684          376          757 
TCGA-43-6770 TCGA-43-7656 TCGA-43-8118 TCGA-43-A56U TCGA-43-A56V TCGA-51-4080 
         310          212         1971          432          366           12 
TCGA-51-4081 TCGA-52-7622 TCGA-52-7810 TCGA-56-5898 TCGA-56-7223 TCGA-56-7580 
         911          541          923          555           30           40 
TCGA-56-7582 TCGA-56-7730 TCGA-56-8503 TCGA-56-8626 TCGA-56-8629 TCGA-56-A49D 
          26            6           41           17           34           38 
TCGA-56-A4BY TCGA-56-A4ZK TCGA-58-8391 TCGA-58-8393 TCGA-58-A46M TCGA-60-2695 
          30            4         2167         1058         1072          642 
TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 
        1950         1943         1958         1963         1505         1963 
TCGA-60-2719 TCGA-60-2722 TCGA-60-2723 TCGA-63-7020 TCGA-66-2737 TCGA-66-2753 
        1297          908         1092         1957           61           31 
TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2766 
          61           28           30          639          762           31 
TCGA-66-2770 TCGA-66-2771 TCGA-66-2777 TCGA-66-2780 TCGA-66-2786 TCGA-66-2787 
         700          578           61         1956          790         1217 
TCGA-66-2788 TCGA-66-2789 TCGA-66-2791 TCGA-66-2793 TCGA-66-2800 TCGA-68-7755 
         699         1955         1977         1952         1492           83 
TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59J TCGA-77-6842 
         202          211          244           96          104         1950 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7338 
        1952         1959         1968           15         1286         1952 
TCGA-77-7465 TCGA-77-8009 TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 
         479         1641         1945         1941         1947         1946 
TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8153 TCGA-77-8156 TCGA-77-A5G3 
        1951         1962          833         1684           10         1959 
TCGA-77-A5G6 TCGA-77-A5G8 TCGA-77-A5GB TCGA-77-A5GF TCGA-85-6798 TCGA-85-7696 
        1955         1290         1939          839           34           18 
TCGA-85-7699 TCGA-85-7844 TCGA-85-7950 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 
           1          911           60           16          960          428 
TCGA-85-8277 TCGA-85-8287 TCGA-85-8351 TCGA-85-8353 TCGA-85-8479 TCGA-85-8580 
          11           13           55           54           22          445 
TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A512 TCGA-85-A5B5 TCGA-90-7769 
        1960           25         1973         1987          111          358 
TCGA-90-A4EE TCGA-92-8063 TCGA-92-8064 TCGA-94-7033 TCGA-96-8170 TCGA-96-A4JK 
         331          122          160           87          211          273 
TCGA-98-8021 TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 
         413          308          222           35          449           36 
TCGA-MF-A522 
          83 

$`DEL PEAK 27(10P15.2) WILD-TYPE`
TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3412 TCGA-18-3414 
         136         2464         2417          146          345          396 
TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-4086 TCGA-18-4721 
        1810          862          758           50           85         2754 
TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1078 TCGA-21-1081 TCGA-21-1083 
          92         3636         1426          474          284          267 
TCGA-21-5784 TCGA-21-5787 TCGA-22-0944 TCGA-22-1002 TCGA-22-1005 TCGA-22-1012 
        1268          329          223          131         1952          429 
TCGA-22-1017 TCGA-22-4594 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 
        1485         1470         1057          399         1946          587 
TCGA-22-5472 TCGA-22-5473 TCGA-22-5480 TCGA-22-5481 TCGA-22-5485 TCGA-22-5489 
        1964         1933         1952         1952          916         1912 
TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 
         506           29         2524         2979         1311         5287 
TCGA-33-4587 TCGA-33-4589 TCGA-33-6738 TCGA-34-2600 TCGA-34-2604 TCGA-34-2608 
        1970         1948          822         1874          958         1000 
TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5241 
         951         1528         2062         1715          707          428 
TCGA-34-5928 TCGA-37-3783 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 
         552          120          200          247          227          238 
TCGA-37-4141 TCGA-37-5819 TCGA-39-5016 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 
          12          103         2253         1996         1964           52 
TCGA-39-5035 TCGA-39-5040 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 
         474         1964         1176          822         1007          349 
TCGA-43-5670 TCGA-43-6771 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 
         849         1936          236         1970          407          358 
TCGA-43-A474 TCGA-43-A475 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-52-7809 
         353          296          324          423           12         1948 
TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-6545 TCGA-56-6546 
        1958         1967          881            3           62           26 
TCGA-56-7221 TCGA-56-7222 TCGA-56-7579 TCGA-56-7731 TCGA-56-7822 TCGA-56-8504 
          30           13           44         1961            1          178 
TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8628 TCGA-56-A4BW TCGA-56-A4BX 
          55           36           63           16            2           46 
TCGA-56-A4ZJ TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 TCGA-58-A46J 
          25            4            8          378          911         2589 
TCGA-58-A46L TCGA-58-A46N TCGA-60-2696 TCGA-60-2698 TCGA-60-2707 TCGA-60-2711 
        1723          910          109          311          661         1260 
TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2720 
         274         1731         1531         1075         1475           97 
TCGA-60-2721 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-63-7021 
         983          717          816          358         1973         1955 
TCGA-63-7022 TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 TCGA-66-2742 TCGA-66-2744 
        1947         1952         1967         1311          641           30 
TCGA-66-2756 TCGA-66-2763 TCGA-66-2765 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 
          30           30           61           61           61         1947 
TCGA-66-2773 TCGA-66-2778 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 
        1946          578          121         1954          759           60 
TCGA-66-2790 TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 TCGA-68-A59I TCGA-77-6843 
         699          913         1645          122          121         1941 
TCGA-77-6844 TCGA-77-7335 TCGA-77-7337 TCGA-77-7463 TCGA-77-8007 TCGA-77-8008 
        1942         1954         1942         1954         1960         1945 
TCGA-77-8128 TCGA-77-8131 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8154 
        1953         1941         1943          293         1961         1092 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G7 TCGA-77-A5GA TCGA-77-A5GH TCGA-85-6560 
        1953         1942         1963         1280          713          364 
TCGA-85-6561 TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 TCGA-85-7843 TCGA-85-8048 
         395           10           49         1965           35           26 
TCGA-85-8049 TCGA-85-8072 TCGA-85-8276 TCGA-85-8288 TCGA-85-8350 TCGA-85-8352 
          60          513           13           54           60           67 
TCGA-85-8354 TCGA-85-8355 TCGA-85-8481 TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 
          61           61           21          424            3          475 
TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A50M TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 
          15         1972           19         1967         1972           24 
TCGA-85-A53L TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7964 TCGA-90-A4ED 
          13          758          289           89          428          244 
TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8065 TCGA-94-7943 TCGA-94-A4VJ 
         269           82          106           70          356          430 
TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8022 
        1213         1344          189          183          256          224 
TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HI 
        1722         1548         1135 

  DEL PEAK 27(10P15.2) MUTATED DEL PEAK 27(10P15.2) WILD-TYPE 
                             1                              1 
  DEL PEAK 27(10P15.2) MUTATED DEL PEAK 27(10P15.2) WILD-TYPE 
                          3724                           5287 
  DEL PEAK 27(10P15.2) MUTATED DEL PEAK 27(10P15.2) WILD-TYPE 
                           700                            552 
[1] "1.0 - 3724.0 (700.0)" "1.0 - 5287.0 (552.0)"
[1] "hr=" "1.1"
D57V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 27(10P15.2) MUTATED         1       30       68        0        21
  DEL PEAK 27(10P15.2) WILD-TYPE       0       42       69        1        31
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 27(10P15.2) MUTATED          32         26          8        0
  DEL PEAK 27(10P15.2) WILD-TYPE        39         31         12        6
D57V3, multiclass
            clus
vv           DEL PEAK 27(10P15.2) MUTATED DEL PEAK 27(10P15.2) WILD-TYPE
  STAGE I                               1                              0
  STAGE IA                             30                             42
  STAGE IB                             68                             69
  STAGE II                              0                              1
  STAGE IIA                            21                             31
  STAGE IIB                            32                             39
  STAGE IIIA                           26                             31
  STAGE IIIB                            8                             12
  STAGE IV                              0                              6
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 27(10P15.2) MUTATED    44 116  19   7
  DEL PEAK 27(10P15.2) WILD-TYPE  54 138  29  13
D57V4, multiclass
    clus
vv   DEL PEAK 27(10P15.2) MUTATED DEL PEAK 27(10P15.2) WILD-TYPE
  T1                           44                             54
  T2                          116                            138
  T3                           19                             29
  T4                            7                             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 27(10P15.2) MUTATED   119  47  17   2
  DEL PEAK 27(10P15.2) WILD-TYPE 142  66  18   3
D57V5, multiclass
    clus
vv   DEL PEAK 27(10P15.2) MUTATED DEL PEAK 27(10P15.2) WILD-TYPE
  N0                          119                            142
  N1                           47                             66
  N2                           17                             18
  N3                            2                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A  MX
  DEL PEAK 27(10P15.2) MUTATED   161   0   0  22
  DEL PEAK 27(10P15.2) WILD-TYPE 197   5   1  28
D57V6, multiclass
     clus
vv    DEL PEAK 27(10P15.2) MUTATED DEL PEAK 27(10P15.2) WILD-TYPE
  M0                           161                            197
  M1                             0                              5
  M1A                            0                              1
  MX                            22                             28
[1] 4 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 27(10P15.2) MUTATED    45 141
  DEL PEAK 27(10P15.2) WILD-TYPE  62 172
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(10P15.2) MUTATED     45  141
  DEL PEAK 27(10P15.2) WILD-TYPE   62  172
        clus
vv       DEL PEAK 27(10P15.2) MUTATED DEL PEAK 27(10P15.2) WILD-TYPE
  FEMALE                           45                             62
  MALE                            141                            172
[1] 2 2
[1] FALSE
D57V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 27(10P15.2) MUTATED                                       5
  DEL PEAK 27(10P15.2) WILD-TYPE                                     7
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 27(10P15.2) MUTATED                                        2
  DEL PEAK 27(10P15.2) WILD-TYPE                                      4
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 27(10P15.2) MUTATED                                         0
  DEL PEAK 27(10P15.2) WILD-TYPE                                       1
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 27(10P15.2) MUTATED                                                           179
  DEL PEAK 27(10P15.2) WILD-TYPE                                                         222
D57V9, multiclass
                                                             clus
vv                                                            DEL PEAK 27(10P15.2) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          179
                                                             clus
vv                                                            DEL PEAK 27(10P15.2) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            222
[1] 4 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 27(10P15.2) MUTATED     6 180
  DEL PEAK 27(10P15.2) WILD-TYPE   7 227
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(10P15.2) MUTATED      6  180
  DEL PEAK 27(10P15.2) WILD-TYPE    7  227
     clus
vv    DEL PEAK 27(10P15.2) MUTATED DEL PEAK 27(10P15.2) WILD-TYPE
  NO                             6                              7
  YES                          180                            227
[1] 2 2
[1] FALSE
D57V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 27(10P15.2) MUTATED   153   4   1   8
  DEL PEAK 27(10P15.2) WILD-TYPE 189   4   3  10
D57V12, multiclass
    clus
vv   DEL PEAK 27(10P15.2) MUTATED DEL PEAK 27(10P15.2) WILD-TYPE
  R0                          153                            189
  R1                            4                              4
  R2                            1                              3
  RX                            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                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 27(10P15.2) MUTATED       2                         8   135
  DEL PEAK 27(10P15.2) WILD-TYPE     7                         9   163
D57V13, multiclass
                           clus
vv                          DEL PEAK 27(10P15.2) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            8
  WHITE                                              135
                           clus
vv                          DEL PEAK 27(10P15.2) WILD-TYPE
  ASIAN                                                  7
  BLACK OR AFRICAN AMERICAN                              9
  WHITE                                                163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V14, binary
                                cls
clus                               0   1
  DEL PEAK 27(10P15.2) MUTATED     3 115
  DEL PEAK 27(10P15.2) WILD-TYPE   5 152
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(10P15.2) MUTATED      3  115
  DEL PEAK 27(10P15.2) WILD-TYPE    5  152
                        clus
vv                       DEL PEAK 27(10P15.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          115
                        clus
vv                       DEL PEAK 27(10P15.2) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            152
[1] 2 2
[1] FALSE

Clustering(58) Variable = DEL PEAK 28(10Q23.31) MUTATION ANALYSIS
D58V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 28(10Q23.31) MUTATED   139  65
  DEL PEAK 28(10Q23.31) WILD-TYPE 126  58
  DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE 
                            204                             184 
  DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE 
                             65                              58 
$`DEL PEAK 28(10Q23.31) MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 
         370          136          146         1415          345         1810 
TCGA-18-4083 TCGA-18-4721 TCGA-18-5592 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 
         187         2754           92         1426         3016         2134 
TCGA-21-1076 TCGA-21-1077 TCGA-21-1081 TCGA-21-1082 TCGA-21-A5DI TCGA-22-0940 
        1852         1058          284         3644          979          608 
TCGA-22-0944 TCGA-22-1000 TCGA-22-1005 TCGA-22-1011 TCGA-22-4593 TCGA-22-4594 
         223         1945         1952           53         1067         1470 
TCGA-22-4595 TCGA-22-4599 TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 TCGA-22-5478 
         734         1161          358         1933          445           24 
TCGA-22-5479 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 
        1651          357          573          916         1912         1713 
TCGA-33-4533 TCGA-33-4538 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 
        1940         2979         1966         1941          428         1970 
TCGA-33-6738 TCGA-34-2596 TCGA-34-2605 TCGA-34-5927 TCGA-37-3792 TCGA-37-4135 
         822           80          881          941           12          207 
TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5027 
         103         1454         2253         1361         1947         1849 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5036 TCGA-39-5037 TCGA-39-5040 
         740           59          833         1084         1086         1964 
TCGA-43-2576 TCGA-43-2578 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-6770 
        1223          684          822         1007          349          310 
TCGA-43-7658 TCGA-43-A474 TCGA-43-A56U TCGA-43-A56V TCGA-46-6025 TCGA-51-4079 
        1970          353          432          366          324           12 
TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-56-1622 
          12          911          541         1948          923          881 
TCGA-56-5897 TCGA-56-5898 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7580 
           3          555           30           13           30           40 
TCGA-56-7582 TCGA-56-7730 TCGA-56-8622 TCGA-56-8625 TCGA-56-8628 TCGA-56-8629 
          26            6           55           63           16           34 
TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZK TCGA-58-8388 TCGA-58-8391 TCGA-58-8393 
          46           30            4          378         2167         1058 
TCGA-58-A46J TCGA-58-A46M TCGA-60-2695 TCGA-60-2698 TCGA-60-2704 TCGA-60-2706 
        2589         1072          642          311         1943         1958 
TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2715 TCGA-60-2719 
        1963         1505         1963         1731         1075         1297 
TCGA-60-2720 TCGA-60-2722 TCGA-60-2725 TCGA-63-7020 TCGA-63-7022 TCGA-66-2727 
          97          908          816         1957         1947         1967 
TCGA-66-2737 TCGA-66-2753 TCGA-66-2754 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 
          61           31           61           30           30          639 
TCGA-66-2759 TCGA-66-2763 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2778 
         762           30          700          578         1946          578 
TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2787 TCGA-66-2789 TCGA-66-2791 
        1954          759           60         1217         1955         1977 
TCGA-66-2792 TCGA-66-2793 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 
         913         1952         1492           83          202          211 
TCGA-68-8250 TCGA-68-8251 TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-7139 
         244           96          104         1950         1941         1968 
TCGA-77-7337 TCGA-77-7463 TCGA-77-7465 TCGA-77-8009 TCGA-77-8130 TCGA-77-8133 
        1942         1954          479         1641         1945         1941 
TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8148 
        1947         1946         1951         1962          833          293 
TCGA-77-8150 TCGA-77-8153 TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5G7 TCGA-77-A5GB 
        1961         1684           10         1959         1963         1939 
TCGA-77-A5GF TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7698 
         839          364          395           34           18           49 
TCGA-85-7699 TCGA-85-7844 TCGA-85-7950 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 
           1          911           60           60           16          960 
TCGA-85-8277 TCGA-85-8351 TCGA-85-8353 TCGA-85-8354 TCGA-85-8479 TCGA-85-8580 
          11           55           54           61           22          445 
TCGA-85-8664 TCGA-85-A4CL TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 
           3           15         1960           19         1973         1967 
TCGA-85-A511 TCGA-85-A53L TCGA-85-A5B5 TCGA-92-7341 TCGA-92-8064 TCGA-94-7033 
        1972           13          111          106          160           87 
TCGA-94-7943 TCGA-96-7545 TCGA-96-8170 TCGA-96-A4JK TCGA-98-8021 TCGA-98-8023 
         356         1344          211          273          413          308 
TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HI 
         222           35          449           36           83         1135 

$`DEL PEAK 28(10Q23.31) WILD-TYPE`
TCGA-18-3408 TCGA-18-3409 TCGA-18-3414 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 
        2464         2417          396          862          758           50 
TCGA-18-3421 TCGA-18-4086 TCGA-18-5595 TCGA-21-1070 TCGA-21-1078 TCGA-21-1079 
        1331           85          827         3636          474          965 
TCGA-21-1080 TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 
        3724          267          962         1268         1032          329 
TCGA-22-1002 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4596 
         131          429          822         1485          623           17 
TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-5471 TCGA-22-5472 
        1057          399         1946          587          965         1964 
TCGA-22-5477 TCGA-22-5480 TCGA-22-5481 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 
        1346         1952         1952          506           29         2524 
TCGA-33-4547 TCGA-33-4566 TCGA-33-4589 TCGA-34-2600 TCGA-34-2604 TCGA-34-2608 
        1311         5287         1948         1874          958         1000 
TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 
         951         1528         2062         1715          707          365 
TCGA-34-5241 TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 
         428          552          166          120           13          200 
TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4141 TCGA-39-5022 TCGA-39-5024 
         247          227          238           12         1996         1964 
TCGA-39-5028 TCGA-39-5034 TCGA-39-5035 TCGA-39-5039 TCGA-43-2581 TCGA-43-5670 
          52         1107          474          544         1176          849 
TCGA-43-6143 TCGA-43-6647 TCGA-43-6771 TCGA-43-7656 TCGA-43-7657 TCGA-43-8115 
         376          757         1936          212          236          407 
TCGA-43-8116 TCGA-43-8118 TCGA-43-A475 TCGA-46-6026 TCGA-52-7811 TCGA-52-7812 
         358         1971          296          423         1958         1967 
TCGA-56-6545 TCGA-56-6546 TCGA-56-7579 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 
          62           26           44         1961            1           41 
TCGA-56-8504 TCGA-56-8624 TCGA-56-8626 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4ZJ 
         178           36           17           38            2           25 
TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8390 TCGA-58-A46L TCGA-58-A46N TCGA-60-2696 
           4            8          911         1723          910          109 
TCGA-60-2703 TCGA-60-2707 TCGA-60-2711 TCGA-60-2712 TCGA-60-2714 TCGA-60-2716 
        1950          661         1260          274         1531         1475 
TCGA-60-2721 TCGA-60-2723 TCGA-60-2724 TCGA-60-2726 TCGA-63-6202 TCGA-63-7021 
         983         1092          717          358         1973         1955 
TCGA-63-7023 TCGA-66-2734 TCGA-66-2742 TCGA-66-2744 TCGA-66-2755 TCGA-66-2765 
        1952         1311          641           30           28           61 
TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2777 TCGA-66-2780 
          31           61           61         1947           61         1956 
TCGA-66-2781 TCGA-66-2786 TCGA-66-2788 TCGA-66-2790 TCGA-66-2794 TCGA-66-2795 
         121          790          699          699         1645          122 
TCGA-68-A59I TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7141 TCGA-77-7142 
         121         1942         1952         1959           15         1286 
TCGA-77-7335 TCGA-77-7338 TCGA-77-8007 TCGA-77-8008 TCGA-77-8128 TCGA-77-8131 
        1954         1952         1960         1945         1953         1941 
TCGA-77-8145 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G8 
        1943         1092         1953         1942         1955         1290 
TCGA-77-A5GA TCGA-77-A5GH TCGA-85-7697 TCGA-85-7710 TCGA-85-7843 TCGA-85-8048 
        1280          713           10         1965           35           26 
TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 
         428          513           13           13           54           60 
TCGA-85-8352 TCGA-85-8355 TCGA-85-8481 TCGA-85-8582 TCGA-85-8666 TCGA-85-A4PA 
          67           61           21          424          475         1972 
TCGA-85-A4QR TCGA-85-A512 TCGA-85-A513 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 
          25         1987           24          758          289           89 
TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 
         358          428          244          331          269           82 
TCGA-92-8063 TCGA-92-8065 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8169 TCGA-96-A4JL 
         122           70          430         1213          189          183 
TCGA-98-7454 TCGA-98-8022 TCGA-NC-A5HE TCGA-NC-A5HG 
         256          224         1722         1548 

  DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE 
                              1                               1 
  DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE 
                           3644                            5287 
  DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE 
                            692                             605 
[1] "1.0 - 3644.0 (692.0)" "1.0 - 5287.0 (605.0)"
[1] "hr=" "1"  
D58V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 28(10Q23.31) MUTATED         1       37       77        0        26
  DEL PEAK 28(10Q23.31) WILD-TYPE       0       35       60        1        26
                                 vv
clus                              STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 28(10Q23.31) MUTATED          36         31         11        1
  DEL PEAK 28(10Q23.31) WILD-TYPE        35         26          9        5
D58V3, multiclass
            clus
vv           DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE
  STAGE I                                1                               0
  STAGE IA                              37                              35
  STAGE IB                              77                              60
  STAGE II                               0                               1
  STAGE IIA                             26                              26
  STAGE IIB                             36                              35
  STAGE IIIA                            31                              26
  STAGE IIIB                            11                               9
  STAGE IV                               1                               5
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  DEL PEAK 28(10Q23.31) MUTATED    54 137  24   7
  DEL PEAK 28(10Q23.31) WILD-TYPE  44 117  24  13
D58V4, multiclass
    clus
vv   DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE
  T1                            54                              44
  T2                           137                             117
  T3                            24                              24
  T4                             7                              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 28(10Q23.31) MUTATED   138  58  18   4
  DEL PEAK 28(10Q23.31) WILD-TYPE 123  55  17   1
D58V5, multiclass
    clus
vv   DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE
  N0                           138                             123
  N1                            58                              55
  N2                            18                              17
  N3                             4                               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               M0  M1 M1A  MX
  DEL PEAK 28(10Q23.31) MUTATED   192   1   0  24
  DEL PEAK 28(10Q23.31) WILD-TYPE 166   4   1  26
D58V6, multiclass
     clus
vv    DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE
  M0                            192                             166
  M1                              1                               4
  M1A                             0                               1
  MX                             24                              26
[1] 4 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 28(10Q23.31) MUTATED    49 173
  DEL PEAK 28(10Q23.31) WILD-TYPE  58 140
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(10Q23.31) MUTATED     49  173
  DEL PEAK 28(10Q23.31) WILD-TYPE   58  140
        clus
vv       DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE
  FEMALE                            49                              58
  MALE                             173                             140
[1] 2 2
[1] FALSE
D58V8, continuous
                                 vv
clus                              LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 28(10Q23.31) MUTATED                                       6
  DEL PEAK 28(10Q23.31) WILD-TYPE                                     6
                                 vv
clus                              LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 28(10Q23.31) MUTATED                                        2
  DEL PEAK 28(10Q23.31) WILD-TYPE                                      4
                                 vv
clus                              LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 28(10Q23.31) MUTATED                                         1
  DEL PEAK 28(10Q23.31) WILD-TYPE                                       0
                                 vv
clus                              LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 28(10Q23.31) MUTATED                                                           213
  DEL PEAK 28(10Q23.31) WILD-TYPE                                                         188
D58V9, multiclass
                                                             clus
vv                                                            DEL PEAK 28(10Q23.31) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           213
                                                             clus
vv                                                            DEL PEAK 28(10Q23.31) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                     6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                    4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             188
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V10, binary
                                 cls
clus                                0   1
  DEL PEAK 28(10Q23.31) MUTATED     6 216
  DEL PEAK 28(10Q23.31) WILD-TYPE   7 191
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(10Q23.31) MUTATED      6  216
  DEL PEAK 28(10Q23.31) WILD-TYPE    7  191
     clus
vv    DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE
  NO                              6                               7
  YES                           216                             191
[1] 2 2
[1] FALSE
D58V11, continuous
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 28(10Q23.31) MUTATED   185   2   2   9
  DEL PEAK 28(10Q23.31) WILD-TYPE 157   6   2   9
D58V12, multiclass
    clus
vv   DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE
  R0                           185                             157
  R1                             2                               6
  R2                             2                               2
  RX                             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                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 28(10Q23.31) MUTATED       5                         8   157
  DEL PEAK 28(10Q23.31) WILD-TYPE     4                         9   141
D58V13, multiclass
                           clus
vv                          DEL PEAK 28(10Q23.31) MUTATED
  ASIAN                                                 5
  BLACK OR AFRICAN AMERICAN                             8
  WHITE                                               157
                           clus
vv                          DEL PEAK 28(10Q23.31) WILD-TYPE
  ASIAN                                                   4
  BLACK OR AFRICAN AMERICAN                               9
  WHITE                                                 141
[1] 3 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 28(10Q23.31) MUTATED     4 137
  DEL PEAK 28(10Q23.31) WILD-TYPE   4 130
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(10Q23.31) MUTATED      4  137
  DEL PEAK 28(10Q23.31) WILD-TYPE    4  130
                        clus
vv                       DEL PEAK 28(10Q23.31) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           137
                        clus
vv                       DEL PEAK 28(10Q23.31) WILD-TYPE
  HISPANIC OR LATINO                                   4
  NOT HISPANIC OR LATINO                             130
[1] 2 2
[1] FALSE

Clustering(59) Variable = DEL PEAK 29(11P15.5) MUTATION ANALYSIS
D59V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 29(11P15.5) MUTATED   135  58
  DEL PEAK 29(11P15.5) WILD-TYPE 130  65
  DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE 
                           193                            195 
  DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE 
                            58                             65 
$`DEL PEAK 29(11P15.5) MUTATED`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3412 TCGA-18-3414 
         370         2464         2417          146          345          396 
TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-5592 TCGA-21-1070 
         862          758           50         1331           92         3636 
TCGA-21-1071 TCGA-21-1076 TCGA-21-1077 TCGA-21-1080 TCGA-21-1082 TCGA-21-1083 
        1426         1852         1058         3724         3644          267 
TCGA-21-5782 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-1017 TCGA-22-4593 
         962         1032          329          979         1485         1067 
TCGA-22-4595 TCGA-22-4596 TCGA-22-4601 TCGA-22-4607 TCGA-22-5471 TCGA-22-5473 
         734           17         1057          587          965         1933 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 
        1346           24         1651         1952          357          573 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4582 
          29         2524         1940         2979         1311         1966 
TCGA-33-4587 TCGA-33-6738 TCGA-34-2600 TCGA-34-2605 TCGA-34-5231 TCGA-34-5232 
        1970          822         1874          881         1528         2062 
TCGA-34-5241 TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-4130 
         428          552          166          120           13          247 
TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-39-5011 TCGA-39-5019 
         227          238          207           12         1454         1361 
TCGA-39-5022 TCGA-39-5027 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5037 
        1996         1849          833         1107          474         1086 
TCGA-43-2578 TCGA-43-2581 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 
         684         1176         1007          349          849          376 
TCGA-43-7656 TCGA-43-7657 TCGA-43-8115 TCGA-43-A474 TCGA-43-A56V TCGA-46-6025 
         212          236          407          353          366          324 
TCGA-46-6026 TCGA-52-7809 TCGA-52-7810 TCGA-56-1622 TCGA-56-6545 TCGA-56-7222 
         423         1948          923          881           62           13 
TCGA-56-7579 TCGA-56-7580 TCGA-56-7822 TCGA-56-8503 TCGA-56-8624 TCGA-56-8628 
          44           40            1           41           36           16 
TCGA-56-8629 TCGA-56-A49D TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-58-8390 
          34           38           25            4            4          911 
TCGA-58-8391 TCGA-60-2695 TCGA-60-2698 TCGA-60-2703 TCGA-60-2708 TCGA-60-2712 
        2167          642          311         1950         1963          274 
TCGA-60-2714 TCGA-60-2720 TCGA-60-2721 TCGA-60-2723 TCGA-60-2724 TCGA-60-2726 
        1531           97          983         1092          717          358 
TCGA-63-6202 TCGA-63-7020 TCGA-66-2742 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 
        1973         1957          641          639          762           30 
TCGA-66-2766 TCGA-66-2768 TCGA-66-2769 TCGA-66-2771 TCGA-66-2773 TCGA-66-2780 
          31           61         1947          578         1946         1956 
TCGA-66-2781 TCGA-66-2782 TCGA-66-2785 TCGA-66-2788 TCGA-66-2789 TCGA-66-2791 
         121         1954           60          699         1955         1977 
TCGA-66-2792 TCGA-66-2793 TCGA-66-2795 TCGA-66-2800 TCGA-68-7757 TCGA-68-8250 
         913         1952          122         1492          211          244 
TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6844 TCGA-77-6845 TCGA-77-7139 
          96          121          104         1942         1952         1968 
TCGA-77-7141 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 
          15         1942         1952         1954          479         1960 
TCGA-77-8008 TCGA-77-8009 TCGA-77-8130 TCGA-77-8133 TCGA-77-8138 TCGA-77-8140 
        1945         1641         1945         1941         1946         1962 
TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5G6 
         293         1961         1684         1092           10         1955 
TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GF TCGA-85-6561 TCGA-85-7696 
        1963         1290         1280          839          395           18 
TCGA-85-7697 TCGA-85-7699 TCGA-85-7843 TCGA-85-7950 TCGA-85-8048 TCGA-85-8276 
          10            1           35           60           26           13 
TCGA-85-8288 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8479 TCGA-85-8481 
          54           55           67           54           22           21 
TCGA-85-A4CL TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A512 TCGA-85-A5B5 TCGA-90-7769 
          15         1960           25         1987          111          358 
TCGA-90-7964 TCGA-90-A59Q TCGA-92-8063 TCGA-92-8065 TCGA-94-7033 TCGA-94-A4VJ 
         428          269          122           70           87          430 
TCGA-96-7544 TCGA-96-8169 TCGA-98-8023 TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HG 
        1213          189          308           83         1722         1548 
TCGA-NC-A5HI 
        1135 

$`DEL PEAK 29(11P15.5) WILD-TYPE`
TCGA-18-3407 TCGA-18-3411 TCGA-18-3415 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 
         136         1415         1810          187           85         2754 
TCGA-18-5595 TCGA-21-1072 TCGA-21-1075 TCGA-21-1078 TCGA-21-1079 TCGA-21-1081 
         827         3016         2134          474          965          284 
TCGA-21-5784 TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 
        1268          608          223         1945          131         1952 
TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4594 TCGA-22-4599 
          53          429          822          623         1470         1161 
TCGA-22-4604 TCGA-22-4605 TCGA-22-4613 TCGA-22-5472 TCGA-22-5474 TCGA-22-5480 
         399         1946          358         1964          445         1952 
TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4566 TCGA-33-4583 
         916         1912         1713          506         5287         1941 
TCGA-33-4586 TCGA-33-4589 TCGA-34-2596 TCGA-34-2604 TCGA-34-2608 TCGA-34-2609 
         428         1948           80          958         1000          951 
TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5927 TCGA-37-3792 TCGA-37-4129 
        1715          707          365          941           12          200 
TCGA-37-5819 TCGA-39-5016 TCGA-39-5021 TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 
         103         2253         1947         1964           52          740 
TCGA-39-5030 TCGA-39-5036 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-3394 
          59         1084          544         1964         1223          822 
TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-7658 TCGA-43-8116 TCGA-43-8118 
         757          310         1936         1970          358         1971 
TCGA-43-A475 TCGA-43-A56U TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 
         296          432           12           12          911          541 
TCGA-52-7811 TCGA-52-7812 TCGA-56-5897 TCGA-56-5898 TCGA-56-6546 TCGA-56-7221 
        1958         1967            3          555           26           30 
TCGA-56-7223 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-8504 TCGA-56-8622 
          30           26            6         1961          178           55 
TCGA-56-8625 TCGA-56-8626 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A5DS 
          63           17            2           46           30            8 
TCGA-58-8388 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N 
         378         1058         2589         1723         1072          910 
TCGA-60-2696 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2709 TCGA-60-2710 
         109         1943         1958          661         1505         1963 
TCGA-60-2711 TCGA-60-2713 TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2722 
        1260         1731         1075         1475         1297          908 
TCGA-60-2725 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 
         816         1955         1947         1952         1967         1311 
TCGA-66-2737 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 
          61           30           31           61           28           30 
TCGA-66-2757 TCGA-66-2765 TCGA-66-2767 TCGA-66-2770 TCGA-66-2777 TCGA-66-2778 
          30           61           61          700           61          578 
TCGA-66-2783 TCGA-66-2786 TCGA-66-2787 TCGA-66-2790 TCGA-66-2794 TCGA-68-7755 
         759          790         1217          699         1645           83 
TCGA-68-7756 TCGA-77-6842 TCGA-77-6843 TCGA-77-7138 TCGA-77-7142 TCGA-77-7335 
         202         1950         1941         1959         1286         1954 
TCGA-77-8128 TCGA-77-8131 TCGA-77-8136 TCGA-77-8139 TCGA-77-8144 TCGA-77-8145 
        1953         1941         1947         1951          833         1943 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6560 
        1953         1942         1959         1939          713          364 
TCGA-85-6798 TCGA-85-7698 TCGA-85-7710 TCGA-85-7844 TCGA-85-8049 TCGA-85-8052 
          34           49         1965          911           60           16 
TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8277 TCGA-85-8287 TCGA-85-8350 
         960          428          513           11           13           60 
TCGA-85-8354 TCGA-85-8355 TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 
          61           61          445          424            3          475 
TCGA-85-A4PA TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 
        1972           19         1973         1967         1972           24 
TCGA-85-A53L TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-A4ED TCGA-90-A4EE 
          13          758          289           89          244          331 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8064 TCGA-94-7943 TCGA-96-7545 TCGA-96-8170 
          82          106          160          356         1344          211 
TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-J1-A4AH 
         273          183          256          413          224          222 
TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 
          35          449           36 

  DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE 
                             1                              2 
  DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE 
                          3724                           5287 
  DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE 
                           642                            623 
[1] "1.0 - 3724.0 (642.0)" "2.0 - 5287.0 (623.0)"
[1] "hr=" "1.1"
D59V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 29(11P15.5) MUTATED         1       28       64        0        26
  DEL PEAK 29(11P15.5) WILD-TYPE       0       44       73        1        26
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 29(11P15.5) MUTATED          39         32          9        4
  DEL PEAK 29(11P15.5) WILD-TYPE        32         25         11        2
D59V3, multiclass
            clus
vv           DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE
  STAGE I                               1                              0
  STAGE IA                             28                             44
  STAGE IB                             64                             73
  STAGE II                              0                              1
  STAGE IIA                            26                             26
  STAGE IIB                            39                             32
  STAGE IIIA                           32                             25
  STAGE IIIB                            9                             11
  STAGE IV                              4                              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 29(11P15.5) MUTATED    43 122  30  10
  DEL PEAK 29(11P15.5) WILD-TYPE  55 132  18  10
D59V4, multiclass
    clus
vv   DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE
  T1                           43                             55
  T2                          122                            132
  T3                           30                             18
  T4                           10                             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 29(11P15.5) MUTATED   126  60  16   2
  DEL PEAK 29(11P15.5) WILD-TYPE 135  53  19   3
D59V5, multiclass
    clus
vv   DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE
  N0                          126                            135
  N1                           60                             53
  N2                           16                             19
  N3                            2                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A  MX
  DEL PEAK 29(11P15.5) MUTATED   177   4   0  21
  DEL PEAK 29(11P15.5) WILD-TYPE 181   1   1  29
D59V6, multiclass
     clus
vv    DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE
  M0                           177                            181
  M1                             4                              1
  M1A                            0                              1
  MX                            21                             29
[1] 4 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 29(11P15.5) MUTATED    48 157
  DEL PEAK 29(11P15.5) WILD-TYPE  59 156
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(11P15.5) MUTATED     48  157
  DEL PEAK 29(11P15.5) WILD-TYPE   59  156
        clus
vv       DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE
  FEMALE                           48                             59
  MALE                            157                            156
[1] 2 2
[1] FALSE
D59V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 29(11P15.5) MUTATED                                       5
  DEL PEAK 29(11P15.5) WILD-TYPE                                     7
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 29(11P15.5) MUTATED                                        3
  DEL PEAK 29(11P15.5) WILD-TYPE                                      3
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 29(11P15.5) MUTATED                                         1
  DEL PEAK 29(11P15.5) WILD-TYPE                                       0
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 29(11P15.5) MUTATED                                                           196
  DEL PEAK 29(11P15.5) WILD-TYPE                                                         205
D59V9, multiclass
                                                             clus
vv                                                            DEL PEAK 29(11P15.5) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          196
                                                             clus
vv                                                            DEL PEAK 29(11P15.5) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            205
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V10, binary
                                cls
clus                               0   1
  DEL PEAK 29(11P15.5) MUTATED     8 197
  DEL PEAK 29(11P15.5) WILD-TYPE   5 210
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(11P15.5) MUTATED      8  197
  DEL PEAK 29(11P15.5) WILD-TYPE    5  210
     clus
vv    DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE
  NO                             8                              5
  YES                          197                            210
[1] 2 2
[1] FALSE
D59V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 29(11P15.5) MUTATED   168   5   2   7
  DEL PEAK 29(11P15.5) WILD-TYPE 174   3   2  11
D59V12, multiclass
    clus
vv   DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE
  R0                          168                            174
  R1                            5                              3
  R2                            2                              2
  RX                            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                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 29(11P15.5) MUTATED       2                         9   144
  DEL PEAK 29(11P15.5) WILD-TYPE     7                         8   154
D59V13, multiclass
                           clus
vv                          DEL PEAK 29(11P15.5) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            9
  WHITE                                              144
                           clus
vv                          DEL PEAK 29(11P15.5) WILD-TYPE
  ASIAN                                                  7
  BLACK OR AFRICAN AMERICAN                              8
  WHITE                                                154
[1] 3 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 29(11P15.5) MUTATED     2 126
  DEL PEAK 29(11P15.5) WILD-TYPE   6 141
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(11P15.5) MUTATED      2  126
  DEL PEAK 29(11P15.5) WILD-TYPE    6  141
                        clus
vv                       DEL PEAK 29(11P15.5) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          126
                        clus
vv                       DEL PEAK 29(11P15.5) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            141
[1] 2 2
[1] FALSE

Clustering(60) Variable = DEL PEAK 30(11Q22.1) MUTATION ANALYSIS
D60V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 30(11Q22.1) MUTATED    90  39
  DEL PEAK 30(11Q22.1) WILD-TYPE 175  84
  DEL PEAK 30(11Q22.1) MUTATED DEL PEAK 30(11Q22.1) WILD-TYPE 
                           129                            259 
  DEL PEAK 30(11Q22.1) MUTATED DEL PEAK 30(11Q22.1) WILD-TYPE 
                            39                             84 
$`DEL PEAK 30(11Q22.1) MUTATED`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3412 TCGA-18-3416 TCGA-18-3417 TCGA-18-3421 
         370         2417          345          862          758         1331 
TCGA-18-5595 TCGA-21-1076 TCGA-21-1080 TCGA-21-5787 TCGA-22-0940 TCGA-22-1002 
         827         1852         3724          329          608          131 
TCGA-22-1011 TCGA-22-1012 TCGA-22-4593 TCGA-22-4601 TCGA-22-4613 TCGA-22-5473 
          53          429         1067         1057          358         1933 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5481 TCGA-33-4589 TCGA-34-2596 TCGA-34-2600 
        1346           24         1952         1948           80         1874 
TCGA-34-2605 TCGA-34-5232 TCGA-34-5239 TCGA-34-5928 TCGA-34-8454 TCGA-37-4130 
         881         2062          707          552          166          247 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5027 TCGA-39-5031 
        2253         1361         1947         1996         1849          833 
TCGA-39-5037 TCGA-43-2581 TCGA-43-3920 TCGA-43-6771 TCGA-43-7657 TCGA-43-8116 
        1086         1176         1007         1936          236          358 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 
        1971          353          366          324          423           12 
TCGA-52-7809 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7580 TCGA-56-7582 
        1948           30           13           30           40           26 
TCGA-56-7822 TCGA-56-8503 TCGA-56-8504 TCGA-56-8624 TCGA-56-8629 TCGA-56-A4BW 
           1           41          178           36           34            2 
TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZK TCGA-58-8390 TCGA-58-8391 TCGA-60-2695 
          46           30            4          911         2167          642 
TCGA-60-2698 TCGA-60-2708 TCGA-60-2712 TCGA-60-2722 TCGA-60-2723 TCGA-60-2725 
         311         1963          274          908         1092          816 
TCGA-60-2726 TCGA-63-7023 TCGA-66-2727 TCGA-66-2758 TCGA-66-2766 TCGA-66-2767 
         358         1952         1967          639           31           61 
TCGA-66-2768 TCGA-66-2781 TCGA-66-2790 TCGA-66-2794 TCGA-68-8250 TCGA-68-8251 
          61          121          699         1645          244           96 
TCGA-68-A59J TCGA-77-7139 TCGA-77-7338 TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 
         104         1968         1952          479         1945         1641 
TCGA-77-8128 TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8148 
        1953         1945         1941         1947         1946          293 
TCGA-77-8150 TCGA-77-8153 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-85-6798 TCGA-85-7696 
        1961         1684         1959         1955           34           18 
TCGA-85-7699 TCGA-85-8048 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 
           1           26          428          513           13           11 
TCGA-85-8352 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8664 TCGA-85-A4QQ 
          67           61           61           22            3         1960 
TCGA-85-A50M TCGA-85-A511 TCGA-85-A5B5 TCGA-90-7766 TCGA-90-7767 TCGA-90-A4EE 
          19         1972          111          289           89          331 
TCGA-90-A59Q TCGA-92-7341 TCGA-92-8064 TCGA-96-7545 TCGA-96-8169 TCGA-96-A4JL 
         269          106          160         1344          189          183 
TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HG 
          83         1722         1548 

$`DEL PEAK 30(11Q22.1) WILD-TYPE`
TCGA-18-3407 TCGA-18-3408 TCGA-18-3410 TCGA-18-3411 TCGA-18-3414 TCGA-18-3415 
         136         2464          146         1415          396         1810 
TCGA-18-3419 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 
          50          187           85         2754           92         3636 
TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 
        1426         3016         2134         1058          474          965 
TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 
         284         3644          267          962         1268         1032 
TCGA-21-A5DI TCGA-22-0944 TCGA-22-1000 TCGA-22-1005 TCGA-22-1016 TCGA-22-1017 
         979          223         1945         1952          822         1485 
TCGA-22-4591 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4604 
         623         1470          734           17         1161          399 
TCGA-22-4605 TCGA-22-4607 TCGA-22-5471 TCGA-22-5472 TCGA-22-5474 TCGA-22-5479 
        1946          587          965         1964          445         1651 
TCGA-22-5480 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 
        1952          357          573          916         1912         1713 
TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 
         506           29         2524         1940         2979         1311 
TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-6738 
        5287         1966         1941          428         1970          822 
TCGA-34-2604 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5234 TCGA-34-5240 
         958         1000          951         1528         1715          365 
TCGA-34-5241 TCGA-34-5927 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 
         428          941          120           13           12          200 
TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 
         227          238          207           12          103         1454 
TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5034 TCGA-39-5035 
        1964           52          740           59         1107          474 
TCGA-39-5036 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-3394 
        1084          544         1964         1223          684          822 
TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-7656 
         349          849          376          757          310          212 
TCGA-43-7658 TCGA-43-8115 TCGA-43-A475 TCGA-43-A56U TCGA-51-4080 TCGA-51-4081 
        1970          407          296          432           12          911 
TCGA-52-7622 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 
         541          923         1958         1967          881            3 
TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7579 TCGA-56-7730 TCGA-56-7731 
         555           62           26           44            6         1961 
TCGA-56-8622 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-A49D TCGA-56-A4ZJ 
          55           63           17           16           38           25 
TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8388 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L 
           4            8          378         1058         2589         1723 
TCGA-58-A46M TCGA-58-A46N TCGA-60-2696 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 
        1072          910          109         1950         1943         1958 
TCGA-60-2707 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2713 TCGA-60-2714 
         661         1505         1963         1260         1731         1531 
TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2724 
        1075         1475         1297           97          983          717 
TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-66-2734 TCGA-66-2737 
        1973         1957         1955         1947         1311           61 
TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 
         641           30           31           61           28           30 
TCGA-66-2757 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2769 TCGA-66-2770 
          30          762           30           61         1947          700 
TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2782 
         578         1946           61          578         1956         1954 
TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 
         759           60          790         1217          699         1955 
TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 
        1977          913         1952          122         1492           83 
TCGA-68-7756 TCGA-68-7757 TCGA-68-A59I TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 
         202          211          121         1950         1941         1942 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 
        1952         1959           15         1286         1954         1942 
TCGA-77-7463 TCGA-77-8007 TCGA-77-8131 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 
        1954         1960         1941         1951         1962          833 
TCGA-77-8145 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G7 
        1943         1092           10         1953         1942         1963 
TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 
        1290         1280         1939          839          713          364 
TCGA-85-6561 TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 
         395           10           49         1965           35          911 
TCGA-85-7950 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8287 TCGA-85-8288 
          60           60           16          960           13           54 
TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 
          60           55           54           21          445          424 
TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A510 
         475           15         1972           25         1973         1967 
TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 TCGA-90-7769 TCGA-90-7964 
        1987           24           13          758          358          428 
TCGA-90-A4ED TCGA-92-7340 TCGA-92-8063 TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 
         244           82          122           70           87          356 
TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8170 TCGA-96-A4JK TCGA-98-7454 TCGA-98-8021 
         430         1213          211          273          256          413 
TCGA-98-8022 TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 
         224          308          222           35          449           36 
TCGA-NC-A5HI 
        1135 

  DEL PEAK 30(11Q22.1) MUTATED DEL PEAK 30(11Q22.1) WILD-TYPE 
                             1                              3 
  DEL PEAK 30(11Q22.1) MUTATED DEL PEAK 30(11Q22.1) WILD-TYPE 
                          3724                           5287 
  DEL PEAK 30(11Q22.1) MUTATED DEL PEAK 30(11Q22.1) WILD-TYPE 
                           428                            734 
[1] "1.0 - 3724.0 (428.0)" "3.0 - 5287.0 (734.0)"
[1] "hr=" "1.1"
D60V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 30(11Q22.1) MUTATED         0       19       42        0        21
  DEL PEAK 30(11Q22.1) WILD-TYPE       1       53       95        1        31
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 30(11Q22.1) MUTATED          25         19          5        2
  DEL PEAK 30(11Q22.1) WILD-TYPE        46         38         15        4
D60V3, multiclass
            clus
vv           DEL PEAK 30(11Q22.1) MUTATED DEL PEAK 30(11Q22.1) WILD-TYPE
  STAGE I                               0                              1
  STAGE IA                             19                             53
  STAGE IB                             42                             95
  STAGE II                              0                              1
  STAGE IIA                            21                             31
  STAGE IIB                            25                             46
  STAGE IIIA                           19                             38
  STAGE IIIB                            5                             15
  STAGE IV                              2                              4
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 30(11Q22.1) MUTATED    28  90  13   5
  DEL PEAK 30(11Q22.1) WILD-TYPE  70 164  35  15
D60V4, multiclass
    clus
vv   DEL PEAK 30(11Q22.1) MUTATED DEL PEAK 30(11Q22.1) WILD-TYPE
  T1                           28                             70
  T2                           90                            164
  T3                           13                             35
  T4                            5                             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 30(11Q22.1) MUTATED    76  48  10   1
  DEL PEAK 30(11Q22.1) WILD-TYPE 185  65  25   4
D60V5, multiclass
    clus
vv   DEL PEAK 30(11Q22.1) MUTATED DEL PEAK 30(11Q22.1) WILD-TYPE
  N0                           76                            185
  N1                           48                             65
  N2                           10                             25
  N3                            1                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A  MX
  DEL PEAK 30(11Q22.1) MUTATED   113   2   0  18
  DEL PEAK 30(11Q22.1) WILD-TYPE 245   3   1  32
D60V6, multiclass
     clus
vv    DEL PEAK 30(11Q22.1) MUTATED DEL PEAK 30(11Q22.1) WILD-TYPE
  M0                           113                            245
  M1                             2                              3
  M1A                            0                              1
  MX                            18                             32
[1] 4 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 30(11Q22.1) MUTATED    31 105
  DEL PEAK 30(11Q22.1) WILD-TYPE  76 208
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(11Q22.1) MUTATED     31  105
  DEL PEAK 30(11Q22.1) WILD-TYPE   76  208
        clus
vv       DEL PEAK 30(11Q22.1) MUTATED DEL PEAK 30(11Q22.1) WILD-TYPE
  FEMALE                           31                             76
  MALE                            105                            208
[1] 2 2
[1] FALSE
D60V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 30(11Q22.1) MUTATED                                       5
  DEL PEAK 30(11Q22.1) WILD-TYPE                                     7
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 30(11Q22.1) MUTATED                                        1
  DEL PEAK 30(11Q22.1) WILD-TYPE                                      5
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 30(11Q22.1) MUTATED                                         0
  DEL PEAK 30(11Q22.1) WILD-TYPE                                       1
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 30(11Q22.1) MUTATED                                                           130
  DEL PEAK 30(11Q22.1) WILD-TYPE                                                         271
D60V9, multiclass
                                                             clus
vv                                                            DEL PEAK 30(11Q22.1) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          130
                                                             clus
vv                                                            DEL PEAK 30(11Q22.1) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            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"
D60V10, binary
                                cls
clus                               0   1
  DEL PEAK 30(11Q22.1) MUTATED     4 132
  DEL PEAK 30(11Q22.1) WILD-TYPE   9 275
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(11Q22.1) MUTATED      4  132
  DEL PEAK 30(11Q22.1) WILD-TYPE    9  275
     clus
vv    DEL PEAK 30(11Q22.1) MUTATED DEL PEAK 30(11Q22.1) WILD-TYPE
  NO                             4                              9
  YES                          132                            275
[1] 2 2
[1] FALSE
D60V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 30(11Q22.1) MUTATED   113   2   1   4
  DEL PEAK 30(11Q22.1) WILD-TYPE 229   6   3  14
D60V12, multiclass
    clus
vv   DEL PEAK 30(11Q22.1) MUTATED DEL PEAK 30(11Q22.1) WILD-TYPE
  R0                          113                            229
  R1                            2                              6
  R2                            1                              3
  RX                            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                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 30(11Q22.1) MUTATED       2                         7    98
  DEL PEAK 30(11Q22.1) WILD-TYPE     7                        10   200
D60V13, multiclass
                           clus
vv                          DEL PEAK 30(11Q22.1) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            7
  WHITE                                               98
                           clus
vv                          DEL PEAK 30(11Q22.1) WILD-TYPE
  ASIAN                                                  7
  BLACK OR AFRICAN AMERICAN                             10
  WHITE                                                200
[1] 3 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 30(11Q22.1) MUTATED     2  90
  DEL PEAK 30(11Q22.1) WILD-TYPE   6 177
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(11Q22.1) MUTATED      2   90
  DEL PEAK 30(11Q22.1) WILD-TYPE    6  177
                        clus
vv                       DEL PEAK 30(11Q22.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           90
                        clus
vv                       DEL PEAK 30(11Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            177
[1] 2 2
[1] FALSE

Clustering(61) Variable = DEL PEAK 31(11Q25) MUTATION ANALYSIS
D61V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 31(11Q25) MUTATED   103  43
  DEL PEAK 31(11Q25) WILD-TYPE 162  80
  DEL PEAK 31(11Q25) MUTATED DEL PEAK 31(11Q25) WILD-TYPE 
                         146                          242 
  DEL PEAK 31(11Q25) MUTATED DEL PEAK 31(11Q25) WILD-TYPE 
                          43                           80 
$`DEL PEAK 31(11Q25) MUTATED`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3409 TCGA-18-3412 TCGA-18-3414 TCGA-18-3416 
         370         2464         2417          345          396          862 
TCGA-18-3417 TCGA-18-3421 TCGA-18-5595 TCGA-21-1076 TCGA-21-1080 TCGA-21-1082 
         758         1331          827         1852         3724         3644 
TCGA-21-5787 TCGA-22-0940 TCGA-22-1002 TCGA-22-1011 TCGA-22-1016 TCGA-22-4593 
         329          608          131           53          822         1067 
TCGA-22-4601 TCGA-22-4613 TCGA-22-5473 TCGA-22-5477 TCGA-22-5478 TCGA-22-5481 
        1057          358         1933         1346           24         1952 
TCGA-22-5489 TCGA-33-4532 TCGA-33-4533 TCGA-33-4587 TCGA-33-4589 TCGA-34-2596 
        1912         2524         1940         1970         1948           80 
TCGA-34-2600 TCGA-34-2605 TCGA-34-5232 TCGA-34-5239 TCGA-34-5928 TCGA-37-3789 
        1874          881         2062          707          552           13 
TCGA-37-4135 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5027 
         207         2253         1361         1947         1996         1849 
TCGA-39-5031 TCGA-39-5037 TCGA-43-2581 TCGA-43-3920 TCGA-43-6647 TCGA-43-6770 
         833         1086         1176         1007          757          310 
TCGA-43-6771 TCGA-43-7657 TCGA-43-7658 TCGA-43-8116 TCGA-43-A474 TCGA-43-A56V 
        1936          236         1970          358          353          366 
TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-52-7809 TCGA-56-7221 TCGA-56-7222 
         324          423           12         1948           30           13 
TCGA-56-7223 TCGA-56-7580 TCGA-56-7582 TCGA-56-7822 TCGA-56-8504 TCGA-56-8624 
          30           40           26            1          178           36 
TCGA-56-8625 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZK 
          63           34            2           46           30            4 
TCGA-58-8390 TCGA-58-A46J TCGA-60-2695 TCGA-60-2698 TCGA-60-2708 TCGA-60-2712 
         911         2589          642          311         1963          274 
TCGA-60-2715 TCGA-60-2722 TCGA-60-2725 TCGA-60-2726 TCGA-63-7023 TCGA-66-2727 
        1075          908          816          358         1952         1967 
TCGA-66-2753 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2765 
          31           30           30          639          762           61 
TCGA-66-2767 TCGA-66-2768 TCGA-66-2773 TCGA-66-2790 TCGA-66-2792 TCGA-66-2794 
          61           61         1946          699          913         1645 
TCGA-66-2800 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59J TCGA-77-7139 TCGA-77-7142 
        1492          244           96          104         1968         1286 
TCGA-77-7338 TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 
        1952          479         1945         1641         1953         1945 
TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8148 TCGA-77-8150 
        1941         1941         1947         1946          293         1961 
TCGA-77-8153 TCGA-77-A5G3 TCGA-85-6798 TCGA-85-7696 TCGA-85-7698 TCGA-85-7699 
        1684         1959           34           18           49            1 
TCGA-85-8048 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 
          26          428          513           13           11           13 
TCGA-85-8352 TCGA-85-8354 TCGA-85-8355 TCGA-85-8481 TCGA-85-8664 TCGA-85-A50M 
          67           61           61           21            3           19 
TCGA-85-A50Z TCGA-85-A511 TCGA-85-A5B5 TCGA-90-7766 TCGA-90-7767 TCGA-90-A4EE 
        1973         1972          111          289           89          331 
TCGA-90-A59Q TCGA-92-7341 TCGA-92-8063 TCGA-96-7545 TCGA-98-8023 TCGA-MF-A522 
         269          106          122         1344          308           83 
TCGA-NC-A5HE TCGA-NC-A5HG 
        1722         1548 

$`DEL PEAK 31(11Q25) WILD-TYPE`
TCGA-18-3407 TCGA-18-3410 TCGA-18-3411 TCGA-18-3415 TCGA-18-3419 TCGA-18-4083 
         136          146         1415         1810           50          187 
TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 
          85         2754           92         3636         1426         3016 
TCGA-21-1075 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1081 TCGA-21-1083 
        2134         1058          474          965          284          267 
TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-21-A5DI TCGA-22-0944 TCGA-22-1000 
         962         1268         1032          979          223         1945 
TCGA-22-1005 TCGA-22-1012 TCGA-22-1017 TCGA-22-4591 TCGA-22-4594 TCGA-22-4595 
        1952          429         1485          623         1470          734 
TCGA-22-4596 TCGA-22-4599 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-5471 
          17         1161          399         1946          587          965 
TCGA-22-5472 TCGA-22-5474 TCGA-22-5479 TCGA-22-5480 TCGA-22-5482 TCGA-22-5483 
        1964          445         1651         1952          357          573 
TCGA-22-5485 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4538 TCGA-33-4547 
         916         1713          506           29         2979         1311 
TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-6738 TCGA-34-2604 
        5287         1966         1941          428          822          958 
TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5234 TCGA-34-5240 TCGA-34-5241 
        1000          951         1528         1715          365          428 
TCGA-34-5927 TCGA-34-8454 TCGA-37-3783 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 
         941          166          120           12          200          247 
TCGA-37-4132 TCGA-37-4133 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 TCGA-39-5024 
         227          238           12          103         1454         1964 
TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 
          52          740           59         1107          474         1084 
TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-3394 TCGA-43-5668 
         544         1964         1223          684          822          349 
TCGA-43-5670 TCGA-43-6143 TCGA-43-7656 TCGA-43-8115 TCGA-43-8118 TCGA-43-A475 
         849          376          212          407         1971          296 
TCGA-43-A56U TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7810 TCGA-52-7811 
         432           12          911          541          923         1958 
TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 
        1967          881            3          555           62           26 
TCGA-56-7579 TCGA-56-7730 TCGA-56-7731 TCGA-56-8503 TCGA-56-8622 TCGA-56-8626 
          44            6         1961           41           55           17 
TCGA-56-8628 TCGA-56-A49D TCGA-56-A4ZJ TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8388 
          16           38           25            4            8          378 
TCGA-58-8391 TCGA-58-8393 TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2696 
        2167         1058         1723         1072          910          109 
TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2709 TCGA-60-2710 
        1950         1943         1958          661         1505         1963 
TCGA-60-2711 TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 
        1260         1731         1531         1475         1297           97 
TCGA-60-2721 TCGA-60-2723 TCGA-60-2724 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 
         983         1092          717         1973         1957         1955 
TCGA-63-7022 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2754 
        1947         1311           61          641           30           61 
TCGA-66-2755 TCGA-66-2763 TCGA-66-2766 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 
          28           30           31         1947          700          578 
TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 
          61          578         1956          121         1954          759 
TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2791 
          60          790         1217          699         1955         1977 
TCGA-66-2793 TCGA-66-2795 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-A59I 
        1952          122           83          202          211          121 
TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7141 
        1950         1941         1942         1952         1959           15 
TCGA-77-7335 TCGA-77-7337 TCGA-77-7463 TCGA-77-8007 TCGA-77-8139 TCGA-77-8140 
        1954         1942         1954         1960         1951         1962 
TCGA-77-8144 TCGA-77-8145 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 
         833         1943         1092           10         1953         1942 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF 
        1955         1963         1290         1280         1939          839 
TCGA-77-A5GH TCGA-85-6560 TCGA-85-6561 TCGA-85-7697 TCGA-85-7710 TCGA-85-7843 
         713          364          395           10         1965           35 
TCGA-85-7844 TCGA-85-7950 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8288 
         911           60           60           16          960           54 
TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 TCGA-85-8479 TCGA-85-8580 TCGA-85-8582 
          60           55           54           22          445          424 
TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A510 
         475           15         1972         1960           25         1967 
TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 TCGA-90-7769 TCGA-90-7964 
        1987           24           13          758          358          428 
TCGA-90-A4ED TCGA-92-7340 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 
         244           82          160           70           87          356 
TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL 
         430         1213          189          211          273          183 
TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 
         256          413          224          222           35          449 
TCGA-LA-A446 TCGA-NC-A5HI 
          36         1135 

  DEL PEAK 31(11Q25) MUTATED DEL PEAK 31(11Q25) WILD-TYPE 
                           1                            3 
  DEL PEAK 31(11Q25) MUTATED DEL PEAK 31(11Q25) WILD-TYPE 
                        3724                         5287 
  DEL PEAK 31(11Q25) MUTATED DEL PEAK 31(11Q25) WILD-TYPE 
                       580.0                        691.5 
[1] "1.0 - 3724.0 (580.0)" "3.0 - 5287.0 (691.5)"
[1] "hr=" "1.1"
D61V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 31(11Q25) MUTATED         0       21       50        0        20
  DEL PEAK 31(11Q25) WILD-TYPE       1       51       87        1        32
                              vv
clus                           STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 31(11Q25) MUTATED          30         21          8        2
  DEL PEAK 31(11Q25) WILD-TYPE        41         36         12        4
D61V3, multiclass
            clus
vv           DEL PEAK 31(11Q25) MUTATED DEL PEAK 31(11Q25) WILD-TYPE
  STAGE I                             0                            1
  STAGE IA                           21                           51
  STAGE IB                           50                           87
  STAGE II                            0                            1
  STAGE IIA                          20                           32
  STAGE IIB                          30                           41
  STAGE IIIA                         21                           36
  STAGE IIIB                          8                           12
  STAGE IV                            2                            4
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            T1  T2  T3  T4
  DEL PEAK 31(11Q25) MUTATED    30 102  15   8
  DEL PEAK 31(11Q25) WILD-TYPE  68 152  33  12
D61V4, multiclass
    clus
vv   DEL PEAK 31(11Q25) MUTATED DEL PEAK 31(11Q25) WILD-TYPE
  T1                         30                           68
  T2                        102                          152
  T3                         15                           33
  T4                          8                           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 31(11Q25) MUTATED    89  54  10   1
  DEL PEAK 31(11Q25) WILD-TYPE 172  59  25   4
D61V5, multiclass
    clus
vv   DEL PEAK 31(11Q25) MUTATED DEL PEAK 31(11Q25) WILD-TYPE
  N0                         89                          172
  N1                         54                           59
  N2                         10                           25
  N3                          1                            4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            M0  M1 M1A  MX
  DEL PEAK 31(11Q25) MUTATED   127   2   0  22
  DEL PEAK 31(11Q25) WILD-TYPE 231   3   1  28
D61V6, multiclass
     clus
vv    DEL PEAK 31(11Q25) MUTATED DEL PEAK 31(11Q25) WILD-TYPE
  M0                         127                          231
  M1                           2                            3
  M1A                          0                            1
  MX                          22                           28
[1] 4 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 31(11Q25) MUTATED    33 122
  DEL PEAK 31(11Q25) WILD-TYPE  74 191
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 31(11Q25) MUTATED     33  122
  DEL PEAK 31(11Q25) WILD-TYPE   74  191
        clus
vv       DEL PEAK 31(11Q25) MUTATED DEL PEAK 31(11Q25) WILD-TYPE
  FEMALE                         33                           74
  MALE                          122                          191
[1] 2 2
[1] FALSE
D61V8, continuous
                              vv
clus                           LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 31(11Q25) MUTATED                                       5
  DEL PEAK 31(11Q25) WILD-TYPE                                     7
                              vv
clus                           LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 31(11Q25) MUTATED                                        1
  DEL PEAK 31(11Q25) WILD-TYPE                                      5
                              vv
clus                           LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 31(11Q25) MUTATED                                         1
  DEL PEAK 31(11Q25) WILD-TYPE                                       0
                              vv
clus                           LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 31(11Q25) MUTATED                                                           148
  DEL PEAK 31(11Q25) WILD-TYPE                                                         253
D61V9, multiclass
                                                             clus
vv                                                            DEL PEAK 31(11Q25) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                               1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                              1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                        148
                                                             clus
vv                                                            DEL PEAK 31(11Q25) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          253
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V10, binary
                              cls
clus                             0   1
  DEL PEAK 31(11Q25) MUTATED     5 150
  DEL PEAK 31(11Q25) WILD-TYPE   8 257
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 31(11Q25) MUTATED      5  150
  DEL PEAK 31(11Q25) WILD-TYPE    8  257
     clus
vv    DEL PEAK 31(11Q25) MUTATED DEL PEAK 31(11Q25) WILD-TYPE
  NO                           5                            8
  YES                        150                          257
[1] 2 2
[1] FALSE
D61V11, continuous
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 31(11Q25) MUTATED   126   2   1   9
  DEL PEAK 31(11Q25) WILD-TYPE 216   6   3   9
D61V12, multiclass
    clus
vv   DEL PEAK 31(11Q25) MUTATED DEL PEAK 31(11Q25) WILD-TYPE
  R0                        126                          216
  R1                          2                            6
  R2                          1                            3
  RX                          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                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 31(11Q25) MUTATED       3                         9   109
  DEL PEAK 31(11Q25) WILD-TYPE     6                         8   189
D61V13, multiclass
                           clus
vv                          DEL PEAK 31(11Q25) MUTATED
  ASIAN                                              3
  BLACK OR AFRICAN AMERICAN                          9
  WHITE                                            109
                           clus
vv                          DEL PEAK 31(11Q25) WILD-TYPE
  ASIAN                                                6
  BLACK OR AFRICAN AMERICAN                            8
  WHITE                                              189
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V14, binary
                              cls
clus                             0   1
  DEL PEAK 31(11Q25) MUTATED     2  99
  DEL PEAK 31(11Q25) WILD-TYPE   6 168
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 31(11Q25) MUTATED      2   99
  DEL PEAK 31(11Q25) WILD-TYPE    6  168
                        clus
vv                       DEL PEAK 31(11Q25) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                         99
                        clus
vv                       DEL PEAK 31(11Q25) WILD-TYPE
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          168
[1] 2 2
[1] FALSE

Clustering(62) Variable = DEL PEAK 32(12Q24.31) MUTATION ANALYSIS
D62V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 32(12Q24.31) MUTATED    52  18
  DEL PEAK 32(12Q24.31) WILD-TYPE 213 105
  DEL PEAK 32(12Q24.31) MUTATED DEL PEAK 32(12Q24.31) WILD-TYPE 
                             70                             318 
  DEL PEAK 32(12Q24.31) MUTATED DEL PEAK 32(12Q24.31) WILD-TYPE 
                             18                             105 
$`DEL PEAK 32(12Q24.31) MUTATED`
TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3415 TCGA-18-4083 TCGA-18-4086 
         136         2464         2417         1810          187           85 
TCGA-21-1072 TCGA-21-1082 TCGA-22-4595 TCGA-22-5473 TCGA-22-5478 TCGA-22-5479 
        3016         3644          734         1933           24         1651 
TCGA-22-5485 TCGA-33-4533 TCGA-34-5232 TCGA-37-4129 TCGA-37-4141 TCGA-43-2581 
         916         1940         2062          200           12         1176 
TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-A56V TCGA-46-6026 TCGA-52-7809 
         349          849          376          366          423         1948 
TCGA-56-5898 TCGA-56-7222 TCGA-56-7223 TCGA-56-7822 TCGA-56-8624 TCGA-56-A49D 
         555           13           30            1           36           38 
TCGA-60-2698 TCGA-60-2703 TCGA-60-2722 TCGA-60-2723 TCGA-60-2725 TCGA-66-2763 
         311         1950          908         1092          816           30 
TCGA-66-2766 TCGA-66-2773 TCGA-66-2781 TCGA-68-7757 TCGA-68-8250 TCGA-77-7138 
          31         1946          121          211          244         1959 
TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8130 TCGA-77-8131 TCGA-77-8138 
        1960         1945         1641         1945         1941         1946 
TCGA-77-8139 TCGA-77-8144 TCGA-77-8148 TCGA-77-8153 TCGA-77-A5GA TCGA-77-A5GB 
        1951          833          293         1684         1280         1939 
TCGA-77-A5GH TCGA-85-6560 TCGA-85-7696 TCGA-85-7710 TCGA-85-8350 TCGA-85-8353 
         713          364           18         1965           60           54 
TCGA-85-8354 TCGA-85-A50M TCGA-85-A50Z TCGA-85-A513 TCGA-90-A4ED TCGA-94-7033 
          61           19         1973           24          244           87 
TCGA-94-A4VJ TCGA-98-8021 TCGA-LA-A446 TCGA-MF-A522 
         430          413           36           83 

$`DEL PEAK 32(12Q24.31) WILD-TYPE`
TCGA-18-3406 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3416 
         370          146         1415          345          396          862 
TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 
         758           50         1331         2754           92          827 
TCGA-21-1070 TCGA-21-1071 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 
        3636         1426         2134         1852         1058          474 
TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 
         965         3724          284          267          962         1268 
TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 
        1032          329          979          608          223         1945 
TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 
         131         1952           53          429          822         1485 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 
         623         1067         1470           17         1161         1057 
TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 
         399         1946          587          358          965         1964 
TCGA-22-5474 TCGA-22-5477 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 
         445         1346         1952         1952          357          573 
TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4538 
        1912         1713          506           29         2524         2979 
TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 
        1311         5287         1966         1941          428         1970 
TCGA-33-4589 TCGA-33-6738 TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 
        1948          822           80         1874          958          881 
TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 
        1000          951         1528         1715          707          365 
TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 
         428          941          552          166          120           13 
TCGA-37-3792 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-5819 
          12          247          227          238          207          103 
TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 
        1454         2253         1361         1947         1996         1964 
TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 
        1849           52          740           59          833         1107 
TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 
         474         1084         1086          544         1964         1223 
TCGA-43-2578 TCGA-43-3394 TCGA-43-3920 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 
         684          822         1007          757          310         1936 
TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 
         212          236         1970          407          358         1971 
TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-46-6025 TCGA-51-4079 TCGA-51-4080 
         353          296          432          324           12           12 
TCGA-51-4081 TCGA-52-7622 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 
         911          541          923         1958         1967          881 
TCGA-56-5897 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7579 TCGA-56-7580 
           3           62           26           30           44           40 
TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 
          26            6         1961           41          178           55 
TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BX 
          63           17           16           34            2           46 
TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8388 
          30           25            4            4            8          378 
TCGA-58-8390 TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M 
         911         2167         1058         2589         1723         1072 
TCGA-58-A46N TCGA-60-2695 TCGA-60-2696 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 
         910          642          109         1943         1958          661 
TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 
        1963         1505         1963         1260          274         1731 
TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 
        1531         1075         1475         1297           97          983 
TCGA-60-2724 TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 
         717          358         1973         1957         1955         1947 
TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 
        1952         1967         1311           61          641           30 
TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 
          31           61           28           30           30          639 
TCGA-66-2759 TCGA-66-2765 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 
         762           61           61           61         1947          700 
TCGA-66-2771 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2782 TCGA-66-2783 
         578           61          578         1956         1954          759 
TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 
          60          790         1217          699         1955          699 
TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 
        1977          913         1952         1645          122         1492 
TCGA-68-7755 TCGA-68-7756 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 
          83          202           96          121          104         1950 
TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 
        1941         1942         1952         1968           15         1286 
TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8128 
        1954         1942         1952         1954          479         1953 
TCGA-77-8133 TCGA-77-8136 TCGA-77-8140 TCGA-77-8145 TCGA-77-8150 TCGA-77-8154 
        1941         1947         1962         1943         1961         1092 
TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 
          10         1953         1942         1959         1955         1963 
TCGA-77-A5G8 TCGA-77-A5GF TCGA-85-6561 TCGA-85-6798 TCGA-85-7697 TCGA-85-7698 
        1290          839          395           34           10           49 
TCGA-85-7699 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 
           1           35          911           60           26           60 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 
          16          960          428          513           13           11 
TCGA-85-8287 TCGA-85-8288 TCGA-85-8351 TCGA-85-8352 TCGA-85-8355 TCGA-85-8479 
          13           54           55           67           61           22 
TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL 
          21          445          424            3          475           15 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 
        1972         1960           25         1967         1972         1987 
TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 
          13          111          758          289           89          358 
TCGA-90-7964 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 
         428          331          269           82          106          122 
TCGA-92-8064 TCGA-92-8065 TCGA-94-7943 TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 
         160           70          356         1213         1344          189 
TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-8022 TCGA-98-8023 
         211          273          183          256          224          308 
TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HI 
         222           35          449         1722         1548         1135 

  DEL PEAK 32(12Q24.31) MUTATED DEL PEAK 32(12Q24.31) WILD-TYPE 
                              1                               1 
  DEL PEAK 32(12Q24.31) MUTATED DEL PEAK 32(12Q24.31) WILD-TYPE 
                           3644                            5287 
  DEL PEAK 32(12Q24.31) MUTATED DEL PEAK 32(12Q24.31) WILD-TYPE 
                          492.5                           651.5 
[1] "1.0 - 3644.0 (492.5)" "1.0 - 5287.0 (651.5)"
[1] "hr=" "1.3"
D62V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 32(12Q24.31) MUTATED         0       11       32        0         6
  DEL PEAK 32(12Q24.31) WILD-TYPE       1       61      105        1        46
                                 vv
clus                              STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 32(12Q24.31) MUTATED          12          8          0        0
  DEL PEAK 32(12Q24.31) WILD-TYPE        59         49         20        6
D62V3, multiclass
            clus
vv           DEL PEAK 32(12Q24.31) MUTATED DEL PEAK 32(12Q24.31) WILD-TYPE
  STAGE I                                0                               1
  STAGE IA                              11                              61
  STAGE IB                              32                             105
  STAGE II                               0                               1
  STAGE IIA                              6                              46
  STAGE IIB                             12                              59
  STAGE IIIA                             8                              49
  STAGE IIIB                             0                              20
  STAGE IV                               0                               6
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  DEL PEAK 32(12Q24.31) MUTATED    17  46   8   0
  DEL PEAK 32(12Q24.31) WILD-TYPE  81 208  40  20
D62V4, multiclass
    clus
vv   DEL PEAK 32(12Q24.31) MUTATED DEL PEAK 32(12Q24.31) WILD-TYPE
  T1                            17                              81
  T2                            46                             208
  T3                             8                              40
  T4                             0                              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2  N3
  DEL PEAK 32(12Q24.31) MUTATED    47  17   4   0
  DEL PEAK 32(12Q24.31) WILD-TYPE 214  96  31   5
D62V5, multiclass
    clus
vv   DEL PEAK 32(12Q24.31) MUTATED DEL PEAK 32(12Q24.31) WILD-TYPE
  N0                            47                             214
  N1                            17                              96
  N2                             4                              31
  N3                             0                               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               M0  M1 M1A  MX
  DEL PEAK 32(12Q24.31) MUTATED    60   0   0   9
  DEL PEAK 32(12Q24.31) WILD-TYPE 298   5   1  41
D62V6, multiclass
     clus
vv    DEL PEAK 32(12Q24.31) MUTATED DEL PEAK 32(12Q24.31) WILD-TYPE
  M0                             60                             298
  M1                              0                               5
  M1A                             0                               1
  MX                              9                              41
[1] 4 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 32(12Q24.31) MUTATED    14  57
  DEL PEAK 32(12Q24.31) WILD-TYPE  93 256
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(12Q24.31) MUTATED     14   57
  DEL PEAK 32(12Q24.31) WILD-TYPE   93  256
        clus
vv       DEL PEAK 32(12Q24.31) MUTATED DEL PEAK 32(12Q24.31) WILD-TYPE
  FEMALE                            14                              93
  MALE                              57                             256
[1] 2 2
[1] FALSE
D62V8, continuous
                                 vv
clus                              LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 32(12Q24.31) MUTATED                                       3
  DEL PEAK 32(12Q24.31) WILD-TYPE                                     9
                                 vv
clus                              LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 32(12Q24.31) MUTATED                                        0
  DEL PEAK 32(12Q24.31) WILD-TYPE                                      6
                                 vv
clus                              LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 32(12Q24.31) MUTATED                                         0
  DEL PEAK 32(12Q24.31) WILD-TYPE                                       1
                                 vv
clus                              LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 32(12Q24.31) MUTATED                                                            68
  DEL PEAK 32(12Q24.31) WILD-TYPE                                                         333
D62V9, multiclass
                                                             clus
vv                                                            DEL PEAK 32(12Q24.31) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            68
                                                             clus
vv                                                            DEL PEAK 32(12Q24.31) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                     9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                    6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             333
[1] 4 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 32(12Q24.31) MUTATED     2  69
  DEL PEAK 32(12Q24.31) WILD-TYPE  11 338
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(12Q24.31) MUTATED      2   69
  DEL PEAK 32(12Q24.31) WILD-TYPE   11  338
     clus
vv    DEL PEAK 32(12Q24.31) MUTATED DEL PEAK 32(12Q24.31) WILD-TYPE
  NO                              2                              11
  YES                            69                             338
[1] 2 2
[1] FALSE
D62V11, continuous
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 32(12Q24.31) MUTATED    57   0   1   2
  DEL PEAK 32(12Q24.31) WILD-TYPE 285   8   3  16
D62V12, multiclass
    clus
vv   DEL PEAK 32(12Q24.31) MUTATED DEL PEAK 32(12Q24.31) WILD-TYPE
  R0                            57                             285
  R1                             0                               8
  R2                             1                               3
  RX                             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                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 32(12Q24.31) MUTATED       3                         5    40
  DEL PEAK 32(12Q24.31) WILD-TYPE     6                        12   258
D62V13, multiclass
                           clus
vv                          DEL PEAK 32(12Q24.31) MUTATED
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                             5
  WHITE                                                40
                           clus
vv                          DEL PEAK 32(12Q24.31) WILD-TYPE
  ASIAN                                                   6
  BLACK OR AFRICAN AMERICAN                              12
  WHITE                                                 258
[1] 3 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 32(12Q24.31) MUTATED     0  42
  DEL PEAK 32(12Q24.31) WILD-TYPE   8 225
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(12Q24.31) MUTATED      0   42
  DEL PEAK 32(12Q24.31) WILD-TYPE    8  225
                        clus
vv                       DEL PEAK 32(12Q24.31) MUTATED
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                            42
                        clus
vv                       DEL PEAK 32(12Q24.31) WILD-TYPE
  HISPANIC OR LATINO                                   8
  NOT HISPANIC OR LATINO                             225
[1] 2 2
[1] FALSE

Clustering(63) Variable = DEL PEAK 33(13Q12.11) MUTATION ANALYSIS
D63V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 33(13Q12.11) MUTATED   177  81
  DEL PEAK 33(13Q12.11) WILD-TYPE  88  42
  DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE 
                            258                             130 
  DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE 
                             81                              42 
$`DEL PEAK 33(13Q12.11) MUTATED`
TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 TCGA-18-3416 
        2417          146         1415          345         1810          862 
TCGA-18-3419 TCGA-18-4083 TCGA-18-4721 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 
          50          187         2754         3636         1426         3016 
TCGA-21-1075 TCGA-21-1076 TCGA-21-1080 TCGA-21-1082 TCGA-21-5786 TCGA-21-5787 
        2134         1852         3724         3644         1032          329 
TCGA-21-A5DI TCGA-22-0940 TCGA-22-1000 TCGA-22-1002 TCGA-22-1011 TCGA-22-1016 
         979          608         1945          131           53          822 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4601 
         623         1067         1470          734           17         1057 
TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 
         399         1946          587          358          965         1964 
TCGA-22-5473 TCGA-22-5477 TCGA-22-5478 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 
        1933         1346           24         1952         1952          357 
TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 
         916         1912         1713          506           29         2524 
TCGA-33-4538 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-33-6738 
        2979         1941          428         1970         1948          822 
TCGA-34-2596 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 
          80          958          881         1000         1528         2062 
TCGA-34-5928 TCGA-34-8454 TCGA-37-3792 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 
         552          166           12          247          227          238 
TCGA-37-4135 TCGA-37-5819 TCGA-39-5016 TCGA-39-5022 TCGA-39-5028 TCGA-39-5029 
         207          103         2253         1996           52          740 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5036 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 
          59          833         1084         1223          684         1176 
TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 
         822         1007          349          376          757          310 
TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-A474 TCGA-43-A56U TCGA-46-6025 
        1970          407          358          353          432          324 
TCGA-51-4079 TCGA-52-7622 TCGA-52-7809 TCGA-52-7811 TCGA-56-1622 TCGA-56-5898 
          12          541         1948         1958          881          555 
TCGA-56-6545 TCGA-56-6546 TCGA-56-7222 TCGA-56-7579 TCGA-56-7582 TCGA-56-7730 
          62           26           13           44           26            6 
TCGA-56-7822 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 
           1           36           63           17           16           34 
TCGA-56-A49D TCGA-56-A4BY TCGA-56-A4ZK TCGA-58-8388 TCGA-58-8391 TCGA-58-8393 
          38           30            4          378         2167         1058 
TCGA-58-A46M TCGA-60-2696 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 
        1072          109         1950         1943         1958          661 
TCGA-60-2708 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2714 TCGA-60-2719 
        1963         1963         1260          274         1531         1297 
TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 
          97          983          908         1092          717          816 
TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-66-2727 
         358         1973         1957         1955         1947         1967 
TCGA-66-2734 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2758 
        1311           31           61           28           30          639 
TCGA-66-2759 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2771 
         762           31           61           61         1947          578 
TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2782 TCGA-66-2783 
        1946           61          578         1956         1954          759 
TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2790 TCGA-66-2791 
          60          790         1217          699          699         1977 
TCGA-66-2792 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 
         913          122         1492           83          202          211 
TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-77-6842 TCGA-77-6844 TCGA-77-6845 
         244           96          121         1950         1942         1952 
TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7337 TCGA-77-7338 
        1959         1968           15         1286         1942         1952 
TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 
        1954          479         1960         1641         1953         1945 
TCGA-77-8131 TCGA-77-8133 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 
        1941         1941         1946         1951         1962          833 
TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5G1 
         293         1961         1684         1092           10         1942 
TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GF 
        1959         1955         1963         1290         1280          839 
TCGA-85-6560 TCGA-85-6561 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7843 
         364          395           10           49            1           35 
TCGA-85-7844 TCGA-85-7950 TCGA-85-8049 TCGA-85-8070 TCGA-85-8072 TCGA-85-8277 
         911           60           60          960          513           11 
TCGA-85-8287 TCGA-85-8288 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 
          13           54           55           67           54           61 
TCGA-85-8479 TCGA-85-8580 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4QQ TCGA-85-A4QR 
          22          445            3          475         1960           25 
TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A512 TCGA-85-A53L TCGA-85-A5B5 
          19         1973         1967         1987           13          111 
TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4EE TCGA-90-A59Q 
         289           89          358          428          331          269 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-94-7033 TCGA-96-7544 
          82          106          122          160           87         1213 
TCGA-96-7545 TCGA-96-8169 TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 
        1344          189          256          413          224          308 
TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HI 
         222           35          449         1722         1548         1135 

$`DEL PEAK 33(13Q12.11) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3414 TCGA-18-3417 TCGA-18-3421 
         370          136         2464          396          758         1331 
TCGA-18-4086 TCGA-18-5592 TCGA-18-5595 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 
          85           92          827         1058          474          965 
TCGA-21-1081 TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 TCGA-22-0944 TCGA-22-1005 
         284          267          962         1268          223         1952 
TCGA-22-1012 TCGA-22-1017 TCGA-22-4599 TCGA-22-5474 TCGA-22-5479 TCGA-22-5483 
         429         1485         1161          445         1651          573 
TCGA-33-4533 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-34-2600 TCGA-34-2609 
        1940         1311         5287         1966         1874          951 
TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-37-3783 
        1715          707          365          428          941          120 
TCGA-37-3789 TCGA-37-4129 TCGA-37-4141 TCGA-39-5011 TCGA-39-5019 TCGA-39-5021 
          13          200           12         1454         1361         1947 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5034 TCGA-39-5035 TCGA-39-5037 TCGA-39-5039 
        1964         1849         1107          474         1086          544 
TCGA-39-5040 TCGA-43-5670 TCGA-43-6771 TCGA-43-7656 TCGA-43-7657 TCGA-43-8118 
        1964          849         1936          212          236         1971 
TCGA-43-A475 TCGA-43-A56V TCGA-46-6026 TCGA-51-4080 TCGA-51-4081 TCGA-52-7810 
         296          366          423           12          911          923 
TCGA-52-7812 TCGA-56-5897 TCGA-56-7221 TCGA-56-7223 TCGA-56-7580 TCGA-56-7731 
        1967            3           30           30           40         1961 
TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZJ 
          41          178           55            2           46           25 
TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8390 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46N 
           4            8          911         2589         1723          910 
TCGA-60-2695 TCGA-60-2698 TCGA-60-2709 TCGA-60-2713 TCGA-60-2715 TCGA-60-2716 
         642          311         1505         1731         1075         1475 
TCGA-63-7023 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2757 TCGA-66-2763 
        1952           61          641           30           30           30 
TCGA-66-2765 TCGA-66-2770 TCGA-66-2781 TCGA-66-2789 TCGA-66-2793 TCGA-66-2794 
          61          700          121         1955         1952         1645 
TCGA-68-A59J TCGA-77-6843 TCGA-77-7335 TCGA-77-8008 TCGA-77-8136 TCGA-77-8145 
         104         1941         1954         1945         1947         1943 
TCGA-77-A5FZ TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6798 TCGA-85-7696 TCGA-85-7710 
        1953         1939          713           34           18         1965 
TCGA-85-8048 TCGA-85-8052 TCGA-85-8071 TCGA-85-8276 TCGA-85-8350 TCGA-85-8355 
          26           16          428           13           60           61 
TCGA-85-8481 TCGA-85-8582 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A511 TCGA-85-A513 
          21          424           15         1972         1972           24 
TCGA-90-6837 TCGA-90-A4ED TCGA-92-8065 TCGA-94-7943 TCGA-94-A4VJ TCGA-96-8170 
         758          244           70          356          430          211 
TCGA-96-A4JK TCGA-96-A4JL TCGA-LA-A446 TCGA-MF-A522 
         273          183           36           83 

  DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE 
                              1                               2 
  DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE 
                           3724                            5287 
  DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE 
                            699                             509 
[1] "1.0 - 3724.0 (699.0)" "2.0 - 5287.0 (509.0)"
[1] "hr=" "1.2"
D63V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 33(13Q12.11) MUTATED         1       40       92        0        34
  DEL PEAK 33(13Q12.11) WILD-TYPE       0       32       45        1        18
                                 vv
clus                              STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 33(13Q12.11) MUTATED          46         46         11        3
  DEL PEAK 33(13Q12.11) WILD-TYPE        25         11          9        3
D63V3, multiclass
            clus
vv           DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE
  STAGE I                                1                               0
  STAGE IA                              40                              32
  STAGE IB                              92                              45
  STAGE II                               0                               1
  STAGE IIA                             34                              18
  STAGE IIB                             46                              25
  STAGE IIIA                            46                              11
  STAGE IIIB                            11                               9
  STAGE IV                               3                               3
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  DEL PEAK 33(13Q12.11) MUTATED    57 176  30  12
  DEL PEAK 33(13Q12.11) WILD-TYPE  41  78  18   8
D63V4, multiclass
    clus
vv   DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE
  T1                            57                              41
  T2                           176                              78
  T3                            30                              18
  T4                            12                               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2  N3
  DEL PEAK 33(13Q12.11) MUTATED   166  76  26   4
  DEL PEAK 33(13Q12.11) WILD-TYPE  95  37   9   1
D63V5, multiclass
    clus
vv   DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE
  N0                           166                              95
  N1                            76                              37
  N2                            26                               9
  N3                             4                               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               M0  M1 M1A  MX
  DEL PEAK 33(13Q12.11) MUTATED   238   2   1  31
  DEL PEAK 33(13Q12.11) WILD-TYPE 120   3   0  19
D63V6, multiclass
     clus
vv    DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE
  M0                            238                             120
  M1                              2                               3
  M1A                             1                               0
  MX                             31                              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"
D63V7, binary
                                 cls
clus                                0   1
  DEL PEAK 33(13Q12.11) MUTATED    70 205
  DEL PEAK 33(13Q12.11) WILD-TYPE  37 108
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(13Q12.11) MUTATED     70  205
  DEL PEAK 33(13Q12.11) WILD-TYPE   37  108
        clus
vv       DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE
  FEMALE                            70                              37
  MALE                             205                             108
[1] 2 2
[1] FALSE
D63V8, continuous
                                 vv
clus                              LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 33(13Q12.11) MUTATED                                       7
  DEL PEAK 33(13Q12.11) WILD-TYPE                                     5
                                 vv
clus                              LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 33(13Q12.11) MUTATED                                        2
  DEL PEAK 33(13Q12.11) WILD-TYPE                                      4
                                 vv
clus                              LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 33(13Q12.11) MUTATED                                         1
  DEL PEAK 33(13Q12.11) WILD-TYPE                                       0
                                 vv
clus                              LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 33(13Q12.11) MUTATED                                                           265
  DEL PEAK 33(13Q12.11) WILD-TYPE                                                         136
D63V9, multiclass
                                                             clus
vv                                                            DEL PEAK 33(13Q12.11) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           265
                                                             clus
vv                                                            DEL PEAK 33(13Q12.11) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                     5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                    4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             136
[1] 4 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 33(13Q12.11) MUTATED    10 265
  DEL PEAK 33(13Q12.11) WILD-TYPE   3 142
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(13Q12.11) MUTATED     10  265
  DEL PEAK 33(13Q12.11) WILD-TYPE    3  142
     clus
vv    DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE
  NO                             10                               3
  YES                           265                             142
[1] 2 2
[1] FALSE
D63V11, continuous
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 33(13Q12.11) MUTATED   227   6   3  12
  DEL PEAK 33(13Q12.11) WILD-TYPE 115   2   1   6
D63V12, multiclass
    clus
vv   DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE
  R0                           227                             115
  R1                             6                               2
  R2                             3                               1
  RX                            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                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 33(13Q12.11) MUTATED       4                        12   187
  DEL PEAK 33(13Q12.11) WILD-TYPE     5                         5   111
D63V13, multiclass
                           clus
vv                          DEL PEAK 33(13Q12.11) MUTATED
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                            12
  WHITE                                               187
                           clus
vv                          DEL PEAK 33(13Q12.11) WILD-TYPE
  ASIAN                                                   5
  BLACK OR AFRICAN AMERICAN                               5
  WHITE                                                 111
[1] 3 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 33(13Q12.11) MUTATED     7 162
  DEL PEAK 33(13Q12.11) WILD-TYPE   1 105
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(13Q12.11) MUTATED      7  162
  DEL PEAK 33(13Q12.11) WILD-TYPE    1  105
                        clus
vv                       DEL PEAK 33(13Q12.11) MUTATED
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           162
                        clus
vv                       DEL PEAK 33(13Q12.11) WILD-TYPE
  HISPANIC OR LATINO                                   1
  NOT HISPANIC OR LATINO                             105
[1] 2 2
[1] FALSE

Clustering(64) Variable = DEL PEAK 34(13Q14.2) MUTATION ANALYSIS
D64V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 34(13Q14.2) MUTATED   177  89
  DEL PEAK 34(13Q14.2) WILD-TYPE  88  34
  DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE 
                           266                            122 
  DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE 
                            89                             34 
$`DEL PEAK 34(13Q14.2) MUTATED`
TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 
        2417          146          862           50         1331          187 
TCGA-18-4086 TCGA-18-4721 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 
          85         2754         3636         1426         3016         2134 
TCGA-21-1076 TCGA-21-1080 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5786 
        1852         3724         3644          267          962         1032 
TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 TCGA-22-1000 TCGA-22-1002 TCGA-22-1011 
         329          979          608         1945          131           53 
TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 
         822         1485          623         1067         1470          734 
TCGA-22-4596 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 
          17         1057          399         1946          587          358 
TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5477 TCGA-22-5478 TCGA-22-5481 
         965         1964         1933         1346           24         1952 
TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 
         357          573          916         1912         1713          506 
TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4538 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 
          29         1940         2979         1966         1941          428 
TCGA-33-4587 TCGA-33-4589 TCGA-33-6738 TCGA-34-2596 TCGA-34-2604 TCGA-34-2605 
        1970         1948          822           80          958          881 
TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5927 TCGA-34-5928 
        1000          951         1528         2062          941          552 
TCGA-34-8454 TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 TCGA-37-4135 TCGA-37-5819 
         166           12          200          227          207          103 
TCGA-39-5011 TCGA-39-5022 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 
        1454         1996           52          740           59          833 
TCGA-39-5036 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-3920 
        1084         1964         1223          684         1176         1007 
TCGA-43-5668 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-7656 TCGA-43-7657 
         349          376          757          310          212          236 
TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-A474 TCGA-46-6025 TCGA-51-4079 
        1970          407          358          353          324           12 
TCGA-52-7622 TCGA-52-7809 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5898 
         541         1948         1958         1967          881          555 
TCGA-56-6545 TCGA-56-6546 TCGA-56-7222 TCGA-56-7579 TCGA-56-7582 TCGA-56-7730 
          62           26           13           44           26            6 
TCGA-56-8624 TCGA-56-8625 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BY 
          36           63           16           34           38           30 
TCGA-56-A4ZK TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J 
           4          378          911         2167         1058         2589 
TCGA-58-A46M TCGA-60-2696 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 
        1072          109         1950         1943         1958          661 
TCGA-60-2708 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 
        1963         1963         1260          274         1731         1531 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 
        1297           97          983          908         1092          717 
TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 
         816          358         1973         1957         1955         1947 
TCGA-66-2727 TCGA-66-2734 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 
        1967         1311           31           61           28           30 
TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2767 TCGA-66-2768 
          30          639          762           30           61           61 
TCGA-66-2769 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 
        1947          578         1946           61          578         1956 
TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 
         121         1954          759           60          790         1217 
TCGA-66-2788 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2795 
         699          699         1977          913         1952          122 
TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 
        1492           83          202          211          244           96 
TCGA-68-A59I TCGA-77-6842 TCGA-77-6844 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 
         121         1950         1942         1959         1968           15 
TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 
        1286         1954         1942         1952         1954          479 
TCGA-77-8007 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8138 
        1960         1953         1945         1941         1941         1946 
TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 
        1951         1962          833          293         1961         1684 
TCGA-77-8154 TCGA-77-8156 TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 
        1092           10         1942         1959         1955         1963 
TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GF TCGA-85-6561 TCGA-85-7697 TCGA-85-7698 
        1290         1280          839          395           10           49 
TCGA-85-7699 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8049 TCGA-85-8070 
           1           35          911           60           60          960 
TCGA-85-8071 TCGA-85-8072 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8351 
         428          513           11           13           54           55 
TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8479 TCGA-85-8580 TCGA-85-8664 
          67           54           61           22          445            3 
TCGA-85-8666 TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A512 
         475           25           19         1973         1967         1987 
TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 
          13          111          289           89          358          428 
TCGA-90-A4EE TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-94-7033 
         331           82          106          122          160           87 
TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-A4JK TCGA-98-7454 TCGA-98-8021 
        1213         1344          189          273          256          413 
TCGA-98-8022 TCGA-98-8023 TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-NC-A5HE 
         224          308           35          449           36         1722 
TCGA-NC-A5HG TCGA-NC-A5HI 
        1548         1135 

$`DEL PEAK 34(13Q14.2) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
         370          136         2464         1415          345          396 
TCGA-18-3415 TCGA-18-3417 TCGA-18-5592 TCGA-18-5595 TCGA-21-1077 TCGA-21-1078 
        1810          758           92          827         1058          474 
TCGA-21-1079 TCGA-21-1081 TCGA-21-5784 TCGA-22-0944 TCGA-22-1005 TCGA-22-1012 
         965          284         1268          223         1952          429 
TCGA-22-4599 TCGA-22-5474 TCGA-22-5479 TCGA-22-5480 TCGA-33-4532 TCGA-33-4547 
        1161          445         1651         1952         2524         1311 
TCGA-33-4566 TCGA-34-2600 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 
        5287         1874         1715          707          365          428 
TCGA-37-3783 TCGA-37-3789 TCGA-37-4130 TCGA-37-4133 TCGA-37-4141 TCGA-39-5016 
         120           13          247          238           12         2253 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5024 TCGA-39-5027 TCGA-39-5034 TCGA-39-5035 
        1361         1947         1964         1849         1107          474 
TCGA-39-5037 TCGA-39-5039 TCGA-43-3394 TCGA-43-5670 TCGA-43-6771 TCGA-43-8118 
        1086          544          822          849         1936         1971 
TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-6026 TCGA-51-4080 TCGA-51-4081 
         296          432          366          423           12          911 
TCGA-52-7810 TCGA-56-5897 TCGA-56-7221 TCGA-56-7223 TCGA-56-7580 TCGA-56-7731 
         923            3           30           30           40         1961 
TCGA-56-7822 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8626 TCGA-56-A4BW 
           1           41          178           55           17            2 
TCGA-56-A4BX TCGA-56-A4ZJ TCGA-56-A5DR TCGA-56-A5DS TCGA-58-A46L TCGA-58-A46N 
          46           25            4            8         1723          910 
TCGA-60-2695 TCGA-60-2698 TCGA-60-2709 TCGA-60-2715 TCGA-60-2716 TCGA-63-7023 
         642          311         1505         1075         1475         1952 
TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2765 TCGA-66-2766 TCGA-66-2770 
          61          641           30           61           31          700 
TCGA-66-2789 TCGA-66-2794 TCGA-68-A59J TCGA-77-6843 TCGA-77-6845 TCGA-77-8008 
        1955         1645          104         1941         1952         1945 
TCGA-77-8009 TCGA-77-8136 TCGA-77-8145 TCGA-77-A5FZ TCGA-77-A5GB TCGA-77-A5GH 
        1641         1947         1943         1953         1939          713 
TCGA-85-6560 TCGA-85-6798 TCGA-85-7696 TCGA-85-7710 TCGA-85-8048 TCGA-85-8052 
         364           34           18         1965           26           16 
TCGA-85-8276 TCGA-85-8350 TCGA-85-8355 TCGA-85-8481 TCGA-85-8582 TCGA-85-A4CL 
          13           60           61           21          424           15 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A511 TCGA-85-A513 TCGA-90-6837 TCGA-90-A4ED 
        1972         1960         1972           24          758          244 
TCGA-90-A59Q TCGA-92-8065 TCGA-94-7943 TCGA-94-A4VJ TCGA-96-8170 TCGA-96-A4JL 
         269           70          356          430          211          183 
TCGA-J1-A4AH TCGA-MF-A522 
         222           83 

  DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE 
                             1                              1 
  DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE 
                          3724                           5287 
  DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE 
                         725.5                          438.5 
[1] "1.0 - 3724.0 (725.5)" "1.0 - 5287.0 (438.5)"
[1] "hr=" "1"  
D64V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 34(13Q14.2) MUTATED         1       48       94        1        34
  DEL PEAK 34(13Q14.2) WILD-TYPE       0       24       43        0        18
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 34(13Q14.2) MUTATED          45         44         12        3
  DEL PEAK 34(13Q14.2) WILD-TYPE        26         13          8        3
D64V3, multiclass
            clus
vv           DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE
  STAGE I                               1                              0
  STAGE IA                             48                             24
  STAGE IB                             94                             43
  STAGE II                              1                              0
  STAGE IIA                            34                             18
  STAGE IIB                            45                             26
  STAGE IIIA                           44                             13
  STAGE IIIB                           12                              8
  STAGE IV                              3                              3
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 34(13Q14.2) MUTATED    65 177  29  13
  DEL PEAK 34(13Q14.2) WILD-TYPE  33  77  19   7
D64V4, multiclass
    clus
vv   DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE
  T1                           65                             33
  T2                          177                             77
  T3                           29                             19
  T4                           13                              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 34(13Q14.2) MUTATED   174  77  26   4
  DEL PEAK 34(13Q14.2) WILD-TYPE  87  36   9   1
D64V5, multiclass
    clus
vv   DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE
  N0                          174                             87
  N1                           77                             36
  N2                           26                              9
  N3                            4                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A  MX
  DEL PEAK 34(13Q14.2) MUTATED   248   2   1  30
  DEL PEAK 34(13Q14.2) WILD-TYPE 110   3   0  20
D64V6, multiclass
     clus
vv    DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE
  M0                           248                            110
  M1                             2                              3
  M1A                            1                              0
  MX                            30                             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V7, binary
                                cls
clus                               0   1
  DEL PEAK 34(13Q14.2) MUTATED    76 208
  DEL PEAK 34(13Q14.2) WILD-TYPE  31 105
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(13Q14.2) MUTATED     76  208
  DEL PEAK 34(13Q14.2) WILD-TYPE   31  105
        clus
vv       DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE
  FEMALE                           76                             31
  MALE                            208                            105
[1] 2 2
[1] FALSE
D64V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 34(13Q14.2) MUTATED                                       6
  DEL PEAK 34(13Q14.2) WILD-TYPE                                     6
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 34(13Q14.2) MUTATED                                        2
  DEL PEAK 34(13Q14.2) WILD-TYPE                                      4
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 34(13Q14.2) MUTATED                                         1
  DEL PEAK 34(13Q14.2) WILD-TYPE                                       0
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 34(13Q14.2) MUTATED                                                           275
  DEL PEAK 34(13Q14.2) WILD-TYPE                                                         126
D64V9, multiclass
                                                             clus
vv                                                            DEL PEAK 34(13Q14.2) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          275
                                                             clus
vv                                                            DEL PEAK 34(13Q14.2) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            126
[1] 4 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 34(13Q14.2) MUTATED    11 273
  DEL PEAK 34(13Q14.2) WILD-TYPE   2 134
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(13Q14.2) MUTATED     11  273
  DEL PEAK 34(13Q14.2) WILD-TYPE    2  134
     clus
vv    DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE
  NO                            11                              2
  YES                          273                            134
[1] 2 2
[1] FALSE
D64V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 34(13Q14.2) MUTATED   233   6   3  12
  DEL PEAK 34(13Q14.2) WILD-TYPE 109   2   1   6
D64V12, multiclass
    clus
vv   DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE
  R0                          233                            109
  R1                            6                              2
  R2                            3                              1
  RX                           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                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 34(13Q14.2) MUTATED       4                        12   196
  DEL PEAK 34(13Q14.2) WILD-TYPE     5                         5   102
D64V13, multiclass
                           clus
vv                          DEL PEAK 34(13Q14.2) MUTATED
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                           12
  WHITE                                              196
                           clus
vv                          DEL PEAK 34(13Q14.2) WILD-TYPE
  ASIAN                                                  5
  BLACK OR AFRICAN AMERICAN                              5
  WHITE                                                102
[1] 3 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 34(13Q14.2) MUTATED     8 169
  DEL PEAK 34(13Q14.2) WILD-TYPE   0  98
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(13Q14.2) MUTATED      8  169
  DEL PEAK 34(13Q14.2) WILD-TYPE    0   98
                        clus
vv                       DEL PEAK 34(13Q14.2) MUTATED
  HISPANIC OR LATINO                                8
  NOT HISPANIC OR LATINO                          169
                        clus
vv                       DEL PEAK 34(13Q14.2) WILD-TYPE
  HISPANIC OR LATINO                                  0
  NOT HISPANIC OR LATINO                             98
[1] 2 2
[1] FALSE

Clustering(65) Variable = DEL PEAK 35(14Q11.2) MUTATION ANALYSIS
D65V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 35(14Q11.2) MUTATED    90  49
  DEL PEAK 35(14Q11.2) WILD-TYPE 175  74
  DEL PEAK 35(14Q11.2) MUTATED DEL PEAK 35(14Q11.2) WILD-TYPE 
                           139                            249 
  DEL PEAK 35(14Q11.2) MUTATED DEL PEAK 35(14Q11.2) WILD-TYPE 
                            49                             74 
$`DEL PEAK 35(14Q11.2) MUTATED`
TCGA-18-3416 TCGA-18-4086 TCGA-21-1071 TCGA-21-1083 TCGA-21-5784 TCGA-21-5786 
         862           85         1426          267         1268         1032 
TCGA-22-0940 TCGA-22-1012 TCGA-22-1016 TCGA-22-4593 TCGA-22-4594 TCGA-22-4596 
         608          429          822         1067         1470           17 
TCGA-22-4601 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5480 TCGA-22-5481 
        1057         1933          445         1346         1952         1952 
TCGA-22-5483 TCGA-22-5491 TCGA-33-4538 TCGA-33-4547 TCGA-33-4583 TCGA-33-4587 
         573         1713         2979         1311         1941         1970 
TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-5241 TCGA-34-5927 
          80         1874          958          881          428          941 
TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 TCGA-37-4130 TCGA-37-4133 TCGA-37-4135 
         552          166          120          247          238          207 
TCGA-37-5819 TCGA-39-5016 TCGA-39-5024 TCGA-39-5030 TCGA-39-5035 TCGA-39-5040 
         103         2253         1964           59          474         1964 
TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 TCGA-43-6770 TCGA-43-7656 TCGA-43-7657 
         822         1007          849          310          212          236 
TCGA-43-7658 TCGA-43-A475 TCGA-43-A56U TCGA-46-6026 TCGA-51-4079 TCGA-52-7809 
        1970          296          432          423           12         1948 
TCGA-56-5897 TCGA-56-7582 TCGA-56-7822 TCGA-56-A4BW TCGA-56-A4BY TCGA-58-8388 
           3           26            1            2           30          378 
TCGA-58-8390 TCGA-60-2695 TCGA-60-2696 TCGA-60-2704 TCGA-60-2709 TCGA-60-2710 
         911          642          109         1943         1505         1963 
TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 
         274         1731         1531          816          358         1973 
TCGA-63-7023 TCGA-66-2727 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 
        1952         1967           31           61           28           30 
TCGA-66-2758 TCGA-66-2766 TCGA-66-2769 TCGA-66-2773 TCGA-66-2777 TCGA-66-2786 
         639           31         1947         1946           61          790 
TCGA-66-2787 TCGA-66-2789 TCGA-66-2793 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 
        1217         1955         1952          211          244           96 
TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-7139 TCGA-77-7141 TCGA-77-7338 
        1950         1941         1942         1968           15         1952 
TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8140 TCGA-77-8156 TCGA-77-A5G6 
         479         1960         1945         1962           10         1955 
TCGA-77-A5G7 TCGA-77-A5GA TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 TCGA-85-6798 
        1963         1280          839          713          364           34 
TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 
          35          911           60           26           60           16 
TCGA-85-8070 TCGA-85-8072 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8352 
         960          513           11           13           54           67 
TCGA-85-8580 TCGA-85-A511 TCGA-85-A53L TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 
         445         1972           13          289           89          358 
TCGA-90-A4ED TCGA-90-A59Q TCGA-94-7033 TCGA-94-7943 TCGA-96-7545 TCGA-96-A4JL 
         244          269           87          356         1344          183 
TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-J1-A4AH TCGA-LA-A446 
         256          413          224          308          222           36 
TCGA-NC-A5HE 
        1722 

$`DEL PEAK 35(14Q11.2) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
         370          136         2464         2417          146         1415 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 
         345          396         1810          758           50         1331 
TCGA-18-4083 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1072 
         187         2754           92          827         3636         3016 
TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 
        2134         1852         1058          474          965         3724 
TCGA-21-1081 TCGA-21-1082 TCGA-21-5782 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0944 
         284         3644          962          329          979          223 
TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1017 TCGA-22-4591 
        1945          131         1952           53         1485          623 
TCGA-22-4595 TCGA-22-4599 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 
         734         1161          399         1946          587          358 
TCGA-22-5471 TCGA-22-5472 TCGA-22-5478 TCGA-22-5479 TCGA-22-5482 TCGA-22-5485 
         965         1964           24         1651          357          916 
TCGA-22-5489 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4566 
        1912          506           29         2524         1940         5287 
TCGA-33-4582 TCGA-33-4586 TCGA-33-4589 TCGA-33-6738 TCGA-34-2608 TCGA-34-2609 
        1966          428         1948          822         1000          951 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-37-3789 
        1528         2062         1715          707          365           13 
TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 TCGA-37-4141 TCGA-39-5011 TCGA-39-5019 
          12          200          227           12         1454         1361 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5031 
        1947         1996         1849           52          740          833 
TCGA-39-5034 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-43-2576 TCGA-43-2578 
        1107         1084         1086          544         1223          684 
TCGA-43-2581 TCGA-43-5668 TCGA-43-6143 TCGA-43-6647 TCGA-43-6771 TCGA-43-8115 
        1176          349          376          757         1936          407 
TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-46-6025 TCGA-51-4080 
         358         1971          353          366          324           12 
TCGA-51-4081 TCGA-52-7622 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 
         911          541          923         1958         1967          881 
TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 
         555           62           26           30           13           30 
TCGA-56-7579 TCGA-56-7580 TCGA-56-7730 TCGA-56-7731 TCGA-56-8503 TCGA-56-8504 
          44           40            6         1961           41          178 
TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 
          55           36           63           17           16           34 
TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS 
          38           46           25            4            4            8 
TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N 
        2167         1058         2589         1723         1072          910 
TCGA-60-2698 TCGA-60-2703 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2711 
         311         1950         1958          661         1963         1260 
TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 
        1075         1475         1297           97          983          908 
TCGA-60-2723 TCGA-60-2724 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-66-2734 
        1092          717         1957         1955         1947         1311 
TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2756 TCGA-66-2759 TCGA-66-2763 
          61          641           30           30          762           30 
TCGA-66-2765 TCGA-66-2767 TCGA-66-2768 TCGA-66-2770 TCGA-66-2771 TCGA-66-2778 
          61           61           61          700          578          578 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2788 
        1956          121         1954          759           60          699 
TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 
         699         1977          913         1645          122         1492 
TCGA-68-7755 TCGA-68-7756 TCGA-68-A59I TCGA-68-A59J TCGA-77-6845 TCGA-77-7138 
          83          202          121          104         1952         1959 
TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7463 TCGA-77-8009 TCGA-77-8128 
        1286         1954         1942         1954         1641         1953 
TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 
        1945         1941         1941         1947         1946         1951 
TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 
         833         1943          293         1961         1684         1092 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G8 TCGA-77-A5GB TCGA-85-6561 
        1953         1942         1959         1290         1939          395 
TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-8071 
          18           10           49            1         1965          428 
TCGA-85-8276 TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 
          13           60           55           54           61           61 
TCGA-85-8479 TCGA-85-8481 TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL 
          22           21          424            3          475           15 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 
        1972         1960           25           19         1973         1967 
TCGA-85-A512 TCGA-85-A513 TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7964 TCGA-90-A4EE 
        1987           24          111          758          428          331 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-A4VJ 
          82          106          122          160           70          430 
TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-L3-A4E7 TCGA-L3-A524 
        1213          189          211          273           35          449 
TCGA-MF-A522 TCGA-NC-A5HG TCGA-NC-A5HI 
          83         1548         1135 

  DEL PEAK 35(14Q11.2) MUTATED DEL PEAK 35(14Q11.2) WILD-TYPE 
                             1                              1 
  DEL PEAK 35(14Q11.2) MUTATED DEL PEAK 35(14Q11.2) WILD-TYPE 
                          2979                           5287 
  DEL PEAK 35(14Q11.2) MUTATED DEL PEAK 35(14Q11.2) WILD-TYPE 
                           479                            707 
[1] "1.0 - 2979.0 (479.0)" "1.0 - 5287.0 (707.0)"
[1] "hr=" "1.4"
D65V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 35(14Q11.2) MUTATED         0       28       50        0        23
  DEL PEAK 35(14Q11.2) WILD-TYPE       1       44       87        1        29
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 35(14Q11.2) MUTATED          19         21          7        0
  DEL PEAK 35(14Q11.2) WILD-TYPE        52         36         13        6
D65V3, multiclass
            clus
vv           DEL PEAK 35(14Q11.2) MUTATED DEL PEAK 35(14Q11.2) WILD-TYPE
  STAGE I                               0                              1
  STAGE IA                             28                             44
  STAGE IB                             50                             87
  STAGE II                              0                              1
  STAGE IIA                            23                             29
  STAGE IIB                            19                             52
  STAGE IIIA                           21                             36
  STAGE IIIB                            7                             13
  STAGE IV                              0                              6
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 35(14Q11.2) MUTATED    38  92  13   5
  DEL PEAK 35(14Q11.2) WILD-TYPE  60 162  35  15
D65V4, multiclass
    clus
vv   DEL PEAK 35(14Q11.2) MUTATED DEL PEAK 35(14Q11.2) WILD-TYPE
  T1                           38                             60
  T2                           92                            162
  T3                           13                             35
  T4                            5                             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 35(14Q11.2) MUTATED    91  43  12   1
  DEL PEAK 35(14Q11.2) WILD-TYPE 170  70  23   4
D65V5, multiclass
    clus
vv   DEL PEAK 35(14Q11.2) MUTATED DEL PEAK 35(14Q11.2) WILD-TYPE
  N0                           91                            170
  N1                           43                             70
  N2                           12                             23
  N3                            1                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A  MX
  DEL PEAK 35(14Q11.2) MUTATED   127   0   0  20
  DEL PEAK 35(14Q11.2) WILD-TYPE 231   5   1  30
D65V6, multiclass
     clus
vv    DEL PEAK 35(14Q11.2) MUTATED DEL PEAK 35(14Q11.2) WILD-TYPE
  M0                           127                            231
  M1                             0                              5
  M1A                            0                              1
  MX                            20                             30
[1] 4 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 35(14Q11.2) MUTATED    37 111
  DEL PEAK 35(14Q11.2) WILD-TYPE  70 202
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(14Q11.2) MUTATED     37  111
  DEL PEAK 35(14Q11.2) WILD-TYPE   70  202
        clus
vv       DEL PEAK 35(14Q11.2) MUTATED DEL PEAK 35(14Q11.2) WILD-TYPE
  FEMALE                           37                             70
  MALE                            111                            202
[1] 2 2
[1] FALSE
D65V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 35(14Q11.2) MUTATED                                       5
  DEL PEAK 35(14Q11.2) WILD-TYPE                                     7
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 35(14Q11.2) MUTATED                                        0
  DEL PEAK 35(14Q11.2) WILD-TYPE                                      6
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 35(14Q11.2) MUTATED                                         1
  DEL PEAK 35(14Q11.2) WILD-TYPE                                       0
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 35(14Q11.2) MUTATED                                                           142
  DEL PEAK 35(14Q11.2) WILD-TYPE                                                         259
D65V9, multiclass
                                                             clus
vv                                                            DEL PEAK 35(14Q11.2) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          142
                                                             clus
vv                                                            DEL PEAK 35(14Q11.2) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            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"
D65V10, binary
                                cls
clus                               0   1
  DEL PEAK 35(14Q11.2) MUTATED     5 143
  DEL PEAK 35(14Q11.2) WILD-TYPE   8 264
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(14Q11.2) MUTATED      5  143
  DEL PEAK 35(14Q11.2) WILD-TYPE    8  264
     clus
vv    DEL PEAK 35(14Q11.2) MUTATED DEL PEAK 35(14Q11.2) WILD-TYPE
  NO                             5                              8
  YES                          143                            264
[1] 2 2
[1] FALSE
D65V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 35(14Q11.2) MUTATED   122   3   1   6
  DEL PEAK 35(14Q11.2) WILD-TYPE 220   5   3  12
D65V12, multiclass
    clus
vv   DEL PEAK 35(14Q11.2) MUTATED DEL PEAK 35(14Q11.2) WILD-TYPE
  R0                          122                            220
  R1                            3                              5
  R2                            1                              3
  RX                            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                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 35(14Q11.2) MUTATED       4                         8   104
  DEL PEAK 35(14Q11.2) WILD-TYPE     5                         9   194
D65V13, multiclass
                           clus
vv                          DEL PEAK 35(14Q11.2) MUTATED
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                            8
  WHITE                                              104
                           clus
vv                          DEL PEAK 35(14Q11.2) WILD-TYPE
  ASIAN                                                  5
  BLACK OR AFRICAN AMERICAN                              9
  WHITE                                                194
[1] 3 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 35(14Q11.2) MUTATED     2  95
  DEL PEAK 35(14Q11.2) WILD-TYPE   6 172
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(14Q11.2) MUTATED      2   95
  DEL PEAK 35(14Q11.2) WILD-TYPE    6  172
                        clus
vv                       DEL PEAK 35(14Q11.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           95
                        clus
vv                       DEL PEAK 35(14Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            172
[1] 2 2
[1] FALSE

Clustering(66) Variable = DEL PEAK 36(15Q11.2) MUTATION ANALYSIS
D66V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 36(15Q11.2) MUTATED    77  46
  DEL PEAK 36(15Q11.2) WILD-TYPE 188  77
  DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE 
                           123                            265 
  DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE 
                            46                             77 
$`DEL PEAK 36(15Q11.2) MUTATED`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3410 TCGA-18-3412 TCGA-18-3415 TCGA-18-3416 
         370         2464          146          345         1810          862 
TCGA-18-3419 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1083 
          50           92         3636         1426         3016          267 
TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1012 TCGA-22-1016 
         329          608          223         1945          429          822 
TCGA-22-1017 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-5471 
        1485         1470          734           17         1161          965 
TCGA-22-5477 TCGA-22-5480 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4547 
        1346         1952           29         2524         1940         1311 
TCGA-33-4582 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-34-2600 TCGA-34-2604 
        1966          428         1970         1948         1874          958 
TCGA-34-8454 TCGA-37-3783 TCGA-37-4133 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 
         166          120          238           12          103         1454 
TCGA-39-5016 TCGA-39-5021 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 
        2253         1947           52          740           59          833 
TCGA-39-5034 TCGA-39-5040 TCGA-43-2578 TCGA-43-2581 TCGA-43-5668 TCGA-43-5670 
        1107         1964          684         1176          349          849 
TCGA-43-7657 TCGA-43-A56V TCGA-46-6026 TCGA-51-4079 TCGA-52-7809 TCGA-52-7810 
         236          366          423           12         1948          923 
TCGA-56-1622 TCGA-56-7580 TCGA-56-7822 TCGA-56-8625 TCGA-56-A49D TCGA-56-A4BW 
         881           40            1           63           38            2 
TCGA-58-A46J TCGA-60-2698 TCGA-60-2703 TCGA-60-2708 TCGA-60-2712 TCGA-60-2714 
        2589          311         1950         1963          274         1531 
TCGA-60-2720 TCGA-60-2723 TCGA-60-2726 TCGA-63-7022 TCGA-66-2737 TCGA-66-2742 
          97         1092          358         1947           61          641 
TCGA-66-2754 TCGA-66-2766 TCGA-66-2767 TCGA-66-2790 TCGA-66-2791 TCGA-66-2793 
          61           31           61          699         1977         1952 
TCGA-66-2794 TCGA-66-2800 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 TCGA-77-7139 
        1645         1492          121          104         1950         1968 
TCGA-77-7141 TCGA-77-7337 TCGA-77-8007 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 
          15         1942         1960         1641         1953         1945 
TCGA-77-8145 TCGA-77-8153 TCGA-77-8156 TCGA-77-A5GH TCGA-85-6560 TCGA-85-7696 
        1943         1684           10          713          364           18 
TCGA-85-7843 TCGA-85-8072 TCGA-85-8287 TCGA-85-8288 TCGA-85-8352 TCGA-85-8479 
          35          513           13           54           67           22 
TCGA-85-8666 TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L 
         475         1960           19         1972           24           13 
TCGA-90-7767 TCGA-90-A4ED TCGA-90-A4EE TCGA-92-7340 TCGA-92-8064 TCGA-92-8065 
          89          244          331           82          160           70 
TCGA-MF-A522 TCGA-NC-A5HG TCGA-NC-A5HI 
          83         1548         1135 

$`DEL PEAK 36(15Q11.2) WILD-TYPE`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3411 TCGA-18-3414 TCGA-18-3417 TCGA-18-3421 
         136         2417         1415          396          758         1331 
TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5595 TCGA-21-1075 TCGA-21-1076 
         187           85         2754          827         2134         1852 
TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 
        1058          474          965         3724          284         3644 
TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-21-A5DI TCGA-22-1002 TCGA-22-1005 
         962         1268         1032          979          131         1952 
TCGA-22-1011 TCGA-22-4591 TCGA-22-4593 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 
          53          623         1067         1057          399         1946 
TCGA-22-4607 TCGA-22-4613 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5478 
         587          358         1964         1933          445           24 
TCGA-22-5479 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 
        1651         1952          357          573          916         1912 
TCGA-22-5491 TCGA-22-5492 TCGA-33-4538 TCGA-33-4566 TCGA-33-4583 TCGA-33-6738 
        1713          506         2979         5287         1941          822 
TCGA-34-2596 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 
          80          881         1000          951         1528         2062 
TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 
        1715          707          365          428          941          552 
TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4135 
          13           12          200          247          227          207 
TCGA-39-5019 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5035 TCGA-39-5036 
        1361         1996         1964         1849          474         1084 
TCGA-39-5037 TCGA-39-5039 TCGA-43-2576 TCGA-43-3394 TCGA-43-3920 TCGA-43-6143 
        1086          544         1223          822         1007          376 
TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 TCGA-43-7658 TCGA-43-8115 
         757          310         1936          212         1970          407 
TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-46-6025 
         358         1971          353          296          432          324 
TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7811 TCGA-52-7812 TCGA-56-5897 
          12          911          541         1958         1967            3 
TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 
         555           62           26           30           13           30 
TCGA-56-7579 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-8503 TCGA-56-8504 
          44           26            6         1961           41          178 
TCGA-56-8622 TCGA-56-8624 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BX 
          55           36           17           16           34           46 
TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8388 
          30           25            4            4            8          378 
TCGA-58-8390 TCGA-58-8391 TCGA-58-8393 TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N 
         911         2167         1058         1723         1072          910 
TCGA-60-2695 TCGA-60-2696 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2709 
         642          109         1943         1958          661         1505 
TCGA-60-2710 TCGA-60-2711 TCGA-60-2713 TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 
        1963         1260         1731         1075         1475         1297 
TCGA-60-2721 TCGA-60-2722 TCGA-60-2724 TCGA-60-2725 TCGA-63-6202 TCGA-63-7020 
         983          908          717          816         1973         1957 
TCGA-63-7021 TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 TCGA-66-2744 TCGA-66-2753 
        1955         1952         1967         1311           30           31 
TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 
          28           30           30          639          762           30 
TCGA-66-2765 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 
          61           61         1947          700          578         1946 
TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 
          61          578         1956          121         1954          759 
TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2792 
          60          790         1217          699         1955          913 
TCGA-66-2795 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 
         122           83          202          211          244           96 
TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7142 TCGA-77-7335 
        1941         1942         1952         1959         1286         1954 
TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8008 TCGA-77-8131 TCGA-77-8133 
        1952         1954          479         1945         1941         1941 
TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8148 
        1947         1946         1951         1962          833          293 
TCGA-77-8150 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 
        1961         1092         1953         1942         1959         1955 
TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-85-6561 
        1963         1290         1280         1939          839          395 
TCGA-85-6798 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7844 
          34           10           49            1         1965          911 
TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 
          60           26           60           16          960          428 
TCGA-85-8276 TCGA-85-8277 TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 TCGA-85-8354 
          13           11           60           55           54           61 
TCGA-85-8355 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 TCGA-85-A4CL 
          61           21          445          424            3           15 
TCGA-85-A4PA TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A510 TCGA-85-A512 TCGA-85-A5B5 
        1972           25         1973         1967         1987          111 
TCGA-90-6837 TCGA-90-7766 TCGA-90-7769 TCGA-90-7964 TCGA-90-A59Q TCGA-92-7341 
         758          289          358          428          269          106 
TCGA-92-8063 TCGA-94-7033 TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-7545 
         122           87          356          430         1213         1344 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 
         189          211          273          183          256          413 
TCGA-98-8022 TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 
         224          308          222           35          449           36 
TCGA-NC-A5HE 
        1722 

  DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE 
                             1                              1 
  DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE 
                          3636                           5287 
  DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE 
                           641                            642 
[1] "1.0 - 3636.0 (641.0)" "1.0 - 5287.0 (642.0)"
[1] "hr=" "1.3"
D66V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 36(15Q11.2) MUTATED         0       17       37        0        15
  DEL PEAK 36(15Q11.2) WILD-TYPE       1       55      100        1        37
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 36(15Q11.2) MUTATED          28         25          7        2
  DEL PEAK 36(15Q11.2) WILD-TYPE        43         32         13        4
D66V3, multiclass
            clus
vv           DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE
  STAGE I                               0                              1
  STAGE IA                             17                             55
  STAGE IB                             37                            100
  STAGE II                              0                              1
  STAGE IIA                            15                             37
  STAGE IIB                            28                             43
  STAGE IIIA                           25                             32
  STAGE IIIB                            7                             13
  STAGE IV                              2                              4
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 36(15Q11.2) MUTATED    24  83  17   7
  DEL PEAK 36(15Q11.2) WILD-TYPE  74 171  31  13
D66V4, multiclass
    clus
vv   DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE
  T1                           24                             74
  T2                           83                            171
  T3                           17                             31
  T4                            7                             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 36(15Q11.2) MUTATED    67  43  17   2
  DEL PEAK 36(15Q11.2) WILD-TYPE 194  70  18   3
D66V5, multiclass
    clus
vv   DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE
  N0                           67                            194
  N1                           43                             70
  N2                           17                             18
  N3                            2                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A  MX
  DEL PEAK 36(15Q11.2) MUTATED   115   2   0  12
  DEL PEAK 36(15Q11.2) WILD-TYPE 243   3   1  38
D66V6, multiclass
     clus
vv    DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE
  M0                           115                            243
  M1                             2                              3
  M1A                            0                              1
  MX                            12                             38
[1] 4 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 36(15Q11.2) MUTATED    39  92
  DEL PEAK 36(15Q11.2) WILD-TYPE  68 221
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(15Q11.2) MUTATED     39   92
  DEL PEAK 36(15Q11.2) WILD-TYPE   68  221
        clus
vv       DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE
  FEMALE                           39                             68
  MALE                             92                            221
[1] 2 2
[1] FALSE
D66V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 36(15Q11.2) MUTATED                                       3
  DEL PEAK 36(15Q11.2) WILD-TYPE                                     9
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 36(15Q11.2) MUTATED                                        2
  DEL PEAK 36(15Q11.2) WILD-TYPE                                      4
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 36(15Q11.2) MUTATED                                         1
  DEL PEAK 36(15Q11.2) WILD-TYPE                                       0
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 36(15Q11.2) MUTATED                                                           125
  DEL PEAK 36(15Q11.2) WILD-TYPE                                                         276
D66V9, multiclass
                                                             clus
vv                                                            DEL PEAK 36(15Q11.2) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          125
                                                             clus
vv                                                            DEL PEAK 36(15Q11.2) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            276
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V10, binary
                                cls
clus                               0   1
  DEL PEAK 36(15Q11.2) MUTATED     6 125
  DEL PEAK 36(15Q11.2) WILD-TYPE   7 282
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(15Q11.2) MUTATED      6  125
  DEL PEAK 36(15Q11.2) WILD-TYPE    7  282
     clus
vv    DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE
  NO                             6                              7
  YES                          125                            282
[1] 2 2
[1] FALSE
D66V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 36(15Q11.2) MUTATED   107   4   2   5
  DEL PEAK 36(15Q11.2) WILD-TYPE 235   4   2  13
D66V12, multiclass
    clus
vv   DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE
  R0                          107                            235
  R1                            4                              4
  R2                            2                              2
  RX                            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                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 36(15Q11.2) MUTATED       5                         7    91
  DEL PEAK 36(15Q11.2) WILD-TYPE     4                        10   207
D66V13, multiclass
                           clus
vv                          DEL PEAK 36(15Q11.2) MUTATED
  ASIAN                                                5
  BLACK OR AFRICAN AMERICAN                            7
  WHITE                                               91
                           clus
vv                          DEL PEAK 36(15Q11.2) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                             10
  WHITE                                                207
[1] 3 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 36(15Q11.2) MUTATED     2  84
  DEL PEAK 36(15Q11.2) WILD-TYPE   6 183
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(15Q11.2) MUTATED      2   84
  DEL PEAK 36(15Q11.2) WILD-TYPE    6  183
                        clus
vv                       DEL PEAK 36(15Q11.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           84
                        clus
vv                       DEL PEAK 36(15Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            183
[1] 2 2
[1] FALSE

Clustering(67) Variable = DEL PEAK 37(15Q21.1) MUTATION ANALYSIS
D67V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 37(15Q21.1) MUTATED    80  45
  DEL PEAK 37(15Q21.1) WILD-TYPE 185  78
  DEL PEAK 37(15Q21.1) MUTATED DEL PEAK 37(15Q21.1) WILD-TYPE 
                           125                            263 
  DEL PEAK 37(15Q21.1) MUTATED DEL PEAK 37(15Q21.1) WILD-TYPE 
                            45                             78 
$`DEL PEAK 37(15Q21.1) MUTATED`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3412 TCGA-18-3416 TCGA-18-3419 TCGA-18-5592 
         370         2464          345          862           50           92 
TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1080 TCGA-21-5786 TCGA-21-5787 
        3636         1426         3016         3724         1032          329 
TCGA-22-0944 TCGA-22-1000 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 
         223         1945          429          822         1485          623 
TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-5471 TCGA-22-5477 
        1470          734           17         1161          965         1346 
TCGA-22-5480 TCGA-33-4533 TCGA-33-4582 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 
        1952         1940         1966          428         1970         1948 
TCGA-34-2600 TCGA-34-2604 TCGA-34-8454 TCGA-37-3783 TCGA-37-4133 TCGA-37-4141 
        1874          958          166          120          238           12 
TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5021 TCGA-39-5028 TCGA-39-5029 
         103         1454         2253         1947           52          740 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5040 TCGA-43-2578 TCGA-43-2581 
          59          833         1107         1964          684         1176 
TCGA-43-5668 TCGA-43-5670 TCGA-43-7657 TCGA-43-8116 TCGA-43-A56V TCGA-46-6025 
         349          849          236          358          366          324 
TCGA-46-6026 TCGA-51-4079 TCGA-52-7810 TCGA-52-7812 TCGA-56-7580 TCGA-56-7822 
         423           12          923         1967           40            1 
TCGA-56-8625 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-60-2698 TCGA-60-2703 
          63           34           38            2          311         1950 
TCGA-60-2708 TCGA-60-2712 TCGA-60-2714 TCGA-60-2720 TCGA-60-2723 TCGA-60-2726 
        1963          274         1531           97         1092          358 
TCGA-63-7022 TCGA-66-2737 TCGA-66-2742 TCGA-66-2754 TCGA-66-2756 TCGA-66-2766 
        1947           61          641           61           30           31 
TCGA-66-2767 TCGA-66-2790 TCGA-66-2791 TCGA-66-2793 TCGA-66-2794 TCGA-66-2800 
          61          699         1977         1952         1645         1492 
TCGA-68-8250 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 TCGA-77-6845 TCGA-77-7139 
         244          121          104         1950         1952         1968 
TCGA-77-7141 TCGA-77-7337 TCGA-77-8007 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 
          15         1942         1960         1641         1953         1945 
TCGA-77-8145 TCGA-77-8153 TCGA-77-8156 TCGA-77-A5G6 TCGA-77-A5GH TCGA-85-6560 
        1943         1684           10         1955          713          364 
TCGA-85-7696 TCGA-85-7843 TCGA-85-8072 TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 
          18           35          513           13           13           54 
TCGA-85-8479 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A511 
          22          475           15         1960           19         1972 
TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7767 TCGA-90-A4ED TCGA-90-A4EE TCGA-92-8064 
          13          111           89          244          331          160 
TCGA-92-8065 TCGA-96-A4JK TCGA-MF-A522 TCGA-NC-A5HG TCGA-NC-A5HI 
          70          273           83         1548         1135 

$`DEL PEAK 37(15Q21.1) WILD-TYPE`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3414 TCGA-18-3415 
         136         2417          146         1415          396         1810 
TCGA-18-3417 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5595 
         758         1331          187           85         2754          827 
TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1081 
        2134         1852         1058          474          965          284 
TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 TCGA-21-A5DI TCGA-22-0940 
        3644          267          962         1268          979          608 
TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-4593 TCGA-22-4601 TCGA-22-4604 
         131         1952           53         1067         1057          399 
TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 
        1946          587          358         1964         1933          445 
TCGA-22-5478 TCGA-22-5479 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 
          24         1651         1952          357          573          916 
TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4538 
        1912         1713          506           29         2524         2979 
TCGA-33-4547 TCGA-33-4566 TCGA-33-4583 TCGA-33-6738 TCGA-34-2596 TCGA-34-2605 
        1311         5287         1941          822           80          881 
TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 
        1000          951         1528         2062         1715          707 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-37-3789 TCGA-37-3792 
         365          428          941          552           13           12 
TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4135 TCGA-39-5019 TCGA-39-5022 
         200          247          227          207         1361         1996 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 
        1964         1849          474         1084         1086          544 
TCGA-43-2576 TCGA-43-3394 TCGA-43-3920 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 
        1223          822         1007          376          757          310 
TCGA-43-6771 TCGA-43-7656 TCGA-43-7658 TCGA-43-8115 TCGA-43-8118 TCGA-43-A474 
        1936          212         1970          407         1971          353 
TCGA-43-A475 TCGA-43-A56U TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 
         296          432           12          911          541         1948 
TCGA-52-7811 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 
        1958          881            3          555           62           26 
TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7582 TCGA-56-7730 
          30           13           30           44           26            6 
TCGA-56-7731 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 TCGA-56-8626 
        1961           41          178           55           36           17 
TCGA-56-8628 TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR 
          16           46           30           25            4            4 
TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J 
           8          378          911         2167         1058         2589 
TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2696 TCGA-60-2704 
        1723         1072          910          642          109         1943 
TCGA-60-2706 TCGA-60-2707 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2713 
        1958          661         1505         1963         1260         1731 
TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2721 TCGA-60-2722 TCGA-60-2724 
        1075         1475         1297          983          908          717 
TCGA-60-2725 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7023 TCGA-66-2727 
         816         1973         1957         1955         1952         1967 
TCGA-66-2734 TCGA-66-2744 TCGA-66-2753 TCGA-66-2755 TCGA-66-2757 TCGA-66-2758 
        1311           30           31           28           30          639 
TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 
         762           30           61           61         1947          700 
TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 
         578         1946           61          578         1956          121 
TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 
        1954          759           60          790         1217          699 
TCGA-66-2789 TCGA-66-2792 TCGA-66-2795 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 
        1955          913          122           83          202          211 
TCGA-68-8251 TCGA-77-6843 TCGA-77-6844 TCGA-77-7138 TCGA-77-7142 TCGA-77-7335 
          96         1941         1942         1959         1286         1954 
TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8008 TCGA-77-8131 TCGA-77-8133 
        1952         1954          479         1945         1941         1941 
TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8148 
        1947         1946         1951         1962          833          293 
TCGA-77-8150 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G7 
        1961         1092         1953         1942         1959         1963 
TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-85-6561 TCGA-85-6798 
        1290         1280         1939          839          395           34 
TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 
          10           49            1         1965          911           60 
TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8277 
          26           60           16          960          428           11 
TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 
          60           55           67           54           61           61 
TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 TCGA-85-A4PA TCGA-85-A4QR 
          21          445          424            3         1972           25 
TCGA-85-A50Z TCGA-85-A510 TCGA-85-A512 TCGA-85-A513 TCGA-90-6837 TCGA-90-7766 
        1973         1967         1987           24          758          289 
TCGA-90-7769 TCGA-90-7964 TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 
         358          428          269           82          106          122 
TCGA-94-7033 TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 
          87          356          430         1213         1344          189 
TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 
         211          183          256          413          224          308 
TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-NC-A5HE 
         222           35          449           36         1722 

  DEL PEAK 37(15Q21.1) MUTATED DEL PEAK 37(15Q21.1) WILD-TYPE 
                             1                              1 
  DEL PEAK 37(15Q21.1) MUTATED DEL PEAK 37(15Q21.1) WILD-TYPE 
                          3724                           5287 
  DEL PEAK 37(15Q21.1) MUTATED DEL PEAK 37(15Q21.1) WILD-TYPE 
                           513                            699 
[1] "1.0 - 3724.0 (513.0)" "1.0 - 5287.0 (699.0)"
[1] "hr=" "1.2"
D67V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 37(15Q21.1) MUTATED         0       19       34        0        16
  DEL PEAK 37(15Q21.1) WILD-TYPE       1       53      103        1        36
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 37(15Q21.1) MUTATED          29         25          8        2
  DEL PEAK 37(15Q21.1) WILD-TYPE        42         32         12        4
D67V3, multiclass
            clus
vv           DEL PEAK 37(15Q21.1) MUTATED DEL PEAK 37(15Q21.1) WILD-TYPE
  STAGE I                               0                              1
  STAGE IA                             19                             53
  STAGE IB                             34                            103
  STAGE II                              0                              1
  STAGE IIA                            16                             36
  STAGE IIB                            29                             42
  STAGE IIIA                           25                             32
  STAGE IIIB                            8                             12
  STAGE IV                              2                              4
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 37(15Q21.1) MUTATED    26  81  18   8
  DEL PEAK 37(15Q21.1) WILD-TYPE  72 173  30  12
D67V4, multiclass
    clus
vv   DEL PEAK 37(15Q21.1) MUTATED DEL PEAK 37(15Q21.1) WILD-TYPE
  T1                           26                             72
  T2                           81                            173
  T3                           18                             30
  T4                            8                             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 37(15Q21.1) MUTATED    68  43  19   2
  DEL PEAK 37(15Q21.1) WILD-TYPE 193  70  16   3
D67V5, multiclass
    clus
vv   DEL PEAK 37(15Q21.1) MUTATED DEL PEAK 37(15Q21.1) WILD-TYPE
  N0                           68                            193
  N1                           43                             70
  N2                           19                             16
  N3                            2                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A  MX
  DEL PEAK 37(15Q21.1) MUTATED   116   2   0  13
  DEL PEAK 37(15Q21.1) WILD-TYPE 242   3   1  37
D67V6, multiclass
     clus
vv    DEL PEAK 37(15Q21.1) MUTATED DEL PEAK 37(15Q21.1) WILD-TYPE
  M0                           116                            242
  M1                             2                              3
  M1A                            0                              1
  MX                            13                             37
[1] 4 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 37(15Q21.1) MUTATED    37  96
  DEL PEAK 37(15Q21.1) WILD-TYPE  70 217
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(15Q21.1) MUTATED     37   96
  DEL PEAK 37(15Q21.1) WILD-TYPE   70  217
        clus
vv       DEL PEAK 37(15Q21.1) MUTATED DEL PEAK 37(15Q21.1) WILD-TYPE
  FEMALE                           37                             70
  MALE                             96                            217
[1] 2 2
[1] FALSE
D67V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 37(15Q21.1) MUTATED                                       2
  DEL PEAK 37(15Q21.1) WILD-TYPE                                    10
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 37(15Q21.1) MUTATED                                        2
  DEL PEAK 37(15Q21.1) WILD-TYPE                                      4
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 37(15Q21.1) MUTATED                                         1
  DEL PEAK 37(15Q21.1) WILD-TYPE                                       0
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 37(15Q21.1) MUTATED                                                           128
  DEL PEAK 37(15Q21.1) WILD-TYPE                                                         273
D67V9, multiclass
                                                             clus
vv                                                            DEL PEAK 37(15Q21.1) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          128
                                                             clus
vv                                                            DEL PEAK 37(15Q21.1) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   10
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            273
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V10, binary
                                cls
clus                               0   1
  DEL PEAK 37(15Q21.1) MUTATED     6 127
  DEL PEAK 37(15Q21.1) WILD-TYPE   7 280
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(15Q21.1) MUTATED      6  127
  DEL PEAK 37(15Q21.1) WILD-TYPE    7  280
     clus
vv    DEL PEAK 37(15Q21.1) MUTATED DEL PEAK 37(15Q21.1) WILD-TYPE
  NO                             6                              7
  YES                          127                            280
[1] 2 2
[1] FALSE
D67V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 37(15Q21.1) MUTATED   109   3   2   5
  DEL PEAK 37(15Q21.1) WILD-TYPE 233   5   2  13
D67V12, multiclass
    clus
vv   DEL PEAK 37(15Q21.1) MUTATED DEL PEAK 37(15Q21.1) WILD-TYPE
  R0                          109                            233
  R1                            3                              5
  R2                            2                              2
  RX                            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                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 37(15Q21.1) MUTATED       4                         8    93
  DEL PEAK 37(15Q21.1) WILD-TYPE     5                         9   205
D67V13, multiclass
                           clus
vv                          DEL PEAK 37(15Q21.1) MUTATED
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                            8
  WHITE                                               93
                           clus
vv                          DEL PEAK 37(15Q21.1) WILD-TYPE
  ASIAN                                                  5
  BLACK OR AFRICAN AMERICAN                              9
  WHITE                                                205
[1] 3 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 37(15Q21.1) MUTATED     3  84
  DEL PEAK 37(15Q21.1) WILD-TYPE   5 183
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(15Q21.1) MUTATED      3   84
  DEL PEAK 37(15Q21.1) WILD-TYPE    5  183
                        clus
vv                       DEL PEAK 37(15Q21.1) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           84
                        clus
vv                       DEL PEAK 37(15Q21.1) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            183
[1] 2 2
[1] FALSE

Clustering(68) Variable = DEL PEAK 38(16P13.3) MUTATION ANALYSIS
D68V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 38(16P13.3) MUTATED   104  37
  DEL PEAK 38(16P13.3) WILD-TYPE 161  86
  DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE 
                           141                            247 
  DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE 
                            37                             86 
$`DEL PEAK 38(16P13.3) MUTATED`
TCGA-18-3410 TCGA-18-3415 TCGA-18-3417 TCGA-18-3421 TCGA-18-4721 TCGA-18-5592 
         146         1810          758         1331         2754           92 
TCGA-21-1070 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1080 TCGA-21-1082 
        3636         2134         1852         1058         3724         3644 
TCGA-21-5786 TCGA-22-0940 TCGA-22-1002 TCGA-22-1012 TCGA-22-4594 TCGA-22-4595 
        1032          608          131          429         1470          734 
TCGA-22-4599 TCGA-22-4604 TCGA-22-4613 TCGA-22-5478 TCGA-22-5480 TCGA-22-5482 
        1161          399          358           24         1952          357 
TCGA-22-5485 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4582 TCGA-33-4587 TCGA-34-2596 
         916           29         1940         1966         1970           80 
TCGA-34-2609 TCGA-34-5239 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-37-5819 
         951          707          428          941          552          103 
TCGA-39-5011 TCGA-39-5016 TCGA-39-5021 TCGA-39-5027 TCGA-39-5028 TCGA-39-5040 
        1454         2253         1947         1849           52         1964 
TCGA-43-3394 TCGA-43-5670 TCGA-43-6143 TCGA-43-7656 TCGA-43-7657 TCGA-43-8116 
         822          849          376          212          236          358 
TCGA-43-8118 TCGA-43-A56U TCGA-51-4080 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 
        1971          432           12          541         1948          923 
TCGA-52-7812 TCGA-56-1622 TCGA-56-6545 TCGA-56-7579 TCGA-56-7580 TCGA-56-7822 
        1967          881           62           44           40            1 
TCGA-56-8503 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4BY TCGA-58-8393 
          41           34           38           46           30         1058 
TCGA-58-A46J TCGA-58-A46L TCGA-60-2695 TCGA-60-2708 TCGA-60-2719 TCGA-60-2720 
        2589         1723          642         1963         1297           97 
TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-63-7023 
        1092          717          816          358         1973         1952 
TCGA-66-2727 TCGA-66-2734 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 
        1967         1311           31           61           28           30 
TCGA-66-2758 TCGA-66-2763 TCGA-66-2766 TCGA-66-2773 TCGA-66-2781 TCGA-66-2782 
         639           30           31         1946          121         1954 
TCGA-66-2786 TCGA-66-2787 TCGA-66-2792 TCGA-66-2800 TCGA-68-7756 TCGA-68-8251 
         790         1217          913         1492          202           96 
TCGA-68-A59J TCGA-77-6842 TCGA-77-6845 TCGA-77-7139 TCGA-77-7142 TCGA-77-8130 
         104         1950         1952         1968         1286         1945 
TCGA-77-8136 TCGA-77-8140 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5G7 
        1947         1962         1684         1092           10         1963 
TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6798 TCGA-85-7698 TCGA-85-7699 TCGA-85-7843 
         839          713           34           49            1           35 
TCGA-85-7950 TCGA-85-8052 TCGA-85-8070 TCGA-85-8277 TCGA-85-8351 TCGA-85-8352 
          60           16          960           11           55           67 
TCGA-85-8353 TCGA-85-8355 TCGA-85-8479 TCGA-85-8580 TCGA-85-8664 TCGA-85-A4CL 
          54           61           22          445            3           15 
TCGA-85-A4QR TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7767 TCGA-90-A4EE TCGA-92-7340 
          25           13          111           89          331           82 
TCGA-92-8064 TCGA-96-7544 TCGA-96-8169 TCGA-96-A4JK TCGA-98-8023 TCGA-J1-A4AH 
         160         1213          189          273          308          222 
TCGA-L3-A4E7 TCGA-L3-A524 TCGA-NC-A5HG 
          35          449         1548 

$`DEL PEAK 38(16P13.3) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3411 TCGA-18-3412 
         370          136         2464         2417         1415          345 
TCGA-18-3414 TCGA-18-3416 TCGA-18-3419 TCGA-18-4083 TCGA-18-4086 TCGA-18-5595 
         396          862           50          187           85          827 
TCGA-21-1071 TCGA-21-1072 TCGA-21-1078 TCGA-21-1079 TCGA-21-1081 TCGA-21-1083 
        1426         3016          474          965          284          267 
TCGA-21-5782 TCGA-21-5784 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0944 TCGA-22-1000 
         962         1268          329          979          223         1945 
TCGA-22-1005 TCGA-22-1011 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 
        1952           53          822         1485          623         1067 
TCGA-22-4596 TCGA-22-4601 TCGA-22-4605 TCGA-22-4607 TCGA-22-5471 TCGA-22-5472 
          17         1057         1946          587          965         1964 
TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 TCGA-22-5481 TCGA-22-5483 
        1933          445         1346         1651         1952          573 
TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4532 TCGA-33-4538 TCGA-33-4547 
        1912         1713          506         2524         2979         1311 
TCGA-33-4566 TCGA-33-4583 TCGA-33-4586 TCGA-33-4589 TCGA-33-6738 TCGA-34-2600 
        5287         1941          428         1948          822         1874 
TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 
         958          881         1000         1528         2062         1715 
TCGA-34-5240 TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 
         365          166          120           13           12          200 
TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-39-5019 
         247          227          238          207           12         1361 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 
        1996         1964          740           59          833         1107 
TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-43-2576 TCGA-43-2578 
         474         1084         1086          544         1223          684 
TCGA-43-2581 TCGA-43-3920 TCGA-43-5668 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 
        1176         1007          349          757          310         1936 
TCGA-43-7658 TCGA-43-8115 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56V TCGA-46-6025 
        1970          407          353          296          366          324 
TCGA-46-6026 TCGA-51-4079 TCGA-51-4081 TCGA-52-7811 TCGA-56-5897 TCGA-56-5898 
         423           12          911         1958            3          555 
TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7582 TCGA-56-7730 
          26           30           13           30           26            6 
TCGA-56-7731 TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 
        1961          178           55           36           63           17 
TCGA-56-8628 TCGA-56-A4BW TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS 
          16            2           25            4            4            8 
TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-A46M TCGA-58-A46N TCGA-60-2696 
         378          911         2167         1072          910          109 
TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2709 
         311         1950         1943         1958          661         1505 
TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 
        1963         1260          274         1731         1531         1075 
TCGA-60-2716 TCGA-60-2721 TCGA-60-2722 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 
        1475          983          908         1957         1955         1947 
TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2756 TCGA-66-2759 TCGA-66-2765 
          61          641           30           30          762           61 
TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2777 
          61           61         1947          700          578           61 
TCGA-66-2778 TCGA-66-2780 TCGA-66-2783 TCGA-66-2785 TCGA-66-2788 TCGA-66-2789 
         578         1956          759           60          699         1955 
TCGA-66-2790 TCGA-66-2791 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-68-7755 
         699         1977         1952         1645          122           83 
TCGA-68-7757 TCGA-68-8250 TCGA-68-A59I TCGA-77-6843 TCGA-77-6844 TCGA-77-7138 
         211          244          121         1941         1942         1959 
TCGA-77-7141 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 
          15         1954         1942         1952         1954          479 
TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8131 TCGA-77-8133 
        1960         1945         1641         1953         1941         1941 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 
        1946         1951          833         1943          293         1961 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G8 TCGA-77-A5GA 
        1953         1942         1959         1955         1290         1280 
TCGA-77-A5GB TCGA-85-6560 TCGA-85-6561 TCGA-85-7696 TCGA-85-7697 TCGA-85-7710 
        1939          364          395           18           10         1965 
TCGA-85-7844 TCGA-85-8048 TCGA-85-8049 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 
         911           26           60          428          513           13 
TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8354 TCGA-85-8481 TCGA-85-8582 
          13           54           60           61           21          424 
TCGA-85-8666 TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 
         475         1972         1960           19         1973         1967 
TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-90-6837 TCGA-90-7766 TCGA-90-7769 
        1972         1987           24          758          289          358 
TCGA-90-7964 TCGA-90-A4ED TCGA-90-A59Q TCGA-92-7341 TCGA-92-8063 TCGA-92-8065 
         428          244          269          106          122           70 
TCGA-94-7033 TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7545 TCGA-96-8170 TCGA-96-A4JL 
          87          356          430         1344          211          183 
TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE 
         256          413          224           36           83         1722 
TCGA-NC-A5HI 
        1135 

  DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE 
                             1                              2 
  DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE 
                          3724                           5287 
  DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE 
                           552                            699 
[1] "1.0 - 3724.0 (552.0)" "2.0 - 5287.0 (699.0)"
[1] "hr=" "1.3"
D68V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 38(16P13.3) MUTATED         0       25       52        0        21
  DEL PEAK 38(16P13.3) WILD-TYPE       1       47       85        1        31
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 38(16P13.3) MUTATED          26         24          4        3
  DEL PEAK 38(16P13.3) WILD-TYPE        45         33         16        3
D68V3, multiclass
            clus
vv           DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE
  STAGE I                               0                              1
  STAGE IA                             25                             47
  STAGE IB                             52                             85
  STAGE II                              0                              1
  STAGE IIA                            21                             31
  STAGE IIB                            26                             45
  STAGE IIIA                           24                             33
  STAGE IIIB                            4                             16
  STAGE IV                              3                              3
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 38(16P13.3) MUTATED    29  98  21   7
  DEL PEAK 38(16P13.3) WILD-TYPE  69 156  27  13
D68V4, multiclass
    clus
vv   DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE
  T1                           29                             69
  T2                           98                            156
  T3                           21                             27
  T4                            7                             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 38(16P13.3) MUTATED   100  41  13   0
  DEL PEAK 38(16P13.3) WILD-TYPE 161  72  22   5
D68V5, multiclass
    clus
vv   DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE
  N0                          100                            161
  N1                           41                             72
  N2                           13                             22
  N3                            0                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A  MX
  DEL PEAK 38(16P13.3) MUTATED   134   2   1  16
  DEL PEAK 38(16P13.3) WILD-TYPE 224   3   0  34
D68V6, multiclass
     clus
vv    DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE
  M0                           134                            224
  M1                             2                              3
  M1A                            1                              0
  MX                            16                             34
[1] 4 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 38(16P13.3) MUTATED    42 113
  DEL PEAK 38(16P13.3) WILD-TYPE  65 200
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(16P13.3) MUTATED     42  113
  DEL PEAK 38(16P13.3) WILD-TYPE   65  200
        clus
vv       DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE
  FEMALE                           42                             65
  MALE                            113                            200
[1] 2 2
[1] FALSE
D68V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 38(16P13.3) MUTATED                                       8
  DEL PEAK 38(16P13.3) WILD-TYPE                                     4
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 38(16P13.3) MUTATED                                        2
  DEL PEAK 38(16P13.3) WILD-TYPE                                      4
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 38(16P13.3) MUTATED                                         1
  DEL PEAK 38(16P13.3) WILD-TYPE                                       0
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 38(16P13.3) MUTATED                                                           144
  DEL PEAK 38(16P13.3) WILD-TYPE                                                         257
D68V9, multiclass
                                                             clus
vv                                                            DEL PEAK 38(16P13.3) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          144
                                                             clus
vv                                                            DEL PEAK 38(16P13.3) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            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"
D68V10, binary
                                cls
clus                               0   1
  DEL PEAK 38(16P13.3) MUTATED     5 150
  DEL PEAK 38(16P13.3) WILD-TYPE   8 257
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(16P13.3) MUTATED      5  150
  DEL PEAK 38(16P13.3) WILD-TYPE    8  257
     clus
vv    DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE
  NO                             5                              8
  YES                          150                            257
[1] 2 2
[1] FALSE
D68V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 38(16P13.3) MUTATED   131   1   0   5
  DEL PEAK 38(16P13.3) WILD-TYPE 211   7   4  13
D68V12, multiclass
    clus
vv   DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE
  R0                          131                            211
  R1                            1                              7
  R2                            0                              4
  RX                            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                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 38(16P13.3) MUTATED       2                         7   109
  DEL PEAK 38(16P13.3) WILD-TYPE     7                        10   189
D68V13, multiclass
                           clus
vv                          DEL PEAK 38(16P13.3) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            7
  WHITE                                              109
                           clus
vv                          DEL PEAK 38(16P13.3) WILD-TYPE
  ASIAN                                                  7
  BLACK OR AFRICAN AMERICAN                             10
  WHITE                                                189
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V14, binary
                                cls
clus                               0   1
  DEL PEAK 38(16P13.3) MUTATED     3  99
  DEL PEAK 38(16P13.3) WILD-TYPE   5 168
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(16P13.3) MUTATED      3   99
  DEL PEAK 38(16P13.3) WILD-TYPE    5  168
                        clus
vv                       DEL PEAK 38(16P13.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           99
                        clus
vv                       DEL PEAK 38(16P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            168
[1] 2 2
[1] FALSE

Clustering(69) Variable = DEL PEAK 39(16Q23.1) MUTATION ANALYSIS
D69V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 39(16Q23.1) MUTATED   115  39
  DEL PEAK 39(16Q23.1) WILD-TYPE 150  84
  DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE 
                           154                            234 
  DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE 
                            39                             84 
$`DEL PEAK 39(16Q23.1) MUTATED`
TCGA-18-3410 TCGA-18-3415 TCGA-18-3416 TCGA-18-3419 TCGA-18-4083 TCGA-18-5592 
         146         1810          862           50          187           92 
TCGA-21-1070 TCGA-21-1076 TCGA-21-1080 TCGA-21-1083 TCGA-21-5787 TCGA-22-0940 
        3636         1852         3724          267          329          608 
TCGA-22-0944 TCGA-22-1002 TCGA-22-1012 TCGA-22-4594 TCGA-22-4595 TCGA-22-4599 
         223          131          429         1470          734         1161 
TCGA-22-4604 TCGA-22-5473 TCGA-22-5478 TCGA-22-5480 TCGA-22-5481 TCGA-22-5489 
         399         1933           24         1952         1952         1912 
TCGA-33-4533 TCGA-33-4547 TCGA-33-4583 TCGA-33-4586 TCGA-34-2596 TCGA-34-2604 
        1940         1311         1941          428           80          958 
TCGA-34-2609 TCGA-34-5231 TCGA-34-5239 TCGA-34-5927 TCGA-39-5011 TCGA-39-5016 
         951         1528          707          941         1454         2253 
TCGA-39-5019 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 TCGA-39-5040 
        1361         1964         1849           52           59         1964 
TCGA-43-2578 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-7657 
         684          822         1007          349          849          236 
TCGA-43-7658 TCGA-43-8116 TCGA-43-A475 TCGA-43-A56U TCGA-46-6025 TCGA-46-6026 
        1970          358          296          432          324          423 
TCGA-51-4079 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-56-7221 
          12          911          541         1948          923           30 
TCGA-56-7222 TCGA-56-7579 TCGA-56-7580 TCGA-56-7730 TCGA-56-7822 TCGA-56-8503 
          13           44           40            6            1           41 
TCGA-56-8626 TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4BY TCGA-58-8388 TCGA-58-8390 
          17           38           46           30          378          911 
TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-60-2695 
        2167         1058         2589         1723         1072          642 
TCGA-60-2710 TCGA-60-2711 TCGA-60-2713 TCGA-60-2714 TCGA-60-2719 TCGA-60-2720 
        1963         1260         1731         1531         1297           97 
TCGA-60-2723 TCGA-60-2725 TCGA-63-6202 TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 
        1092          816         1973         1952         1967         1311 
TCGA-66-2753 TCGA-66-2755 TCGA-66-2757 TCGA-66-2759 TCGA-66-2763 TCGA-66-2767 
          31           28           30          762           30           61 
TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2778 TCGA-66-2782 TCGA-66-2786 
          61         1947          700          578         1954          790 
TCGA-66-2787 TCGA-66-2789 TCGA-66-2790 TCGA-66-2792 TCGA-66-2793 TCGA-66-2800 
        1217         1955          699          913         1952         1492 
TCGA-68-7756 TCGA-68-8251 TCGA-68-A59J TCGA-77-6842 TCGA-77-7139 TCGA-77-7141 
         202           96          104         1950         1968           15 
TCGA-77-7142 TCGA-77-7463 TCGA-77-7465 TCGA-77-8136 TCGA-77-8139 TCGA-77-8150 
        1286         1954          479         1947         1951         1961 
TCGA-77-8153 TCGA-77-8156 TCGA-77-A5GH TCGA-85-6561 TCGA-85-6798 TCGA-85-7697 
        1684           10          713          395           34           10 
TCGA-85-7698 TCGA-85-7699 TCGA-85-7844 TCGA-85-7950 TCGA-85-8071 TCGA-85-8352 
          49            1          911           60          428           67 
TCGA-85-8353 TCGA-85-8355 TCGA-85-8580 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4QR 
          54           61          445            3          475           25 
TCGA-85-A50M TCGA-85-A50Z TCGA-85-A512 TCGA-85-A5B5 TCGA-90-7766 TCGA-90-7767 
          19         1973         1987          111          289           89 
TCGA-90-A4ED TCGA-90-A4EE TCGA-92-8064 TCGA-92-8065 TCGA-94-A4VJ TCGA-96-8169 
         244          331          160           70          430          189 
TCGA-96-A4JK TCGA-96-A4JL TCGA-J1-A4AH TCGA-NC-A5HG 
         273          183          222         1548 

$`DEL PEAK 39(16Q23.1) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3411 TCGA-18-3412 
         370          136         2464         2417         1415          345 
TCGA-18-3414 TCGA-18-3417 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 TCGA-18-5595 
         396          758         1331           85         2754          827 
TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 
        1426         3016         2134         1058          474          965 
TCGA-21-1081 TCGA-21-1082 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-21-A5DI 
         284         3644          962         1268         1032          979 
TCGA-22-1000 TCGA-22-1005 TCGA-22-1011 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 
        1945         1952           53          822         1485          623 
TCGA-22-4593 TCGA-22-4596 TCGA-22-4601 TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 
        1067           17         1057         1946          587          358 
TCGA-22-5471 TCGA-22-5472 TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 TCGA-22-5482 
         965         1964          445         1346         1651          357 
TCGA-22-5483 TCGA-22-5485 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 
         573          916         1713          506           29         2524 
TCGA-33-4538 TCGA-33-4566 TCGA-33-4582 TCGA-33-4587 TCGA-33-4589 TCGA-33-6738 
        2979         5287         1966         1970         1948          822 
TCGA-34-2600 TCGA-34-2605 TCGA-34-2608 TCGA-34-5232 TCGA-34-5234 TCGA-34-5240 
        1874          881         1000         2062         1715          365 
TCGA-34-5241 TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 
         428          552          166          120           13           12 
TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 
         200          247          227          238          207           12 
TCGA-37-5819 TCGA-39-5021 TCGA-39-5022 TCGA-39-5029 TCGA-39-5031 TCGA-39-5034 
         103         1947         1996          740          833         1107 
TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-43-2576 TCGA-43-2581 
         474         1084         1086          544         1223         1176 
TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 TCGA-43-8115 
         376          757          310         1936          212          407 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-51-4080 TCGA-52-7811 TCGA-52-7812 
        1971          353          366           12         1958         1967 
TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7223 
         881            3          555           62           26           30 
TCGA-56-7582 TCGA-56-7731 TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 
          26         1961          178           55           36           63 
TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR 
          16           34            2           25            4            4 
TCGA-56-A5DS TCGA-58-A46N TCGA-60-2696 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 
           8          910          109          311         1950         1943 
TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2712 TCGA-60-2715 
        1958          661         1963         1505          274         1075 
TCGA-60-2716 TCGA-60-2721 TCGA-60-2722 TCGA-60-2724 TCGA-60-2726 TCGA-63-7020 
        1475          983          908          717          358         1957 
TCGA-63-7021 TCGA-63-7022 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2754 
        1955         1947           61          641           30           61 
TCGA-66-2756 TCGA-66-2758 TCGA-66-2765 TCGA-66-2766 TCGA-66-2771 TCGA-66-2773 
          30          639           61           31          578         1946 
TCGA-66-2777 TCGA-66-2780 TCGA-66-2781 TCGA-66-2783 TCGA-66-2785 TCGA-66-2788 
          61         1956          121          759           60          699 
TCGA-66-2791 TCGA-66-2794 TCGA-66-2795 TCGA-68-7755 TCGA-68-7757 TCGA-68-8250 
        1977         1645          122           83          211          244 
TCGA-68-A59I TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7335 
         121         1941         1942         1952         1959         1954 
TCGA-77-7337 TCGA-77-7338 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 
        1942         1952         1960         1945         1641         1953 
TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8138 TCGA-77-8140 TCGA-77-8144 
        1945         1941         1941         1946         1962          833 
TCGA-77-8145 TCGA-77-8148 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 
        1943          293         1092         1953         1942         1959 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF 
        1955         1963         1290         1280         1939          839 
TCGA-85-6560 TCGA-85-7696 TCGA-85-7710 TCGA-85-7843 TCGA-85-8048 TCGA-85-8049 
         364           18         1965           35           26           60 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 
          16          960          513           13           11           13 
TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8354 TCGA-85-8479 TCGA-85-8481 
          54           60           55           61           22           21 
TCGA-85-8582 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A510 TCGA-85-A511 
         424           15         1972         1960         1967         1972 
TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 TCGA-90-7769 TCGA-90-7964 TCGA-90-A59Q 
          24           13          758          358          428          269 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-94-7033 TCGA-94-7943 TCGA-96-7544 
          82          106          122           87          356         1213 
TCGA-96-7545 TCGA-96-8170 TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 
        1344          211          256          413          224          308 
TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HI 
          35          449           36           83         1722         1135 

  DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE 
                             1                              2 
  DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE 
                          3724                           5287 
  DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE 
                           593                            680 
[1] "1.0 - 3724.0 (593.0)" "2.0 - 5287.0 (680.0)"
[1] "hr=" "1.2"
D69V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 39(16Q23.1) MUTATED         0       25       55        0        22
  DEL PEAK 39(16Q23.1) WILD-TYPE       1       47       82        1        30
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 39(16Q23.1) MUTATED          32         24          8        2
  DEL PEAK 39(16Q23.1) WILD-TYPE        39         33         12        4
D69V3, multiclass
            clus
vv           DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE
  STAGE I                               0                              1
  STAGE IA                             25                             47
  STAGE IB                             55                             82
  STAGE II                              0                              1
  STAGE IIA                            22                             30
  STAGE IIB                            32                             39
  STAGE IIIA                           24                             33
  STAGE IIIB                            8                             12
  STAGE IV                              2                              4
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 39(16Q23.1) MUTATED    33 106  22   9
  DEL PEAK 39(16Q23.1) WILD-TYPE  65 148  26  11
D69V4, multiclass
    clus
vv   DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE
  T1                           33                             65
  T2                          106                            148
  T3                           22                             26
  T4                            9                             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 39(16Q23.1) MUTATED   108  43  14   3
  DEL PEAK 39(16Q23.1) WILD-TYPE 153  70  21   2
D69V5, multiclass
    clus
vv   DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE
  N0                          108                            153
  N1                           43                             70
  N2                           14                             21
  N3                            3                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A  MX
  DEL PEAK 39(16Q23.1) MUTATED   149   1   1  15
  DEL PEAK 39(16Q23.1) WILD-TYPE 209   4   0  35
D69V6, multiclass
     clus
vv    DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE
  M0                           149                            209
  M1                             1                              4
  M1A                            1                              0
  MX                            15                             35
[1] 4 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 39(16Q23.1) MUTATED    50 120
  DEL PEAK 39(16Q23.1) WILD-TYPE  57 193
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(16Q23.1) MUTATED     50  120
  DEL PEAK 39(16Q23.1) WILD-TYPE   57  193
        clus
vv       DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE
  FEMALE                           50                             57
  MALE                            120                            193
[1] 2 2
[1] FALSE
D69V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 39(16Q23.1) MUTATED                                       6
  DEL PEAK 39(16Q23.1) WILD-TYPE                                     6
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 39(16Q23.1) MUTATED                                        0
  DEL PEAK 39(16Q23.1) WILD-TYPE                                      6
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 39(16Q23.1) MUTATED                                         0
  DEL PEAK 39(16Q23.1) WILD-TYPE                                       1
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 39(16Q23.1) MUTATED                                                           164
  DEL PEAK 39(16Q23.1) WILD-TYPE                                                         237
D69V9, multiclass
                                                             clus
vv                                                            DEL PEAK 39(16Q23.1) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          164
                                                             clus
vv                                                            DEL PEAK 39(16Q23.1) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V10, binary
                                cls
clus                               0   1
  DEL PEAK 39(16Q23.1) MUTATED     8 162
  DEL PEAK 39(16Q23.1) WILD-TYPE   5 245
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(16Q23.1) MUTATED      8  162
  DEL PEAK 39(16Q23.1) WILD-TYPE    5  245
     clus
vv    DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE
  NO                             8                              5
  YES                          162                            245
[1] 2 2
[1] FALSE
D69V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 39(16Q23.1) MUTATED   137   3   2   4
  DEL PEAK 39(16Q23.1) WILD-TYPE 205   5   2  14
D69V12, multiclass
    clus
vv   DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE
  R0                          137                            205
  R1                            3                              5
  R2                            2                              2
  RX                            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                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 39(16Q23.1) MUTATED       3                         8   120
  DEL PEAK 39(16Q23.1) WILD-TYPE     6                         9   178
D69V13, multiclass
                           clus
vv                          DEL PEAK 39(16Q23.1) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            8
  WHITE                                              120
                           clus
vv                          DEL PEAK 39(16Q23.1) WILD-TYPE
  ASIAN                                                  6
  BLACK OR AFRICAN AMERICAN                              9
  WHITE                                                178
[1] 3 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 39(16Q23.1) MUTATED     2 110
  DEL PEAK 39(16Q23.1) WILD-TYPE   6 157
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(16Q23.1) MUTATED      2  110
  DEL PEAK 39(16Q23.1) WILD-TYPE    6  157
                        clus
vv                       DEL PEAK 39(16Q23.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          110
                        clus
vv                       DEL PEAK 39(16Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            157
[1] 2 2
[1] FALSE

Clustering(70) Variable = DEL PEAK 40(17P11.2) MUTATION ANALYSIS
D70V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 40(17P11.2) MUTATED   137  73
  DEL PEAK 40(17P11.2) WILD-TYPE 128  50
  DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE 
                           210                            178 
  DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE 
                            73                             50 
$`DEL PEAK 40(17P11.2) MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3410 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 
         370          136          146          345          396         1810 
TCGA-18-3416 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 TCGA-21-1070 
         862           50         1331           85         2754         3636 
TCGA-21-1071 TCGA-21-1075 TCGA-21-1077 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 
        1426         2134         1058         3644          267          962 
TCGA-21-5787 TCGA-21-A5DI TCGA-22-0944 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 
         329          979          223           53          429          822 
TCGA-22-4591 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4604 TCGA-22-4605 
         623          734           17         1161          399         1946 
TCGA-22-4607 TCGA-22-4613 TCGA-22-5472 TCGA-22-5477 TCGA-22-5480 TCGA-22-5481 
         587          358         1964         1346         1952         1952 
TCGA-22-5483 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 
         573         1912         1713          506           29         2524 
TCGA-33-4547 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-34-2600 
        1311         1966         1941          428         1970         1874 
TCGA-34-2604 TCGA-34-2608 TCGA-34-5240 TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 
         958         1000          365          166          120           13 
TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5016 TCGA-39-5029 
         238          207           12          103         2253          740 
TCGA-39-5034 TCGA-39-5035 TCGA-39-5040 TCGA-43-2576 TCGA-43-5670 TCGA-43-6143 
        1107          474         1964         1223          849          376 
TCGA-43-7656 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-A474 TCGA-43-A475 
         212         1970          407          358          353          296 
TCGA-43-A56U TCGA-43-A56V TCGA-46-6025 TCGA-46-6026 TCGA-51-4080 TCGA-52-7622 
         432          366          324          423           12          541 
TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-7223 TCGA-56-7580 
        1967          881            3          555           30           40 
TCGA-56-7582 TCGA-56-7822 TCGA-56-8503 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 
          26            1           41           36           63           17 
TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BY TCGA-56-A4ZJ TCGA-58-8388 
          16           34           38           30           25          378 
TCGA-58-8390 TCGA-58-8391 TCGA-58-8393 TCGA-58-A46L TCGA-58-A46M TCGA-60-2695 
         911         2167         1058         1723         1072          642 
TCGA-60-2696 TCGA-60-2703 TCGA-60-2706 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 
         109         1950         1958          274         1731         1531 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2725 
        1297           97          983          908         1092          816 
TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7023 TCGA-66-2727 
         358         1973         1957         1955         1952         1967 
TCGA-66-2742 TCGA-66-2753 TCGA-66-2754 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 
         641           31           61           30          639          762 
TCGA-66-2763 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2771 
          30           31           61           61         1947          578 
TCGA-66-2773 TCGA-66-2777 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 
        1946           61         1956          121         1954          759 
TCGA-66-2785 TCGA-66-2786 TCGA-66-2788 TCGA-66-2789 TCGA-66-2791 TCGA-66-2793 
          60          790          699         1955         1977         1952 
TCGA-66-2795 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59J TCGA-77-6842 TCGA-77-6844 
         122          211           96          104         1950         1942 
TCGA-77-6845 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7337 TCGA-77-7338 
        1952         1968           15         1286         1942         1952 
TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 
         479         1945         1641         1953         1945         1941 
TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8145 
        1941         1947         1946         1951         1962         1943 
TCGA-77-8148 TCGA-77-8150 TCGA-77-8154 TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 
         293         1961         1092         1942         1959         1955 
TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6560 TCGA-85-7697 TCGA-85-7843 TCGA-85-7844 
        1939          713          364           10           35          911 
TCGA-85-8070 TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 TCGA-85-8479 TCGA-85-A4CL 
         960           13           13           54           22           15 
TCGA-85-A4QQ TCGA-85-A50Z TCGA-85-A510 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L 
        1960         1973         1967         1987           24           13 
TCGA-90-7767 TCGA-90-7964 TCGA-90-A4ED TCGA-92-7341 TCGA-92-8063 TCGA-92-8065 
          89          428          244          106          122           70 
TCGA-94-7033 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-7545 TCGA-96-8170 TCGA-96-A4JK 
          87          430         1213         1344          211          273 
TCGA-98-8021 TCGA-98-8022 TCGA-L3-A4E7 TCGA-L3-A524 TCGA-NC-A5HG TCGA-NC-A5HI 
         413          224           35          449         1548         1135 

$`DEL PEAK 40(17P11.2) WILD-TYPE`
TCGA-18-3408 TCGA-18-3409 TCGA-18-3411 TCGA-18-3417 TCGA-18-4083 TCGA-18-5592 
        2464         2417         1415          758          187           92 
TCGA-18-5595 TCGA-21-1072 TCGA-21-1076 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 
         827         3016         1852          474          965         3724 
TCGA-21-1081 TCGA-21-5784 TCGA-21-5786 TCGA-22-0940 TCGA-22-1000 TCGA-22-1002 
         284         1268         1032          608         1945          131 
TCGA-22-1005 TCGA-22-1017 TCGA-22-4593 TCGA-22-4594 TCGA-22-4601 TCGA-22-5471 
        1952         1485         1067         1470         1057          965 
TCGA-22-5473 TCGA-22-5474 TCGA-22-5478 TCGA-22-5479 TCGA-22-5482 TCGA-22-5485 
        1933          445           24         1651          357          916 
TCGA-33-4533 TCGA-33-4538 TCGA-33-4566 TCGA-33-4589 TCGA-33-6738 TCGA-34-2596 
        1940         2979         5287         1948          822           80 
TCGA-34-2605 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 
         881          951         1528         2062         1715          707 
TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 
         428          941          552           12          200          247 
TCGA-37-4132 TCGA-39-5011 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 
         227         1454         1361         1947         1996         1964 
TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 TCGA-39-5031 TCGA-39-5036 TCGA-39-5037 
        1849           52           59          833         1084         1086 
TCGA-39-5039 TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 
         544          684         1176          822         1007          349 
TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-7657 TCGA-43-8118 TCGA-51-4079 
         757          310         1936          236         1971           12 
TCGA-51-4081 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-56-6545 TCGA-56-6546 
         911         1948          923         1958           62           26 
TCGA-56-7221 TCGA-56-7222 TCGA-56-7579 TCGA-56-7730 TCGA-56-7731 TCGA-56-8504 
          30           13           44            6         1961          178 
TCGA-56-8622 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS 
          55            2           46            4            4            8 
TCGA-58-A46J TCGA-58-A46N TCGA-60-2698 TCGA-60-2704 TCGA-60-2707 TCGA-60-2708 
        2589          910          311         1943          661         1963 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2715 TCGA-60-2716 TCGA-60-2724 
        1505         1963         1260         1075         1475          717 
TCGA-63-7022 TCGA-66-2734 TCGA-66-2737 TCGA-66-2744 TCGA-66-2755 TCGA-66-2756 
        1947         1311           61           30           28           30 
TCGA-66-2765 TCGA-66-2770 TCGA-66-2778 TCGA-66-2787 TCGA-66-2790 TCGA-66-2792 
          61          700          578         1217          699          913 
TCGA-66-2794 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-8250 TCGA-68-A59I 
        1645         1492           83          202          244          121 
TCGA-77-6843 TCGA-77-7138 TCGA-77-7335 TCGA-77-7463 TCGA-77-8007 TCGA-77-8144 
        1941         1959         1954         1954         1960          833 
TCGA-77-8153 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA 
        1684           10         1953         1963         1290         1280 
TCGA-77-A5GF TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7698 TCGA-85-7699 
         839          395           34           18           49            1 
TCGA-85-7710 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8071 
        1965           60           26           60           16          428 
TCGA-85-8072 TCGA-85-8277 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 
         513           11           60           55           67           54 
TCGA-85-8354 TCGA-85-8355 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 
          61           61           21          445          424            3 
TCGA-85-8666 TCGA-85-A4PA TCGA-85-A4QR TCGA-85-A50M TCGA-85-A511 TCGA-85-A5B5 
         475         1972           25           19         1972          111 
TCGA-90-6837 TCGA-90-7766 TCGA-90-7769 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 
         758          289          358          331          269           82 
TCGA-92-8064 TCGA-94-7943 TCGA-96-8169 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8023 
         160          356          189          183          256          308 
TCGA-J1-A4AH TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE 
         222           36           83         1722 

  DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE 
                             1                              1 
  DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE 
                          3644                           5287 
  DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE 
                         640.0                          672.5 
[1] "1.0 - 3644.0 (640.0)" "1.0 - 5287.0 (672.5)"
[1] "hr=" "1.1"
D70V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 40(17P11.2) MUTATED         1       40       67        0        29
  DEL PEAK 40(17P11.2) WILD-TYPE       0       32       70        1        23
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 40(17P11.2) MUTATED          38         31         11        4
  DEL PEAK 40(17P11.2) WILD-TYPE        33         26          9        2
D70V3, multiclass
            clus
vv           DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE
  STAGE I                               1                              0
  STAGE IA                             40                             32
  STAGE IB                             67                             70
  STAGE II                              0                              1
  STAGE IIA                            29                             23
  STAGE IIB                            38                             33
  STAGE IIIA                           31                             26
  STAGE IIIB                           11                              9
  STAGE IV                              4                              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 40(17P11.2) MUTATED    53 135  25   8
  DEL PEAK 40(17P11.2) WILD-TYPE  45 119  23  12
D70V4, multiclass
    clus
vv   DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE
  T1                           53                             45
  T2                          135                            119
  T3                           25                             23
  T4                            8                             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 40(17P11.2) MUTATED   133  58  22   4
  DEL PEAK 40(17P11.2) WILD-TYPE 128  55  13   1
D70V5, multiclass
    clus
vv   DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE
  N0                          133                            128
  N1                           58                             55
  N2                           22                             13
  N3                            4                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A  MX
  DEL PEAK 40(17P11.2) MUTATED   190   3   1  24
  DEL PEAK 40(17P11.2) WILD-TYPE 168   2   0  26
D70V6, multiclass
     clus
vv    DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE
  M0                           190                            168
  M1                             3                              2
  M1A                            1                              0
  MX                            24                             26
[1] 4 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 40(17P11.2) MUTATED    53 168
  DEL PEAK 40(17P11.2) WILD-TYPE  54 145
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(17P11.2) MUTATED     53  168
  DEL PEAK 40(17P11.2) WILD-TYPE   54  145
        clus
vv       DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE
  FEMALE                           53                             54
  MALE                            168                            145
[1] 2 2
[1] FALSE
D70V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 40(17P11.2) MUTATED                                       8
  DEL PEAK 40(17P11.2) WILD-TYPE                                     4
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 40(17P11.2) MUTATED                                        2
  DEL PEAK 40(17P11.2) WILD-TYPE                                      4
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 40(17P11.2) MUTATED                                         1
  DEL PEAK 40(17P11.2) WILD-TYPE                                       0
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 40(17P11.2) MUTATED                                                           210
  DEL PEAK 40(17P11.2) WILD-TYPE                                                         191
D70V9, multiclass
                                                             clus
vv                                                            DEL PEAK 40(17P11.2) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          210
                                                             clus
vv                                                            DEL PEAK 40(17P11.2) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            191
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V10, binary
                                cls
clus                               0   1
  DEL PEAK 40(17P11.2) MUTATED    10 211
  DEL PEAK 40(17P11.2) WILD-TYPE   3 196
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(17P11.2) MUTATED     10  211
  DEL PEAK 40(17P11.2) WILD-TYPE    3  196
     clus
vv    DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE
  NO                            10                              3
  YES                          211                            196
[1] 2 2
[1] FALSE
D70V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 40(17P11.2) MUTATED   191   5   2   7
  DEL PEAK 40(17P11.2) WILD-TYPE 151   3   2  11
D70V12, multiclass
    clus
vv   DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE
  R0                          191                            151
  R1                            5                              3
  R2                            2                              2
  RX                            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                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 40(17P11.2) MUTATED       5                         6   152
  DEL PEAK 40(17P11.2) WILD-TYPE     4                        11   146
D70V13, multiclass
                           clus
vv                          DEL PEAK 40(17P11.2) MUTATED
  ASIAN                                                5
  BLACK OR AFRICAN AMERICAN                            6
  WHITE                                              152
                           clus
vv                          DEL PEAK 40(17P11.2) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                             11
  WHITE                                                146
[1] 3 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 40(17P11.2) MUTATED     4 132
  DEL PEAK 40(17P11.2) WILD-TYPE   4 135
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(17P11.2) MUTATED      4  132
  DEL PEAK 40(17P11.2) WILD-TYPE    4  135
                        clus
vv                       DEL PEAK 40(17P11.2) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          132
                        clus
vv                       DEL PEAK 40(17P11.2) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            135
[1] 2 2
[1] FALSE

Clustering(71) Variable = DEL PEAK 41(17Q11.2) MUTATION ANALYSIS
D71V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 41(17Q11.2) MUTATED    77  30
  DEL PEAK 41(17Q11.2) WILD-TYPE 188  93
  DEL PEAK 41(17Q11.2) MUTATED DEL PEAK 41(17Q11.2) WILD-TYPE 
                           107                            281 
  DEL PEAK 41(17Q11.2) MUTATED DEL PEAK 41(17Q11.2) WILD-TYPE 
                            30                             93 
$`DEL PEAK 41(17Q11.2) MUTATED`
TCGA-18-3410 TCGA-18-3414 TCGA-18-3416 TCGA-21-1070 TCGA-21-1082 TCGA-21-5786 
         146          396          862         3636         3644         1032 
TCGA-21-A5DI TCGA-22-1011 TCGA-22-1016 TCGA-22-4595 TCGA-22-4596 TCGA-22-4607 
         979           53          822          734           17          587 
TCGA-22-5472 TCGA-22-5478 TCGA-22-5492 TCGA-33-4583 TCGA-33-4587 TCGA-34-2600 
        1964           24          506         1941         1970         1874 
TCGA-34-2604 TCGA-34-5239 TCGA-34-5241 TCGA-34-8454 TCGA-37-3789 TCGA-37-4141 
         958          707          428          166           13           12 
TCGA-39-5029 TCGA-39-5035 TCGA-43-2578 TCGA-43-2581 TCGA-43-3920 TCGA-43-5670 
         740          474          684         1176         1007          849 
TCGA-43-6770 TCGA-43-7656 TCGA-43-A56U TCGA-43-A56V TCGA-46-6025 TCGA-52-7810 
         310          212          432          366          324          923 
TCGA-52-7812 TCGA-56-5897 TCGA-56-5898 TCGA-56-7223 TCGA-56-7580 TCGA-56-7822 
        1967            3          555           30           40            1 
TCGA-56-8503 TCGA-56-8624 TCGA-56-8625 TCGA-56-8628 TCGA-56-A49D TCGA-56-A4ZJ 
          41           36           63           16           38           25 
TCGA-58-8391 TCGA-58-8393 TCGA-60-2695 TCGA-60-2696 TCGA-60-2706 TCGA-60-2713 
        2167         1058          642          109         1958         1731 
TCGA-60-2714 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2723 TCGA-60-2724 
        1531         1297           97          983         1092          717 
TCGA-63-6202 TCGA-63-7020 TCGA-66-2753 TCGA-66-2763 TCGA-66-2769 TCGA-66-2771 
        1973         1957           31           30         1947          578 
TCGA-66-2780 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2788 
        1956         1954          759           60          790          699 
TCGA-66-2789 TCGA-66-2793 TCGA-66-2794 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59J 
        1955         1952         1645          244           96          104 
TCGA-77-8008 TCGA-77-8130 TCGA-77-8131 TCGA-77-8136 TCGA-77-8138 TCGA-77-8144 
        1945         1945         1941         1947         1946          833 
TCGA-77-8150 TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5GB TCGA-77-A5GH TCGA-85-7697 
        1961         1942         1955         1939          713           10 
TCGA-85-7950 TCGA-85-8287 TCGA-85-8352 TCGA-85-8479 TCGA-85-A4QQ TCGA-85-A50Z 
          60           13           67           22         1960         1973 
TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-A4ED TCGA-92-8063 TCGA-92-8065 
          24           13          111          244          122           70 
TCGA-94-7033 TCGA-98-8021 TCGA-98-8022 TCGA-L3-A4E7 TCGA-NC-A5HG 
          87          413          224           35         1548 

$`DEL PEAK 41(17Q11.2) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3411 TCGA-18-3412 
         370          136         2464         2417         1415          345 
TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 
        1810          758           50         1331          187           85 
TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 
        2754           92          827         1426         3016         2134 
TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 
        1852         1058          474          965         3724          284 
TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 
         267          962         1268          329          608          223 
TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1012 TCGA-22-1017 TCGA-22-4591 
        1945          131         1952          429         1485          623 
TCGA-22-4593 TCGA-22-4594 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 
        1067         1470         1161         1057          399         1946 
TCGA-22-4613 TCGA-22-5471 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 
         358          965         1933          445         1346         1651 
TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 
        1952         1952          357          573          916         1912 
TCGA-22-5491 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 
        1713           29         2524         1940         2979         1311 
TCGA-33-4566 TCGA-33-4582 TCGA-33-4586 TCGA-33-4589 TCGA-33-6738 TCGA-34-2596 
        5287         1966          428         1948          822           80 
TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 
         881         1000          951         1528         2062         1715 
TCGA-34-5240 TCGA-34-5927 TCGA-34-5928 TCGA-37-3783 TCGA-37-3792 TCGA-37-4129 
         365          941          552          120           12          200 
TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-5819 TCGA-39-5011 
         247          227          238          207          103         1454 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 
        2253         1361         1947         1996         1964         1849 
TCGA-39-5028 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5036 TCGA-39-5037 
          52           59          833         1107         1084         1086 
TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-3394 TCGA-43-5668 TCGA-43-6143 
         544         1964         1223          822          349          376 
TCGA-43-6647 TCGA-43-6771 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 
         757         1936          236         1970          407          358 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 
        1971          353          296          423           12           12 
TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7811 TCGA-56-1622 TCGA-56-6545 
         911          541         1948         1958          881           62 
TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7579 TCGA-56-7582 TCGA-56-7730 
          26           30           13           44           26            6 
TCGA-56-7731 TCGA-56-8504 TCGA-56-8622 TCGA-56-8626 TCGA-56-8629 TCGA-56-A4BW 
        1961          178           55           17           34            2 
TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8388 
          46           30            4            4            8          378 
TCGA-58-8390 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2698 
         911         2589         1723         1072          910          311 
TCGA-60-2703 TCGA-60-2704 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 
        1950         1943          661         1963         1505         1963 
TCGA-60-2711 TCGA-60-2712 TCGA-60-2715 TCGA-60-2716 TCGA-60-2722 TCGA-60-2725 
        1260          274         1075         1475          908          816 
TCGA-60-2726 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 
         358         1955         1947         1952         1967         1311 
TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 
          61          641           30           61           28           30 
TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 
          30          639          762           61           31           61 
TCGA-66-2768 TCGA-66-2770 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2781 
          61          700         1946           61          578          121 
TCGA-66-2787 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2795 TCGA-66-2800 
        1217          699         1977          913          122         1492 
TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-A59I TCGA-77-6842 TCGA-77-6843 
          83          202          211          121         1950         1941 
TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 
        1942         1952         1959         1968           15         1286 
TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 
        1954         1942         1952         1954          479         1960 
TCGA-77-8009 TCGA-77-8128 TCGA-77-8133 TCGA-77-8139 TCGA-77-8140 TCGA-77-8145 
        1641         1953         1941         1951         1962         1943 
TCGA-77-8148 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G3 
         293         1684         1092           10         1953         1959 
TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GF TCGA-85-6560 TCGA-85-6561 
        1963         1290         1280          839          364          395 
TCGA-85-6798 TCGA-85-7696 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 
          34           18           49            1         1965           35 
TCGA-85-7844 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 
         911           26           60           16          960          428 
TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 
         513           13           11           54           60           55 
TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 
          54           61           61           21          445          424 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QR TCGA-85-A50M 
           3          475           15         1972           25           19 
TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 
        1967         1972         1987          758          289           89 
TCGA-90-7769 TCGA-90-7964 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 
         358          428          331          269           82          106 
TCGA-92-8064 TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 
         160          356          430         1213         1344          189 
TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-8023 TCGA-J1-A4AH 
         211          273          183          256          308          222 
TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HI 
         449           36           83         1722         1135 

  DEL PEAK 41(17Q11.2) MUTATED DEL PEAK 41(17Q11.2) WILD-TYPE 
                             1                              1 
  DEL PEAK 41(17Q11.2) MUTATED DEL PEAK 41(17Q11.2) WILD-TYPE 
                          3644                           5287 
  DEL PEAK 41(17Q11.2) MUTATED DEL PEAK 41(17Q11.2) WILD-TYPE 
                           684                            639 
[1] "1.0 - 3644.0 (684.0)" "1.0 - 5287.0 (639.0)"
[1] "hr=" "1.1"
D71V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 41(17Q11.2) MUTATED         1       21       41        0         8
  DEL PEAK 41(17Q11.2) WILD-TYPE       0       51       96        1        44
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 41(17Q11.2) MUTATED          13         20          6        3
  DEL PEAK 41(17Q11.2) WILD-TYPE        58         37         14        3
D71V3, multiclass
            clus
vv           DEL PEAK 41(17Q11.2) MUTATED DEL PEAK 41(17Q11.2) WILD-TYPE
  STAGE I                               1                              0
  STAGE IA                             21                             51
  STAGE IB                             41                             96
  STAGE II                              0                              1
  STAGE IIA                             8                             44
  STAGE IIB                            13                             58
  STAGE IIIA                           20                             37
  STAGE IIIB                            6                             14
  STAGE IV                              3                              3
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 41(17Q11.2) MUTATED    26  62  19   6
  DEL PEAK 41(17Q11.2) WILD-TYPE  72 192  29  14
D71V4, multiclass
    clus
vv   DEL PEAK 41(17Q11.2) MUTATED DEL PEAK 41(17Q11.2) WILD-TYPE
  T1                           26                             72
  T2                           62                            192
  T3                           19                             29
  T4                            6                             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 41(17Q11.2) MUTATED    78  17  12   2
  DEL PEAK 41(17Q11.2) WILD-TYPE 183  96  23   3
D71V5, multiclass
    clus
vv   DEL PEAK 41(17Q11.2) MUTATED DEL PEAK 41(17Q11.2) WILD-TYPE
  N0                           78                            183
  N1                           17                             96
  N2                           12                             23
  N3                            2                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A  MX
  DEL PEAK 41(17Q11.2) MUTATED    92   2   1  16
  DEL PEAK 41(17Q11.2) WILD-TYPE 266   3   0  34
D71V6, multiclass
     clus
vv    DEL PEAK 41(17Q11.2) MUTATED DEL PEAK 41(17Q11.2) WILD-TYPE
  M0                            92                            266
  M1                             2                              3
  M1A                            1                              0
  MX                            16                             34
[1] 4 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 41(17Q11.2) MUTATED    33  80
  DEL PEAK 41(17Q11.2) WILD-TYPE  74 233
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(17Q11.2) MUTATED     33   80
  DEL PEAK 41(17Q11.2) WILD-TYPE   74  233
        clus
vv       DEL PEAK 41(17Q11.2) MUTATED DEL PEAK 41(17Q11.2) WILD-TYPE
  FEMALE                           33                             74
  MALE                             80                            233
[1] 2 2
[1] FALSE
D71V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 41(17Q11.2) MUTATED                                       2
  DEL PEAK 41(17Q11.2) WILD-TYPE                                    10
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 41(17Q11.2) MUTATED                                        1
  DEL PEAK 41(17Q11.2) WILD-TYPE                                      5
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 41(17Q11.2) MUTATED                                         1
  DEL PEAK 41(17Q11.2) WILD-TYPE                                       0
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 41(17Q11.2) MUTATED                                                           109
  DEL PEAK 41(17Q11.2) WILD-TYPE                                                         292
D71V9, multiclass
                                                             clus
vv                                                            DEL PEAK 41(17Q11.2) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          109
                                                             clus
vv                                                            DEL PEAK 41(17Q11.2) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   10
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            292
[1] 4 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 41(17Q11.2) MUTATED     2 111
  DEL PEAK 41(17Q11.2) WILD-TYPE  11 296
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(17Q11.2) MUTATED      2  111
  DEL PEAK 41(17Q11.2) WILD-TYPE   11  296
     clus
vv    DEL PEAK 41(17Q11.2) MUTATED DEL PEAK 41(17Q11.2) WILD-TYPE
  NO                             2                             11
  YES                          111                            296
[1] 2 2
[1] FALSE
D71V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 41(17Q11.2) MUTATED    93   1   1   6
  DEL PEAK 41(17Q11.2) WILD-TYPE 249   7   3  12
D71V12, multiclass
    clus
vv   DEL PEAK 41(17Q11.2) MUTATED DEL PEAK 41(17Q11.2) WILD-TYPE
  R0                           93                            249
  R1                            1                              7
  R2                            1                              3
  RX                            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                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 41(17Q11.2) MUTATED       3                         8    71
  DEL PEAK 41(17Q11.2) WILD-TYPE     6                         9   227
D71V13, multiclass
                           clus
vv                          DEL PEAK 41(17Q11.2) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            8
  WHITE                                               71
                           clus
vv                          DEL PEAK 41(17Q11.2) WILD-TYPE
  ASIAN                                                  6
  BLACK OR AFRICAN AMERICAN                              9
  WHITE                                                227
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V14, binary
                                cls
clus                               0   1
  DEL PEAK 41(17Q11.2) MUTATED     3  74
  DEL PEAK 41(17Q11.2) WILD-TYPE   5 193
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(17Q11.2) MUTATED      3   74
  DEL PEAK 41(17Q11.2) WILD-TYPE    5  193
                        clus
vv                       DEL PEAK 41(17Q11.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           74
                        clus
vv                       DEL PEAK 41(17Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            193
[1] 2 2
[1] FALSE

Clustering(72) Variable = DEL PEAK 42(17Q25.3) MUTATION ANALYSIS
D72V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 42(17Q25.3) MUTATED    58  23
  DEL PEAK 42(17Q25.3) WILD-TYPE 207 100
  DEL PEAK 42(17Q25.3) MUTATED DEL PEAK 42(17Q25.3) WILD-TYPE 
                            81                            307 
  DEL PEAK 42(17Q25.3) MUTATED DEL PEAK 42(17Q25.3) WILD-TYPE 
                            23                            100 
$`DEL PEAK 42(17Q25.3) MUTATED`
TCGA-18-3415 TCGA-18-3421 TCGA-21-1070 TCGA-21-1075 TCGA-21-A5DI TCGA-22-1011 
        1810         1331         3636         2134          979           53 
TCGA-22-1016 TCGA-22-5472 TCGA-22-5482 TCGA-33-4538 TCGA-33-4583 TCGA-34-2600 
         822         1964          357         2979         1941         1874 
TCGA-34-5241 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-5819 TCGA-39-5029 
         428          120           13           12          103          740 
TCGA-43-2581 TCGA-43-5670 TCGA-43-A56U TCGA-51-4080 TCGA-52-7622 TCGA-52-7810 
        1176          849          432           12          541          923 
TCGA-56-5898 TCGA-56-7580 TCGA-56-7822 TCGA-56-8503 TCGA-56-8624 TCGA-56-8626 
         555           40            1           41           36           17 
TCGA-56-8628 TCGA-56-A4ZJ TCGA-56-A5DR TCGA-58-8388 TCGA-58-8393 TCGA-60-2695 
          16           25            4          378         1058          642 
TCGA-60-2696 TCGA-60-2708 TCGA-60-2714 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 
         109         1963         1531         1297           97          983 
TCGA-63-7020 TCGA-63-7023 TCGA-66-2780 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 
        1957         1952         1956         1954          759           60 
TCGA-66-2786 TCGA-66-2789 TCGA-66-2790 TCGA-68-A59J TCGA-77-6842 TCGA-77-6844 
         790         1955          699          104         1950         1942 
TCGA-77-6845 TCGA-77-7337 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8138 
        1952         1942         1953         1945         1941         1946 
TCGA-77-8144 TCGA-77-8150 TCGA-77-A5G1 TCGA-77-A5GB TCGA-77-A5GH TCGA-85-7697 
         833         1961         1942         1939          713           10 
TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 TCGA-85-8070 TCGA-85-8287 TCGA-85-8288 
        1965          911           60          960           13           54 
TCGA-85-8355 TCGA-85-8479 TCGA-85-A4QQ TCGA-85-A50Z TCGA-92-8063 TCGA-96-7544 
          61           22         1960         1973          122         1213 
TCGA-98-8021 TCGA-L3-A4E7 TCGA-MF-A522 
         413           35           83 

$`DEL PEAK 42(17Q25.3) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
         370          136         2464         2417          146         1415 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-4083 
         345          396          862          758           50          187 
TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1071 TCGA-21-1072 
          85         2754           92          827         1426         3016 
TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 
        1852         1058          474          965         3724          284 
TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 
        3644          267          962         1268         1032          329 
TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1012 
         608          223         1945          131         1952          429 
TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 
        1485          623         1067         1470          734           17 
TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 
        1161         1057          399         1946          587          358 
TCGA-22-5471 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 
         965         1933          445         1346           24         1651 
TCGA-22-5480 TCGA-22-5481 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 
        1952         1952          573          916         1912         1713 
TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4547 TCGA-33-4566 
         506           29         2524         1940         1311         5287 
TCGA-33-4582 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-33-6738 TCGA-34-2596 
        1966          428         1970         1948          822           80 
TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 
         958          881         1000          951         1528         2062 
TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5927 TCGA-34-5928 TCGA-34-8454 
        1715          707          365          941          552          166 
TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 
         200          247          227          238          207           12 
TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 
        1454         2253         1361         1947         1996         1964 
TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 
        1849           52           59          833         1107          474 
TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 
        1084         1086          544         1964         1223          684 
TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 
         822         1007          349          376          757          310 
TCGA-43-6771 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 
        1936          212          236         1970          407          358 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56V TCGA-46-6025 TCGA-46-6026 
        1971          353          296          366          324          423 
TCGA-51-4079 TCGA-51-4081 TCGA-52-7809 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 
          12          911         1948         1958         1967          881 
TCGA-56-5897 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 
           3           62           26           30           13           30 
TCGA-56-7579 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-8504 TCGA-56-8622 
          44           26            6         1961          178           55 
TCGA-56-8625 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY 
          63           34           38            2           46           30 
TCGA-56-A4ZK TCGA-56-A5DS TCGA-58-8390 TCGA-58-8391 TCGA-58-A46J TCGA-58-A46L 
           4            8          911         2167         2589         1723 
TCGA-58-A46M TCGA-58-A46N TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 
        1072          910          311         1950         1943         1958 
TCGA-60-2707 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 
         661         1505         1963         1260          274         1731 
TCGA-60-2715 TCGA-60-2716 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 
        1075         1475          908         1092          717          816 
TCGA-60-2726 TCGA-63-6202 TCGA-63-7021 TCGA-63-7022 TCGA-66-2727 TCGA-66-2734 
         358         1973         1955         1947         1967         1311 
TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 
          61          641           30           31           61           28 
TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 
          30           30          639          762           30           61 
TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 
          31           61           61         1947          700          578 
TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2781 TCGA-66-2787 TCGA-66-2788 
        1946           61          578          121         1217          699 
TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 
        1977          913         1952         1645          122         1492 
TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I 
          83          202          211          244           96          121 
TCGA-77-6843 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 
        1941         1959         1968           15         1286         1954 
TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 
        1952         1954          479         1960         1945         1641 
TCGA-77-8133 TCGA-77-8136 TCGA-77-8139 TCGA-77-8140 TCGA-77-8145 TCGA-77-8148 
        1941         1947         1951         1962         1943          293 
TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G3 TCGA-77-A5G6 
        1684         1092           10         1953         1959         1955 
TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GF TCGA-85-6560 TCGA-85-6561 
        1963         1290         1280          839          364          395 
TCGA-85-6798 TCGA-85-7696 TCGA-85-7698 TCGA-85-7699 TCGA-85-7843 TCGA-85-8048 
          34           18           49            1           35           26 
TCGA-85-8049 TCGA-85-8052 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 
          60           16          428          513           13           11 
TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8481 
          60           55           67           54           61           21 
TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4PA 
         445          424            3          475           15         1972 
TCGA-85-A4QR TCGA-85-A50M TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 
          25           19         1967         1972         1987           24 
TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 
          13          111          758          289           89          358 
TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 
         428          244          331          269           82          106 
TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7545 
         160           70           87          356          430         1344 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-8022 
         189          211          273          183          256          224 
TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A524 TCGA-LA-A446 TCGA-NC-A5HE TCGA-NC-A5HG 
         308          222          449           36         1722         1548 
TCGA-NC-A5HI 
        1135 

  DEL PEAK 42(17Q25.3) MUTATED DEL PEAK 42(17Q25.3) WILD-TYPE 
                             1                              1 
  DEL PEAK 42(17Q25.3) MUTATED DEL PEAK 42(17Q25.3) WILD-TYPE 
                          3636                           5287 
  DEL PEAK 42(17Q25.3) MUTATED DEL PEAK 42(17Q25.3) WILD-TYPE 
                           822                            578 
[1] "1.0 - 3636.0 (822.0)" "1.0 - 5287.0 (578.0)"
[1] "hr=" "1.3"
D72V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 42(17Q25.3) MUTATED         1       16       32        0         6
  DEL PEAK 42(17Q25.3) WILD-TYPE       0       56      105        1        46
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 42(17Q25.3) MUTATED          17         11          3        0
  DEL PEAK 42(17Q25.3) WILD-TYPE        54         46         17        6
D72V3, multiclass
            clus
vv           DEL PEAK 42(17Q25.3) MUTATED DEL PEAK 42(17Q25.3) WILD-TYPE
  STAGE I                               1                              0
  STAGE IA                             16                             56
  STAGE IB                             32                            105
  STAGE II                              0                              1
  STAGE IIA                             6                             46
  STAGE IIB                            17                             54
  STAGE IIIA                           11                             46
  STAGE IIIB                            3                             17
  STAGE IV                              0                              6
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 42(17Q25.3) MUTATED    22  49  13   2
  DEL PEAK 42(17Q25.3) WILD-TYPE  76 205  35  18
D72V4, multiclass
    clus
vv   DEL PEAK 42(17Q25.3) MUTATED DEL PEAK 42(17Q25.3) WILD-TYPE
  T1                           22                             76
  T2                           49                            205
  T3                           13                             35
  T4                            2                             18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 42(17Q25.3) MUTATED    59  17   6   2
  DEL PEAK 42(17Q25.3) WILD-TYPE 202  96  29   3
D72V5, multiclass
    clus
vv   DEL PEAK 42(17Q25.3) MUTATED DEL PEAK 42(17Q25.3) WILD-TYPE
  N0                           59                            202
  N1                           17                             96
  N2                            6                             29
  N3                            2                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A  MX
  DEL PEAK 42(17Q25.3) MUTATED    75   0   0   9
  DEL PEAK 42(17Q25.3) WILD-TYPE 283   5   1  41
D72V6, multiclass
     clus
vv    DEL PEAK 42(17Q25.3) MUTATED DEL PEAK 42(17Q25.3) WILD-TYPE
  M0                            75                            283
  M1                             0                              5
  M1A                            0                              1
  MX                             9                             41
[1] 4 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 42(17Q25.3) MUTATED    20  66
  DEL PEAK 42(17Q25.3) WILD-TYPE  87 247
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(17Q25.3) MUTATED     20   66
  DEL PEAK 42(17Q25.3) WILD-TYPE   87  247
        clus
vv       DEL PEAK 42(17Q25.3) MUTATED DEL PEAK 42(17Q25.3) WILD-TYPE
  FEMALE                           20                             87
  MALE                             66                            247
[1] 2 2
[1] FALSE
D72V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 42(17Q25.3) MUTATED                                       3
  DEL PEAK 42(17Q25.3) WILD-TYPE                                     9
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 42(17Q25.3) MUTATED                                        1
  DEL PEAK 42(17Q25.3) WILD-TYPE                                      5
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 42(17Q25.3) MUTATED                                         0
  DEL PEAK 42(17Q25.3) WILD-TYPE                                       1
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 42(17Q25.3) MUTATED                                                            82
  DEL PEAK 42(17Q25.3) WILD-TYPE                                                         319
D72V9, multiclass
                                                             clus
vv                                                            DEL PEAK 42(17Q25.3) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           82
                                                             clus
vv                                                            DEL PEAK 42(17Q25.3) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            319
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V10, binary
                                cls
clus                               0   1
  DEL PEAK 42(17Q25.3) MUTATED     3  83
  DEL PEAK 42(17Q25.3) WILD-TYPE  10 324
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(17Q25.3) MUTATED      3   83
  DEL PEAK 42(17Q25.3) WILD-TYPE   10  324
     clus
vv    DEL PEAK 42(17Q25.3) MUTATED DEL PEAK 42(17Q25.3) WILD-TYPE
  NO                             3                             10
  YES                           83                            324
[1] 2 2
[1] FALSE
D72V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 42(17Q25.3) MUTATED    72   1   1   4
  DEL PEAK 42(17Q25.3) WILD-TYPE 270   7   3  14
D72V12, multiclass
    clus
vv   DEL PEAK 42(17Q25.3) MUTATED DEL PEAK 42(17Q25.3) WILD-TYPE
  R0                           72                            270
  R1                            1                              7
  R2                            1                              3
  RX                            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                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 42(17Q25.3) MUTATED       0                         5    60
  DEL PEAK 42(17Q25.3) WILD-TYPE     9                        12   238
D72V13, multiclass
                           clus
vv                          DEL PEAK 42(17Q25.3) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            5
  WHITE                                               60
                           clus
vv                          DEL PEAK 42(17Q25.3) WILD-TYPE
  ASIAN                                                  9
  BLACK OR AFRICAN AMERICAN                             12
  WHITE                                                238
[1] 3 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 42(17Q25.3) MUTATED     3  57
  DEL PEAK 42(17Q25.3) WILD-TYPE   5 210
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(17Q25.3) MUTATED      3   57
  DEL PEAK 42(17Q25.3) WILD-TYPE    5  210
                        clus
vv                       DEL PEAK 42(17Q25.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           57
                        clus
vv                       DEL PEAK 42(17Q25.3) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            210
[1] 2 2
[1] FALSE

Clustering(73) Variable = DEL PEAK 43(18Q23) MUTATION ANALYSIS
D73V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 43(18Q23) MUTATED   126  50
  DEL PEAK 43(18Q23) WILD-TYPE 139  73
  DEL PEAK 43(18Q23) MUTATED DEL PEAK 43(18Q23) WILD-TYPE 
                         176                          212 
  DEL PEAK 43(18Q23) MUTATED DEL PEAK 43(18Q23) WILD-TYPE 
                          50                           73 
$`DEL PEAK 43(18Q23) MUTATED`
TCGA-18-3412 TCGA-18-3414 TCGA-18-3416 TCGA-18-3417 TCGA-18-3421 TCGA-18-4086 
         345          396          862          758         1331           85 
TCGA-21-1070 TCGA-21-1071 TCGA-21-1079 TCGA-21-1080 TCGA-21-1083 TCGA-21-5782 
        3636         1426          965         3724          267          962 
TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-1000 TCGA-22-1016 TCGA-22-1017 
        1032          329          979         1945          822         1485 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 TCGA-22-4613 
         623         1067          734         1161         1057          358 
TCGA-22-5471 TCGA-22-5473 TCGA-22-5491 TCGA-22-5492 TCGA-33-4533 TCGA-33-4538 
         965         1933         1713          506         1940         2979 
TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4589 TCGA-33-6738 
        1311         5287         1966         1941         1948          822 
TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-5231 TCGA-34-5241 TCGA-34-8454 
         958          881         1000         1528          428          166 
TCGA-37-3792 TCGA-37-4130 TCGA-37-4133 TCGA-39-5016 TCGA-39-5027 TCGA-39-5028 
          12          247          238         2253         1849           52 
TCGA-39-5029 TCGA-39-5036 TCGA-43-2576 TCGA-43-2578 TCGA-43-3394 TCGA-43-5668 
         740         1084         1223          684          822          349 
TCGA-43-5670 TCGA-43-6770 TCGA-43-7656 TCGA-43-8116 TCGA-46-6025 TCGA-51-4079 
         849          310          212          358          324           12 
TCGA-52-7810 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-6545 TCGA-56-7221 
         923         1967          881            3           62           30 
TCGA-56-7222 TCGA-56-7223 TCGA-56-7730 TCGA-56-7822 TCGA-56-8503 TCGA-56-8624 
          13           30            6            1           41           36 
TCGA-56-8626 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BY TCGA-56-A4ZK TCGA-56-A5DR 
          17           34            2           30            4            4 
TCGA-58-A46M TCGA-60-2698 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2714 
        1072          311         1958          661         1963         1531 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2726 TCGA-66-2734 TCGA-66-2737 TCGA-66-2744 
        1297           97          358         1311           61           30 
TCGA-66-2753 TCGA-66-2758 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2768 
          31          639           30           61           31           61 
TCGA-66-2771 TCGA-66-2773 TCGA-66-2780 TCGA-66-2781 TCGA-66-2785 TCGA-66-2787 
         578         1946         1956          121           60         1217 
TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 TCGA-66-2800 TCGA-68-7755 
         699         1977          913         1645         1492           83 
TCGA-68-7757 TCGA-68-A59J TCGA-77-6842 TCGA-77-6845 TCGA-77-7141 TCGA-77-7142 
         211          104         1950         1952           15         1286 
TCGA-77-7337 TCGA-77-8130 TCGA-77-8131 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 
        1942         1945         1941         1947         1946         1951 
TCGA-77-8140 TCGA-77-8144 TCGA-77-8148 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5G1 
        1962          833          293         1092           10         1942 
TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G8 TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 
        1959         1955         1290          364          395           34 
TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 
          18           10           49           35          911           60 
TCGA-85-8049 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 
          60          428          513           13           11           13 
TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8664 
          67           54           61           61           22            3 
TCGA-85-8666 TCGA-85-A4QQ TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A53L 
         475         1960         1967         1972         1987           13 
TCGA-85-A5B5 TCGA-90-7766 TCGA-90-7769 TCGA-90-A4ED TCGA-92-7341 TCGA-92-8063 
         111          289          358          244          106          122 
TCGA-92-8064 TCGA-94-7033 TCGA-94-7943 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK 
         160           87          356          189          211          273 
TCGA-98-7454 TCGA-98-8022 TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A524 TCGA-NC-A5HE 
         256          224          308          222          449         1722 
TCGA-NC-A5HG TCGA-NC-A5HI 
        1548         1135 

$`DEL PEAK 43(18Q23) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
         370          136         2464         2417          146         1415 
TCGA-18-3415 TCGA-18-3419 TCGA-18-4083 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 
        1810           50          187         2754           92          827 
TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1081 
        3016         2134         1852         1058          474          284 
TCGA-21-1082 TCGA-21-5784 TCGA-22-0940 TCGA-22-0944 TCGA-22-1002 TCGA-22-1005 
        3644         1268          608          223          131         1952 
TCGA-22-1011 TCGA-22-1012 TCGA-22-4594 TCGA-22-4596 TCGA-22-4604 TCGA-22-4605 
          53          429         1470           17          399         1946 
TCGA-22-4607 TCGA-22-5472 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 
         587         1964          445         1346           24         1651 
TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 
        1952         1952          357          573          916         1912 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4586 TCGA-33-4587 TCGA-34-2596 TCGA-34-2600 
          29         2524          428         1970           80         1874 
TCGA-34-2609 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5927 
         951         2062         1715          707          365          941 
TCGA-34-5928 TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 TCGA-37-4132 TCGA-37-4135 
         552          120           13          200          227          207 
TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 
          12          103         1454         1361         1947         1996 
TCGA-39-5024 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5037 
        1964           59          833         1107          474         1086 
TCGA-39-5039 TCGA-39-5040 TCGA-43-2581 TCGA-43-3920 TCGA-43-6143 TCGA-43-6647 
         544         1964         1176         1007          376          757 
TCGA-43-6771 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8118 TCGA-43-A474 
        1936          236         1970          407         1971          353 
TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-6026 TCGA-51-4080 TCGA-51-4081 
         296          432          366          423           12          911 
TCGA-52-7622 TCGA-52-7809 TCGA-52-7811 TCGA-56-5898 TCGA-56-6546 TCGA-56-7579 
         541         1948         1958          555           26           44 
TCGA-56-7580 TCGA-56-7582 TCGA-56-7731 TCGA-56-8504 TCGA-56-8622 TCGA-56-8625 
          40           26         1961          178           55           63 
TCGA-56-8628 TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4ZJ TCGA-56-A5DS TCGA-58-8388 
          16           38           46           25            8          378 
TCGA-58-8390 TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46N 
         911         2167         1058         2589         1723          910 
TCGA-60-2695 TCGA-60-2696 TCGA-60-2703 TCGA-60-2704 TCGA-60-2709 TCGA-60-2710 
         642          109         1950         1943         1505         1963 
TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2715 TCGA-60-2716 TCGA-60-2721 
        1260          274         1731         1075         1475          983 
TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-63-6202 TCGA-63-7020 
         908         1092          717          816         1973         1957 
TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-66-2727 TCGA-66-2742 TCGA-66-2754 
        1955         1947         1952         1967          641           61 
TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2759 TCGA-66-2767 TCGA-66-2769 
          28           30           30          762           61         1947 
TCGA-66-2770 TCGA-66-2777 TCGA-66-2778 TCGA-66-2782 TCGA-66-2783 TCGA-66-2786 
         700           61          578         1954          759          790 
TCGA-66-2788 TCGA-66-2789 TCGA-66-2793 TCGA-66-2795 TCGA-68-7756 TCGA-68-8250 
         699         1955         1952          122          202          244 
TCGA-68-8251 TCGA-68-A59I TCGA-77-6843 TCGA-77-6844 TCGA-77-7138 TCGA-77-7139 
          96          121         1941         1942         1959         1968 
TCGA-77-7335 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 
        1954         1952         1954          479         1960         1945 
TCGA-77-8009 TCGA-77-8128 TCGA-77-8133 TCGA-77-8145 TCGA-77-8150 TCGA-77-8153 
        1641         1953         1941         1943         1961         1684 
TCGA-77-A5FZ TCGA-77-A5G7 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH 
        1953         1963         1280         1939          839          713 
TCGA-85-7699 TCGA-85-7710 TCGA-85-8048 TCGA-85-8052 TCGA-85-8070 TCGA-85-8288 
           1         1965           26           16          960           54 
TCGA-85-8350 TCGA-85-8351 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-A4CL 
          60           55           21          445          424           15 
TCGA-85-A4PA TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A513 TCGA-90-6837 
        1972           25           19         1973           24          758 
TCGA-90-7767 TCGA-90-7964 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-8065 
          89          428          331          269           82           70 
TCGA-94-A4VJ TCGA-96-7544 TCGA-96-7545 TCGA-96-A4JL TCGA-98-8021 TCGA-L3-A4E7 
         430         1213         1344          183          413           35 
TCGA-LA-A446 TCGA-MF-A522 
          36           83 

  DEL PEAK 43(18Q23) MUTATED DEL PEAK 43(18Q23) WILD-TYPE 
                           1                            1 
  DEL PEAK 43(18Q23) MUTATED DEL PEAK 43(18Q23) WILD-TYPE 
                        5287                         3644 
  DEL PEAK 43(18Q23) MUTATED DEL PEAK 43(18Q23) WILD-TYPE 
                         462                          737 
[1] "1.0 - 5287.0 (462.0)" "1.0 - 3644.0 (737.0)"
[1] "hr=" "1.1"
D73V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 43(18Q23) MUTATED         1       27       65        0        22
  DEL PEAK 43(18Q23) WILD-TYPE       0       45       72        1        30
                              vv
clus                           STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 43(18Q23) MUTATED          35         29          6        4
  DEL PEAK 43(18Q23) WILD-TYPE        36         28         14        2
D73V3, multiclass
            clus
vv           DEL PEAK 43(18Q23) MUTATED DEL PEAK 43(18Q23) WILD-TYPE
  STAGE I                             1                            0
  STAGE IA                           27                           45
  STAGE IB                           65                           72
  STAGE II                            0                            1
  STAGE IIA                          22                           30
  STAGE IIB                          35                           36
  STAGE IIIA                         29                           28
  STAGE IIIB                          6                           14
  STAGE IV                            4                            2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            T1  T2  T3  T4
  DEL PEAK 43(18Q23) MUTATED    40 115  28   8
  DEL PEAK 43(18Q23) WILD-TYPE  58 139  20  12
D73V4, multiclass
    clus
vv   DEL PEAK 43(18Q23) MUTATED DEL PEAK 43(18Q23) WILD-TYPE
  T1                         40                           58
  T2                        115                          139
  T3                         28                           20
  T4                          8                           12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            N0  N1  N2  N3
  DEL PEAK 43(18Q23) MUTATED   115  54  17   1
  DEL PEAK 43(18Q23) WILD-TYPE 146  59  18   4
D73V5, multiclass
    clus
vv   DEL PEAK 43(18Q23) MUTATED DEL PEAK 43(18Q23) WILD-TYPE
  N0                        115                          146
  N1                         54                           59
  N2                         17                           18
  N3                          1                            4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            M0  M1 M1A  MX
  DEL PEAK 43(18Q23) MUTATED   162   3   1  21
  DEL PEAK 43(18Q23) WILD-TYPE 196   2   0  29
D73V6, multiclass
     clus
vv    DEL PEAK 43(18Q23) MUTATED DEL PEAK 43(18Q23) WILD-TYPE
  M0                         162                          196
  M1                           3                            2
  M1A                          1                            0
  MX                          21                           29
[1] 4 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 43(18Q23) MUTATED    37 154
  DEL PEAK 43(18Q23) WILD-TYPE  70 159
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 43(18Q23) MUTATED     37  154
  DEL PEAK 43(18Q23) WILD-TYPE   70  159
        clus
vv       DEL PEAK 43(18Q23) MUTATED DEL PEAK 43(18Q23) WILD-TYPE
  FEMALE                         37                           70
  MALE                          154                          159
[1] 2 2
[1] FALSE
D73V8, continuous
                              vv
clus                           LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 43(18Q23) MUTATED                                       3
  DEL PEAK 43(18Q23) WILD-TYPE                                     9
                              vv
clus                           LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 43(18Q23) MUTATED                                        3
  DEL PEAK 43(18Q23) WILD-TYPE                                      3
                              vv
clus                           LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 43(18Q23) MUTATED                                         0
  DEL PEAK 43(18Q23) WILD-TYPE                                       1
                              vv
clus                           LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 43(18Q23) MUTATED                                                           185
  DEL PEAK 43(18Q23) WILD-TYPE                                                         216
D73V9, multiclass
                                                             clus
vv                                                            DEL PEAK 43(18Q23) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                               3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                              0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                        185
                                                             clus
vv                                                            DEL PEAK 43(18Q23) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          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"
D73V10, binary
                              cls
clus                             0   1
  DEL PEAK 43(18Q23) MUTATED     6 185
  DEL PEAK 43(18Q23) WILD-TYPE   7 222
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 43(18Q23) MUTATED      6  185
  DEL PEAK 43(18Q23) WILD-TYPE    7  222
     clus
vv    DEL PEAK 43(18Q23) MUTATED DEL PEAK 43(18Q23) WILD-TYPE
  NO                           6                            7
  YES                        185                          222
[1] 2 2
[1] FALSE
D73V11, continuous
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 43(18Q23) MUTATED   156   2   1  10
  DEL PEAK 43(18Q23) WILD-TYPE 186   6   3   8
D73V12, multiclass
    clus
vv   DEL PEAK 43(18Q23) MUTATED DEL PEAK 43(18Q23) WILD-TYPE
  R0                        156                          186
  R1                          2                            6
  R2                          1                            3
  RX                         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                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 43(18Q23) MUTATED       4                         9   135
  DEL PEAK 43(18Q23) WILD-TYPE     5                         8   163
D73V13, multiclass
                           clus
vv                          DEL PEAK 43(18Q23) MUTATED
  ASIAN                                              4
  BLACK OR AFRICAN AMERICAN                          9
  WHITE                                            135
                           clus
vv                          DEL PEAK 43(18Q23) WILD-TYPE
  ASIAN                                                5
  BLACK OR AFRICAN AMERICAN                            8
  WHITE                                              163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V14, binary
                              cls
clus                             0   1
  DEL PEAK 43(18Q23) MUTATED     5 122
  DEL PEAK 43(18Q23) WILD-TYPE   3 145
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 43(18Q23) MUTATED      5  122
  DEL PEAK 43(18Q23) WILD-TYPE    3  145
                        clus
vv                       DEL PEAK 43(18Q23) MUTATED
  HISPANIC OR LATINO                              5
  NOT HISPANIC OR LATINO                        122
                        clus
vv                       DEL PEAK 43(18Q23) WILD-TYPE
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          145
[1] 2 2
[1] FALSE

Clustering(74) Variable = DEL PEAK 44(19P13.3) MUTATION ANALYSIS
D74V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 44(19P13.3) MUTATED   125  57
  DEL PEAK 44(19P13.3) WILD-TYPE 140  66
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                           182                            206 
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                            57                             66 
$`DEL PEAK 44(19P13.3) MUTATED`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3411 TCGA-18-3412 TCGA-18-3417 TCGA-18-5592 
         136         2417         1415          345          758           92 
TCGA-21-1070 TCGA-21-1071 TCGA-21-1077 TCGA-21-1080 TCGA-21-1081 TCGA-21-1083 
        3636         1426         1058         3724          284          267 
TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 TCGA-22-1002 TCGA-22-1005 TCGA-22-1012 
         329          979          608          131         1952          429 
TCGA-22-4591 TCGA-22-4594 TCGA-22-4601 TCGA-22-4605 TCGA-22-4607 TCGA-22-5474 
         623         1470         1057         1946          587          445 
TCGA-22-5478 TCGA-22-5481 TCGA-22-5483 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 
          24         1952          573          506           29         2524 
TCGA-33-4547 TCGA-33-4582 TCGA-33-4586 TCGA-33-4587 TCGA-33-6738 TCGA-34-2604 
        1311         1966          428         1970          822          958 
TCGA-34-2608 TCGA-34-5241 TCGA-34-5928 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 
        1000          428          552           13           12          200 
TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 
         247          227          238          207           12          103 
TCGA-39-5011 TCGA-39-5019 TCGA-39-5021 TCGA-39-5029 TCGA-39-5034 TCGA-39-5035 
        1454         1361         1947          740         1107          474 
TCGA-39-5036 TCGA-39-5037 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-3394 
        1084         1086         1964         1223          684          822 
TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-6770 TCGA-43-7656 
        1007          349          849          376          310          212 
TCGA-43-7657 TCGA-43-8115 TCGA-43-A56V TCGA-46-6025 TCGA-51-4079 TCGA-51-4081 
         236          407          366          324           12          911 
TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 
        1948          923         1958          881            3          555 
TCGA-56-6546 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7730 TCGA-56-7822 
          26           13           30           44            6            1 
TCGA-56-8624 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR 
          36           34           38           25            4            4 
TCGA-58-8388 TCGA-58-8390 TCGA-58-8393 TCGA-58-A46L TCGA-60-2696 TCGA-60-2698 
         378          911         1058         1723          109          311 
TCGA-60-2706 TCGA-60-2707 TCGA-60-2711 TCGA-60-2714 TCGA-60-2720 TCGA-60-2722 
        1958          661         1260         1531           97          908 
TCGA-60-2723 TCGA-63-6202 TCGA-63-7020 TCGA-66-2727 TCGA-66-2734 TCGA-66-2753 
        1092         1973         1957         1967         1311           31 
TCGA-66-2754 TCGA-66-2756 TCGA-66-2758 TCGA-66-2759 TCGA-66-2766 TCGA-66-2768 
          61           30          639          762           31           61 
TCGA-66-2769 TCGA-66-2771 TCGA-66-2777 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 
        1947          578           61         1956          121         1954 
TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 
         759           60          790          699         1955          699 
TCGA-66-2793 TCGA-66-2795 TCGA-68-7756 TCGA-68-8250 TCGA-68-A59I TCGA-77-6843 
        1952          122          202          244          121         1941 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7338 TCGA-77-7463 TCGA-77-8008 TCGA-77-8009 
        1952         1959         1952         1954         1945         1641 
TCGA-77-8130 TCGA-77-8136 TCGA-77-8138 TCGA-77-8144 TCGA-77-8145 TCGA-77-8156 
        1945         1947         1946          833         1943           10 
TCGA-77-A5G1 TCGA-85-6560 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 
        1942          364           18           10           49            1 
TCGA-85-7710 TCGA-85-7843 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 
        1965           35          960          428          513           13 
TCGA-85-8277 TCGA-85-8287 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8354 
          11           13           60           55           67           61 
TCGA-85-8479 TCGA-85-8664 TCGA-85-A4CL TCGA-85-A510 TCGA-85-A53L TCGA-90-7964 
          22            3           15         1967           13          428 
TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7341 TCGA-92-8063 TCGA-92-8065 
         244          331          269          106          122           70 
TCGA-94-7033 TCGA-94-7943 TCGA-94-A4VJ TCGA-96-8169 TCGA-LA-A446 TCGA-MF-A522 
          87          356          430          189           36           83 
TCGA-NC-A5HG TCGA-NC-A5HI 
        1548         1135 

$`DEL PEAK 44(19P13.3) WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3410 TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 
         370         2464          146          396         1810          862 
TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5595 
          50         1331          187           85         2754          827 
TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1078 TCGA-21-1079 TCGA-21-1082 
        3016         2134         1852          474          965         3644 
TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-22-0944 TCGA-22-1000 TCGA-22-1011 
         962         1268         1032          223         1945           53 
TCGA-22-1016 TCGA-22-1017 TCGA-22-4593 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 
         822         1485         1067          734           17         1161 
TCGA-22-4604 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5477 
         399          358          965         1964         1933         1346 
TCGA-22-5479 TCGA-22-5480 TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 
        1651         1952          357          916         1912         1713 
TCGA-33-4533 TCGA-33-4538 TCGA-33-4566 TCGA-33-4583 TCGA-33-4589 TCGA-34-2596 
        1940         2979         5287         1941         1948           80 
TCGA-34-2600 TCGA-34-2605 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 
        1874          881          951         1528         2062         1715 
TCGA-34-5239 TCGA-34-5240 TCGA-34-5927 TCGA-34-8454 TCGA-37-3783 TCGA-39-5016 
         707          365          941          166          120         2253 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 TCGA-39-5031 
        1996         1964         1849           52           59          833 
TCGA-39-5039 TCGA-43-2581 TCGA-43-6647 TCGA-43-6771 TCGA-43-7658 TCGA-43-8116 
         544         1176          757         1936         1970          358 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-46-6026 TCGA-51-4080 
        1971          353          296          432          423           12 
TCGA-52-7622 TCGA-52-7812 TCGA-56-6545 TCGA-56-7221 TCGA-56-7580 TCGA-56-7582 
         541         1967           62           30           40           26 
TCGA-56-7731 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8625 TCGA-56-8626 
        1961           41          178           55           63           17 
TCGA-56-8628 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A5DS TCGA-58-8391 
          16            2           46           30            8         2167 
TCGA-58-A46J TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2703 TCGA-60-2704 
        2589         1072          910          642         1950         1943 
TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2712 TCGA-60-2713 TCGA-60-2715 
        1963         1505         1963          274         1731         1075 
TCGA-60-2716 TCGA-60-2719 TCGA-60-2721 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 
        1475         1297          983          717          816          358 
TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 
        1955         1947         1952           61          641           30 
TCGA-66-2755 TCGA-66-2757 TCGA-66-2763 TCGA-66-2765 TCGA-66-2767 TCGA-66-2770 
          28           30           30           61           61          700 
TCGA-66-2773 TCGA-66-2778 TCGA-66-2787 TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 
        1946          578         1217         1977          913         1645 
TCGA-66-2800 TCGA-68-7755 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59J TCGA-77-6842 
        1492           83          211           96          104         1950 
TCGA-77-6844 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 
        1942         1968           15         1286         1954         1942 
TCGA-77-7465 TCGA-77-8007 TCGA-77-8128 TCGA-77-8131 TCGA-77-8133 TCGA-77-8139 
         479         1960         1953         1941         1941         1951 
TCGA-77-8140 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-A5FZ 
        1962          293         1961         1684         1092         1953 
TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB 
        1959         1955         1963         1290         1280         1939 
TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6561 TCGA-85-6798 TCGA-85-7844 TCGA-85-7950 
         839          713          395           34          911           60 
TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8288 TCGA-85-8353 TCGA-85-8355 
          26           60           16           54           54           61 
TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8666 TCGA-85-A4PA TCGA-85-A4QQ 
          21          445          424          475         1972         1960 
TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 
          25           19         1973         1972         1987           24 
TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-92-7340 
         111          758          289           89          358           82 
TCGA-92-8064 TCGA-96-7544 TCGA-96-7545 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL 
         160         1213         1344          211          273          183 
TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A4E7 
         256          413          224          308          222           35 
TCGA-L3-A524 TCGA-NC-A5HE 
         449         1722 

  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                             1                              2 
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                          3724                           5287 
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                         437.5                          836.0 
[1] "1.0 - 3724.0 (437.5)" "2.0 - 5287.0 (836.0)"
[1] "hr=" "1.4"
D74V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 44(19P13.3) MUTATED         1       29       66        0        25
  DEL PEAK 44(19P13.3) WILD-TYPE       0       43       71        1        27
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 44(19P13.3) MUTATED          27         32          9        2
  DEL PEAK 44(19P13.3) WILD-TYPE        44         25         11        4
D74V3, multiclass
            clus
vv           DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  STAGE I                               1                              0
  STAGE IA                             29                             43
  STAGE IB                             66                             71
  STAGE II                              0                              1
  STAGE IIA                            25                             27
  STAGE IIB                            27                             44
  STAGE IIIA                           32                             25
  STAGE IIIB                            9                             11
  STAGE IV                              2                              4
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 44(19P13.3) MUTATED    45 118  21   9
  DEL PEAK 44(19P13.3) WILD-TYPE  53 136  27  11
D74V4, multiclass
    clus
vv   DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  T1                           45                             53
  T2                          118                            136
  T3                           21                             27
  T4                            9                             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 44(19P13.3) MUTATED   125  44  21   2
  DEL PEAK 44(19P13.3) WILD-TYPE 136  69  14   3
D74V5, multiclass
    clus
vv   DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  N0                          125                            136
  N1                           44                             69
  N2                           21                             14
  N3                            2                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A  MX
  DEL PEAK 44(19P13.3) MUTATED   162   2   0  26
  DEL PEAK 44(19P13.3) WILD-TYPE 196   3   1  24
D74V6, multiclass
     clus
vv    DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  M0                           162                            196
  M1                             2                              3
  M1A                            0                              1
  MX                            26                             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V7, binary
                                cls
clus                               0   1
  DEL PEAK 44(19P13.3) MUTATED    46 147
  DEL PEAK 44(19P13.3) WILD-TYPE  61 166
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(19P13.3) MUTATED     46  147
  DEL PEAK 44(19P13.3) WILD-TYPE   61  166
        clus
vv       DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  FEMALE                           46                             61
  MALE                            147                            166
[1] 2 2
[1] FALSE
D74V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 44(19P13.3) MUTATED                                       6
  DEL PEAK 44(19P13.3) WILD-TYPE                                     6
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 44(19P13.3) MUTATED                                        3
  DEL PEAK 44(19P13.3) WILD-TYPE                                      3
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 44(19P13.3) MUTATED                                         1
  DEL PEAK 44(19P13.3) WILD-TYPE                                       0
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 44(19P13.3) MUTATED                                                           183
  DEL PEAK 44(19P13.3) WILD-TYPE                                                         218
D74V9, multiclass
                                                             clus
vv                                                            DEL PEAK 44(19P13.3) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          183
                                                             clus
vv                                                            DEL PEAK 44(19P13.3) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            218
[1] 4 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 44(19P13.3) MUTATED     6 187
  DEL PEAK 44(19P13.3) WILD-TYPE   7 220
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(19P13.3) MUTATED      6  187
  DEL PEAK 44(19P13.3) WILD-TYPE    7  220
     clus
vv    DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  NO                             6                              7
  YES                          187                            220
[1] 2 2
[1] FALSE
D74V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 44(19P13.3) MUTATED   152   4   1   8
  DEL PEAK 44(19P13.3) WILD-TYPE 190   4   3  10
D74V12, multiclass
    clus
vv   DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  R0                          152                            190
  R1                            4                              4
  R2                            1                              3
  RX                            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                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 44(19P13.3) MUTATED       3                        12   133
  DEL PEAK 44(19P13.3) WILD-TYPE     6                         5   165
D74V13, multiclass
                           clus
vv                          DEL PEAK 44(19P13.3) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                           12
  WHITE                                              133
                           clus
vv                          DEL PEAK 44(19P13.3) WILD-TYPE
  ASIAN                                                  6
  BLACK OR AFRICAN AMERICAN                              5
  WHITE                                                165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V14, binary
                                cls
clus                               0   1
  DEL PEAK 44(19P13.3) MUTATED     3 128
  DEL PEAK 44(19P13.3) WILD-TYPE   5 139
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(19P13.3) MUTATED      3  128
  DEL PEAK 44(19P13.3) WILD-TYPE    5  139
                        clus
vv                       DEL PEAK 44(19P13.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          128
                        clus
vv                       DEL PEAK 44(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            139
[1] 2 2
[1] FALSE

Clustering(75) Variable = DEL PEAK 45(19Q13.32) MUTATION ANALYSIS
D75V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 45(19Q13.32) MUTATED    84  26
  DEL PEAK 45(19Q13.32) WILD-TYPE 181  97
  DEL PEAK 45(19Q13.32) MUTATED DEL PEAK 45(19Q13.32) WILD-TYPE 
                            110                             278 
  DEL PEAK 45(19Q13.32) MUTATED DEL PEAK 45(19Q13.32) WILD-TYPE 
                             26                              97 
$`DEL PEAK 45(19Q13.32) MUTATED`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 TCGA-18-3416 
         370         2417          146         1415          345          862 
TCGA-18-5592 TCGA-21-1076 TCGA-21-1077 TCGA-21-1080 TCGA-22-0944 TCGA-22-1005 
          92         1852         1058         3724          223         1952 
TCGA-22-1017 TCGA-22-4594 TCGA-22-4595 TCGA-22-4607 TCGA-22-4613 TCGA-22-5478 
        1485         1470          734          587          358           24 
TCGA-33-4532 TCGA-33-4538 TCGA-33-4586 TCGA-34-2600 TCGA-34-5241 TCGA-34-5927 
        2524         2979          428         1874          428          941 
TCGA-37-4129 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-39-5016 TCGA-39-5036 
         200          238          207           12         2253         1084 
TCGA-43-3394 TCGA-43-6770 TCGA-43-7657 TCGA-43-8116 TCGA-43-A474 TCGA-46-6026 
         822          310          236          358          353          423 
TCGA-51-4081 TCGA-52-7809 TCGA-52-7810 TCGA-56-5897 TCGA-56-7221 TCGA-56-7222 
         911         1948          923            3           30           13 
TCGA-56-7579 TCGA-56-7822 TCGA-56-8622 TCGA-56-A4BX TCGA-58-A46L TCGA-60-2695 
          44            1           55           46         1723          642 
TCGA-60-2696 TCGA-60-2698 TCGA-60-2706 TCGA-60-2707 TCGA-60-2714 TCGA-60-2719 
         109          311         1958          661         1531         1297 
TCGA-60-2726 TCGA-63-7023 TCGA-66-2727 TCGA-66-2753 TCGA-66-2766 TCGA-66-2777 
         358         1952         1967           31           31           61 
TCGA-66-2781 TCGA-66-2783 TCGA-66-2792 TCGA-66-2794 TCGA-66-2800 TCGA-68-7755 
         121          759          913         1645         1492           83 
TCGA-68-7756 TCGA-77-6845 TCGA-77-7141 TCGA-77-7142 TCGA-77-7338 TCGA-77-7463 
         202         1952           15         1286         1952         1954 
TCGA-77-8128 TCGA-77-8144 TCGA-77-8148 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 
        1953          833          293         1684         1092           10 
TCGA-77-A5G8 TCGA-77-A5GA TCGA-85-6560 TCGA-85-6561 TCGA-85-7696 TCGA-85-7697 
        1290         1280          364          395           18           10 
TCGA-85-7843 TCGA-85-7950 TCGA-85-8048 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 
          35           60           26          960          428          513 
TCGA-85-8287 TCGA-85-8351 TCGA-85-8353 TCGA-85-8355 TCGA-85-8664 TCGA-85-A4CL 
          13           55           54           61            3           15 
TCGA-85-A4QR TCGA-85-A512 TCGA-85-A53L TCGA-90-A4ED TCGA-92-7341 TCGA-94-7943 
          25         1987           13          244          106          356 
TCGA-96-7545 TCGA-96-A4JK TCGA-98-8021 TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 
        1344          273          413          449           36           83 
TCGA-NC-A5HG TCGA-NC-A5HI 
        1548         1135 

$`DEL PEAK 45(19Q13.32) WILD-TYPE`
TCGA-18-3407 TCGA-18-3408 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 
         136         2464          396         1810          758           50 
TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5595 TCGA-21-1070 
        1331          187           85         2754          827         3636 
TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1078 TCGA-21-1079 TCGA-21-1081 
        1426         3016         2134          474          965          284 
TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 
        3644          267          962         1268         1032          329 
TCGA-21-A5DI TCGA-22-0940 TCGA-22-1000 TCGA-22-1002 TCGA-22-1011 TCGA-22-1012 
         979          608         1945          131           53          429 
TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 
         822          623         1067           17         1161         1057 
TCGA-22-4604 TCGA-22-4605 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 
         399         1946          965         1964         1933          445 
TCGA-22-5477 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 
        1346         1651         1952         1952          357          573 
TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4533 
         916         1912         1713          506           29         1940 
TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4587 TCGA-33-4589 
        1311         5287         1966         1941         1970         1948 
TCGA-33-6738 TCGA-34-2596 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 
         822           80          958          881         1000          951 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5928 
        1528         2062         1715          707          365          552 
TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4130 TCGA-37-4132 
         166          120           13           12          247          227 
TCGA-37-5819 TCGA-39-5011 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 
         103         1454         1361         1947         1996         1964 
TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 
        1849           52          740           59          833         1107 
TCGA-39-5035 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 
         474         1086          544         1964         1223          684 
TCGA-43-2581 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 
        1176         1007          349          849          376          757 
TCGA-43-6771 TCGA-43-7656 TCGA-43-7658 TCGA-43-8115 TCGA-43-8118 TCGA-43-A475 
        1936          212         1970          407         1971          296 
TCGA-43-A56U TCGA-43-A56V TCGA-46-6025 TCGA-51-4079 TCGA-51-4080 TCGA-52-7622 
         432          366          324           12           12          541 
TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 
        1958         1967          881          555           62           26 
TCGA-56-7223 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-8503 
          30           40           26            6         1961           41 
TCGA-56-8504 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 
         178           36           63           17           16           34 
TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR 
          38            2           30           25            4            4 
TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J 
           8          378          911         2167         1058         2589 
TCGA-58-A46M TCGA-58-A46N TCGA-60-2703 TCGA-60-2704 TCGA-60-2708 TCGA-60-2709 
        1072          910         1950         1943         1963         1505 
TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2715 TCGA-60-2716 
        1963         1260          274         1731         1075         1475 
TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 
          97          983          908         1092          717          816 
TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-66-2734 TCGA-66-2737 
        1973         1957         1955         1947         1311           61 
TCGA-66-2742 TCGA-66-2744 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 
         641           30           61           28           30           30 
TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2767 TCGA-66-2768 
         639          762           30           61           61           61 
TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2778 TCGA-66-2780 
        1947          700          578         1946          578         1956 
TCGA-66-2782 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 
        1954           60          790         1217          699         1955 
TCGA-66-2790 TCGA-66-2791 TCGA-66-2793 TCGA-66-2795 TCGA-68-7757 TCGA-68-8250 
         699         1977         1952          122          211          244 
TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 
          96          121          104         1950         1941         1942 
TCGA-77-7138 TCGA-77-7139 TCGA-77-7335 TCGA-77-7337 TCGA-77-7465 TCGA-77-8007 
        1959         1968         1954         1942          479         1960 
TCGA-77-8008 TCGA-77-8009 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 
        1945         1641         1945         1941         1941         1947 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8145 TCGA-77-8150 TCGA-77-A5FZ 
        1946         1951         1962         1943         1961         1953 
TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5GB TCGA-77-A5GF 
        1942         1959         1955         1963         1939          839 
TCGA-77-A5GH TCGA-85-6798 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7844 
         713           34           49            1         1965          911 
TCGA-85-8049 TCGA-85-8052 TCGA-85-8276 TCGA-85-8277 TCGA-85-8288 TCGA-85-8350 
          60           16           13           11           54           60 
TCGA-85-8352 TCGA-85-8354 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 
          67           61           22           21          445          424 
TCGA-85-8666 TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 
         475         1972         1960           19         1973         1967 
TCGA-85-A511 TCGA-85-A513 TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 
        1972           24          111          758          289           89 
TCGA-90-7769 TCGA-90-7964 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-8063 
         358          428          331          269           82          122 
TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8169 
         160           70           87          430         1213          189 
TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8022 TCGA-98-8023 TCGA-J1-A4AH 
         211          183          256          224          308          222 
TCGA-L3-A4E7 TCGA-NC-A5HE 
          35         1722 

  DEL PEAK 45(19Q13.32) MUTATED DEL PEAK 45(19Q13.32) WILD-TYPE 
                              1                               1 
  DEL PEAK 45(19Q13.32) MUTATED DEL PEAK 45(19Q13.32) WILD-TYPE 
                           3724                            5287 
  DEL PEAK 45(19Q13.32) MUTATED DEL PEAK 45(19Q13.32) WILD-TYPE 
                          404.0                           748.5 
[1] "1.0 - 3724.0 (404.0)" "1.0 - 5287.0 (748.5)"
[1] "hr=" "1.1"
D75V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 45(19Q13.32) MUTATED         0       22       41        1        17
  DEL PEAK 45(19Q13.32) WILD-TYPE       1       50       96        0        35
                                 vv
clus                              STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 45(19Q13.32) MUTATED          16         15          5        1
  DEL PEAK 45(19Q13.32) WILD-TYPE        55         42         15        5
D75V3, multiclass
            clus
vv           DEL PEAK 45(19Q13.32) MUTATED DEL PEAK 45(19Q13.32) WILD-TYPE
  STAGE I                                0                               1
  STAGE IA                              22                              50
  STAGE IB                              41                              96
  STAGE II                               1                               0
  STAGE IIA                             17                              35
  STAGE IIB                             16                              55
  STAGE IIIA                            15                              42
  STAGE IIIB                             5                              15
  STAGE IV                               1                               5
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  DEL PEAK 45(19Q13.32) MUTATED    30  72  14   5
  DEL PEAK 45(19Q13.32) WILD-TYPE  68 182  34  15
D75V4, multiclass
    clus
vv   DEL PEAK 45(19Q13.32) MUTATED DEL PEAK 45(19Q13.32) WILD-TYPE
  T1                            30                              68
  T2                            72                             182
  T3                            14                              34
  T4                             5                              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 45(19Q13.32) MUTATED    81  25  11   1
  DEL PEAK 45(19Q13.32) WILD-TYPE 180  88  24   4
D75V5, multiclass
    clus
vv   DEL PEAK 45(19Q13.32) MUTATED DEL PEAK 45(19Q13.32) WILD-TYPE
  N0                            81                             180
  N1                            25                              88
  N2                            11                              24
  N3                             1                               4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               M0  M1 M1A  MX
  DEL PEAK 45(19Q13.32) MUTATED   106   1   0  11
  DEL PEAK 45(19Q13.32) WILD-TYPE 252   4   1  39
D75V6, multiclass
     clus
vv    DEL PEAK 45(19Q13.32) MUTATED DEL PEAK 45(19Q13.32) WILD-TYPE
  M0                            106                             252
  M1                              1                               4
  M1A                             0                               1
  MX                             11                              39
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V7, binary
                                 cls
clus                                0   1
  DEL PEAK 45(19Q13.32) MUTATED    23  98
  DEL PEAK 45(19Q13.32) WILD-TYPE  84 215
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 45(19Q13.32) MUTATED     23   98
  DEL PEAK 45(19Q13.32) WILD-TYPE   84  215
        clus
vv       DEL PEAK 45(19Q13.32) MUTATED DEL PEAK 45(19Q13.32) WILD-TYPE
  FEMALE                            23                              84
  MALE                              98                             215
[1] 2 2
[1] FALSE
D75V8, continuous
                                 vv
clus                              LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 45(19Q13.32) MUTATED                                       6
  DEL PEAK 45(19Q13.32) WILD-TYPE                                     6
                                 vv
clus                              LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 45(19Q13.32) MUTATED                                        2
  DEL PEAK 45(19Q13.32) WILD-TYPE                                      4
                                 vv
clus                              LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 45(19Q13.32) MUTATED                                         0
  DEL PEAK 45(19Q13.32) WILD-TYPE                                       1
                                 vv
clus                              LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 45(19Q13.32) MUTATED                                                           113
  DEL PEAK 45(19Q13.32) WILD-TYPE                                                         288
D75V9, multiclass
                                                             clus
vv                                                            DEL PEAK 45(19Q13.32) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           113
                                                             clus
vv                                                            DEL PEAK 45(19Q13.32) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                     6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                    4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             288
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V10, binary
                                 cls
clus                                0   1
  DEL PEAK 45(19Q13.32) MUTATED     5 116
  DEL PEAK 45(19Q13.32) WILD-TYPE   8 291
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 45(19Q13.32) MUTATED      5  116
  DEL PEAK 45(19Q13.32) WILD-TYPE    8  291
     clus
vv    DEL PEAK 45(19Q13.32) MUTATED DEL PEAK 45(19Q13.32) WILD-TYPE
  NO                              5                               8
  YES                           116                             291
[1] 2 2
[1] FALSE
D75V11, continuous
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 45(19Q13.32) MUTATED    92   2   2   7
  DEL PEAK 45(19Q13.32) WILD-TYPE 250   6   2  11
D75V12, multiclass
    clus
vv   DEL PEAK 45(19Q13.32) MUTATED DEL PEAK 45(19Q13.32) WILD-TYPE
  R0                            92                             250
  R1                             2                               6
  R2                             2                               2
  RX                             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                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 45(19Q13.32) MUTATED       2                         5    84
  DEL PEAK 45(19Q13.32) WILD-TYPE     7                        12   214
D75V13, multiclass
                           clus
vv                          DEL PEAK 45(19Q13.32) MUTATED
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             5
  WHITE                                                84
                           clus
vv                          DEL PEAK 45(19Q13.32) WILD-TYPE
  ASIAN                                                   7
  BLACK OR AFRICAN AMERICAN                              12
  WHITE                                                 214
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V14, binary
                                 cls
clus                                0   1
  DEL PEAK 45(19Q13.32) MUTATED     2  75
  DEL PEAK 45(19Q13.32) WILD-TYPE   6 192
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 45(19Q13.32) MUTATED      2   75
  DEL PEAK 45(19Q13.32) WILD-TYPE    6  192
                        clus
vv                       DEL PEAK 45(19Q13.32) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            75
                        clus
vv                       DEL PEAK 45(19Q13.32) WILD-TYPE
  HISPANIC OR LATINO                                   6
  NOT HISPANIC OR LATINO                             192
[1] 2 2
[1] FALSE

Clustering(76) Variable = DEL PEAK 46(21Q11.2) MUTATION ANALYSIS
D76V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 46(21Q11.2) MUTATED   125  60
  DEL PEAK 46(21Q11.2) WILD-TYPE 140  63
  DEL PEAK 46(21Q11.2) MUTATED DEL PEAK 46(21Q11.2) WILD-TYPE 
                           185                            203 
  DEL PEAK 46(21Q11.2) MUTATED DEL PEAK 46(21Q11.2) WILD-TYPE 
                            60                             63 
$`DEL PEAK 46(21Q11.2) MUTATED`
TCGA-18-3408 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-4721 
        2464          345          396         1810          862         2754 
TCGA-21-1070 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1079 TCGA-21-1083 
        3636         3016         2134         1852          965          267 
TCGA-21-5786 TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 TCGA-22-1002 TCGA-22-1012 
        1032          329          608          223          131          429 
TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4599 
         822         1485          623         1067         1470         1161 
TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 
         358         1933          445         1346           24         1651 
TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5491 TCGA-22-A5C4 
        1952         1952          357          573         1713           29 
TCGA-33-4532 TCGA-33-4538 TCGA-33-4547 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 
        2524         2979         1311          428         1970         1948 
TCGA-34-2596 TCGA-34-2604 TCGA-34-5231 TCGA-34-5234 TCGA-34-5927 TCGA-34-5928 
          80          958         1528         1715          941          552 
TCGA-37-3792 TCGA-37-4130 TCGA-37-5819 TCGA-39-5016 TCGA-39-5019 TCGA-39-5029 
          12          247          103         2253         1361          740 
TCGA-39-5031 TCGA-39-5034 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-43-3920 
         833         1107         1084         1086          544         1007 
TCGA-43-5668 TCGA-43-6647 TCGA-43-6771 TCGA-43-7656 TCGA-43-A56V TCGA-46-6026 
         349          757         1936          212          366          423 
TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-56-5897 
          12          911          541         1948          923            3 
TCGA-56-5898 TCGA-56-6546 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 
         555           26           13           30           44           40 
TCGA-56-7582 TCGA-56-7822 TCGA-56-8503 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BX 
          26            1           41           34           38           46 
TCGA-56-A4ZJ TCGA-58-8388 TCGA-58-8390 TCGA-60-2703 TCGA-60-2707 TCGA-60-2711 
          25          378          911         1950          661         1260 
TCGA-60-2712 TCGA-60-2715 TCGA-60-2719 TCGA-60-2721 TCGA-60-2723 TCGA-60-2725 
         274         1075         1297          983         1092          816 
TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7023 TCGA-66-2734 
         358         1973         1957         1955         1952         1311 
TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 
         641           30           31           61           28           30 
TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2771 
         639          762           30           61           31          578 
TCGA-66-2777 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2786 TCGA-66-2788 
          61         1956          121         1954          790          699 
TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2795 TCGA-68-7755 TCGA-68-7756 
        1977          913         1952          122           83          202 
TCGA-68-8250 TCGA-68-8251 TCGA-77-6842 TCGA-77-7138 TCGA-77-7335 TCGA-77-7463 
         244           96         1950         1959         1954         1954 
TCGA-77-7465 TCGA-77-8008 TCGA-77-8128 TCGA-77-8136 TCGA-77-8140 TCGA-77-8145 
         479         1945         1953         1947         1962         1943 
TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5G3 
         293         1961         1684         1092           10         1959 
TCGA-77-A5G6 TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 TCGA-85-6798 TCGA-85-7696 
        1955          839          713          364           34           18 
TCGA-85-7698 TCGA-85-7843 TCGA-85-8048 TCGA-85-8070 TCGA-85-8071 TCGA-85-8276 
          49           35           26          960          428           13 
TCGA-85-8287 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8354 TCGA-85-8355 
          13           60           55           67           61           61 
TCGA-85-8481 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4QR TCGA-85-A50Z 
          21            3          475           15           25         1973 
TCGA-85-A510 TCGA-85-A511 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7766 TCGA-90-7767 
        1967         1972           13          111          289           89 
TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE TCGA-92-7341 TCGA-92-8064 TCGA-94-7943 
         358          244          331          106          160          356 
TCGA-96-A4JK TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-L3-A524 
         273          413          224          308          449 

$`DEL PEAK 46(21Q11.2) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3417 
         370          136         2417          146         1415          758 
TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-5592 TCGA-18-5595 
          50         1331          187           85           92          827 
TCGA-21-1071 TCGA-21-1077 TCGA-21-1078 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 
        1426         1058          474         3724          284         3644 
TCGA-21-5782 TCGA-21-5784 TCGA-21-A5DI TCGA-22-1000 TCGA-22-1005 TCGA-22-1011 
         962         1268          979         1945         1952           53 
TCGA-22-4595 TCGA-22-4596 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 
         734           17         1057          399         1946          587 
TCGA-22-5471 TCGA-22-5472 TCGA-22-5485 TCGA-22-5489 TCGA-22-5492 TCGA-33-4533 
         965         1964          916         1912          506         1940 
TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-6738 TCGA-34-2600 TCGA-34-2605 
        5287         1966         1941          822         1874          881 
TCGA-34-2608 TCGA-34-2609 TCGA-34-5232 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 
        1000          951         2062          707          365          428 
TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 TCGA-37-4132 TCGA-37-4133 
         166          120           13          200          227          238 
TCGA-37-4135 TCGA-37-4141 TCGA-39-5011 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 
         207           12         1454         1947         1996         1964 
TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 TCGA-39-5035 TCGA-39-5040 TCGA-43-2576 
        1849           52           59          474         1964         1223 
TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 TCGA-43-5670 TCGA-43-6143 TCGA-43-6770 
         684         1176          822          849          376          310 
TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 
         236         1970          407          358         1971          353 
TCGA-43-A475 TCGA-43-A56U TCGA-46-6025 TCGA-51-4079 TCGA-52-7811 TCGA-52-7812 
         296          432          324           12         1958         1967 
TCGA-56-1622 TCGA-56-6545 TCGA-56-7221 TCGA-56-7730 TCGA-56-7731 TCGA-56-8504 
         881           62           30            6         1961          178 
TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-A4BW 
          55           36           63           17           16            2 
TCGA-56-A4BY TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8391 TCGA-58-8393 
          30            4            4            8         2167         1058 
TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2696 
        2589         1723         1072          910          642          109 
TCGA-60-2698 TCGA-60-2704 TCGA-60-2706 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 
         311         1943         1958         1963         1505         1963 
TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 TCGA-60-2720 TCGA-60-2722 TCGA-60-2724 
        1731         1531         1475           97          908          717 
TCGA-63-7022 TCGA-66-2727 TCGA-66-2737 TCGA-66-2756 TCGA-66-2767 TCGA-66-2768 
        1947         1967           61           30           61           61 
TCGA-66-2769 TCGA-66-2770 TCGA-66-2773 TCGA-66-2778 TCGA-66-2783 TCGA-66-2785 
        1947          700         1946          578          759           60 
TCGA-66-2787 TCGA-66-2789 TCGA-66-2790 TCGA-66-2794 TCGA-66-2800 TCGA-68-7757 
        1217         1955          699         1645         1492          211 
TCGA-68-A59I TCGA-68-A59J TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7139 
         121          104         1941         1942         1952         1968 
TCGA-77-7141 TCGA-77-7142 TCGA-77-7337 TCGA-77-7338 TCGA-77-8007 TCGA-77-8009 
          15         1286         1942         1952         1960         1641 
TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8138 TCGA-77-8139 TCGA-77-8144 
        1945         1941         1941         1946         1951          833 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB 
        1953         1942         1963         1290         1280         1939 
TCGA-85-6561 TCGA-85-7697 TCGA-85-7699 TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 
         395           10            1         1965          911           60 
TCGA-85-8049 TCGA-85-8052 TCGA-85-8072 TCGA-85-8277 TCGA-85-8288 TCGA-85-8353 
          60           16          513           11           54           54 
TCGA-85-8479 TCGA-85-8580 TCGA-85-8582 TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M 
          22          445          424         1972         1960           19 
TCGA-85-A512 TCGA-85-A513 TCGA-90-6837 TCGA-90-7964 TCGA-90-A59Q TCGA-92-7340 
        1987           24          758          428          269           82 
TCGA-92-8063 TCGA-92-8065 TCGA-94-7033 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-7545 
         122           70           87          430         1213         1344 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-J1-A4AH TCGA-L3-A4E7 
         189          211          183          256          222           35 
TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HI 
          36           83         1722         1548         1135 

  DEL PEAK 46(21Q11.2) MUTATED DEL PEAK 46(21Q11.2) WILD-TYPE 
                             1                              1 
  DEL PEAK 46(21Q11.2) MUTATED DEL PEAK 46(21Q11.2) WILD-TYPE 
                          3636                           5287 
  DEL PEAK 46(21Q11.2) MUTATED DEL PEAK 46(21Q11.2) WILD-TYPE 
                           552                            758 
[1] "1.0 - 3636.0 (552.0)" "1.0 - 5287.0 (758.0)"
[1] "hr=" "1.2"
D76V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 46(21Q11.2) MUTATED         0       36       63        1        29
  DEL PEAK 46(21Q11.2) WILD-TYPE       1       36       74        0        23
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 46(21Q11.2) MUTATED          34         26          7        4
  DEL PEAK 46(21Q11.2) WILD-TYPE        37         31         13        2
D76V3, multiclass
            clus
vv           DEL PEAK 46(21Q11.2) MUTATED DEL PEAK 46(21Q11.2) WILD-TYPE
  STAGE I                               0                              1
  STAGE IA                             36                             36
  STAGE IB                             63                             74
  STAGE II                              1                              0
  STAGE IIA                            29                             23
  STAGE IIB                            34                             37
  STAGE IIIA                           26                             31
  STAGE IIIB                            7                             13
  STAGE IV                              4                              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 46(21Q11.2) MUTATED    49 121  22   9
  DEL PEAK 46(21Q11.2) WILD-TYPE  49 133  26  11
D76V4, multiclass
    clus
vv   DEL PEAK 46(21Q11.2) MUTATED DEL PEAK 46(21Q11.2) WILD-TYPE
  T1                           49                             49
  T2                          121                            133
  T3                           22                             26
  T4                            9                             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 46(21Q11.2) MUTATED   122  60  16   1
  DEL PEAK 46(21Q11.2) WILD-TYPE 139  53  19   4
D76V5, multiclass
    clus
vv   DEL PEAK 46(21Q11.2) MUTATED DEL PEAK 46(21Q11.2) WILD-TYPE
  N0                          122                            139
  N1                           60                             53
  N2                           16                             19
  N3                            1                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A  MX
  DEL PEAK 46(21Q11.2) MUTATED   175   3   1  20
  DEL PEAK 46(21Q11.2) WILD-TYPE 183   2   0  30
D76V6, multiclass
     clus
vv    DEL PEAK 46(21Q11.2) MUTATED DEL PEAK 46(21Q11.2) WILD-TYPE
  M0                           175                            183
  M1                             3                              2
  M1A                            1                              0
  MX                            20                             30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V7, binary
                                cls
clus                               0   1
  DEL PEAK 46(21Q11.2) MUTATED    42 159
  DEL PEAK 46(21Q11.2) WILD-TYPE  65 154
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 46(21Q11.2) MUTATED     42  159
  DEL PEAK 46(21Q11.2) WILD-TYPE   65  154
        clus
vv       DEL PEAK 46(21Q11.2) MUTATED DEL PEAK 46(21Q11.2) WILD-TYPE
  FEMALE                           42                             65
  MALE                            159                            154
[1] 2 2
[1] FALSE
D76V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 46(21Q11.2) MUTATED                                       4
  DEL PEAK 46(21Q11.2) WILD-TYPE                                     8
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 46(21Q11.2) MUTATED                                        2
  DEL PEAK 46(21Q11.2) WILD-TYPE                                      4
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 46(21Q11.2) MUTATED                                         1
  DEL PEAK 46(21Q11.2) WILD-TYPE                                       0
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 46(21Q11.2) MUTATED                                                           194
  DEL PEAK 46(21Q11.2) WILD-TYPE                                                         207
D76V9, multiclass
                                                             clus
vv                                                            DEL PEAK 46(21Q11.2) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          194
                                                             clus
vv                                                            DEL PEAK 46(21Q11.2) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            207
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V10, binary
                                cls
clus                               0   1
  DEL PEAK 46(21Q11.2) MUTATED     4 197
  DEL PEAK 46(21Q11.2) WILD-TYPE   9 210
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 46(21Q11.2) MUTATED      4  197
  DEL PEAK 46(21Q11.2) WILD-TYPE    9  210
     clus
vv    DEL PEAK 46(21Q11.2) MUTATED DEL PEAK 46(21Q11.2) WILD-TYPE
  NO                             4                              9
  YES                          197                            210
[1] 2 2
[1] FALSE
D76V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 46(21Q11.2) MUTATED   169   3   1   7
  DEL PEAK 46(21Q11.2) WILD-TYPE 173   5   3  11
D76V12, multiclass
    clus
vv   DEL PEAK 46(21Q11.2) MUTATED DEL PEAK 46(21Q11.2) WILD-TYPE
  R0                          169                            173
  R1                            3                              5
  R2                            1                              3
  RX                            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                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 46(21Q11.2) MUTATED       3                         7   139
  DEL PEAK 46(21Q11.2) WILD-TYPE     6                        10   159
D76V13, multiclass
                           clus
vv                          DEL PEAK 46(21Q11.2) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            7
  WHITE                                              139
                           clus
vv                          DEL PEAK 46(21Q11.2) WILD-TYPE
  ASIAN                                                  6
  BLACK OR AFRICAN AMERICAN                             10
  WHITE                                                159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V14, binary
                                cls
clus                               0   1
  DEL PEAK 46(21Q11.2) MUTATED     6 122
  DEL PEAK 46(21Q11.2) WILD-TYPE   2 145
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 46(21Q11.2) MUTATED      6  122
  DEL PEAK 46(21Q11.2) WILD-TYPE    2  145
                        clus
vv                       DEL PEAK 46(21Q11.2) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          122
                        clus
vv                       DEL PEAK 46(21Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            145
[1] 2 2
[1] FALSE

Clustering(77) Variable = DEL PEAK 47(21Q22.3) MUTATION ANALYSIS
D77V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 47(21Q22.3) MUTATED   150  67
  DEL PEAK 47(21Q22.3) WILD-TYPE 115  56
  DEL PEAK 47(21Q22.3) MUTATED DEL PEAK 47(21Q22.3) WILD-TYPE 
                           217                            171 
  DEL PEAK 47(21Q22.3) MUTATED DEL PEAK 47(21Q22.3) WILD-TYPE 
                            67                             56 
$`DEL PEAK 47(21Q22.3) MUTATED`
TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 
        2464         1415          345          396         1810          862 
TCGA-18-3417 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-21-1070 TCGA-21-1072 
         758          187           85         2754         3636         3016 
TCGA-21-1075 TCGA-21-1076 TCGA-21-1079 TCGA-21-1083 TCGA-21-5786 TCGA-21-5787 
        2134         1852          965          267         1032          329 
TCGA-22-0944 TCGA-22-1002 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 
         223          131          429          822         1485          623 
TCGA-22-4593 TCGA-22-4594 TCGA-22-4599 TCGA-22-4604 TCGA-22-4613 TCGA-22-5471 
        1067         1470         1161          399          358          965 
TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 
        1933          445         1346           24         1651         1952 
TCGA-22-5482 TCGA-22-5483 TCGA-22-5491 TCGA-22-5492 TCGA-33-4532 TCGA-33-4538 
         357          573         1713          506         2524         2979 
TCGA-33-4547 TCGA-33-4582 TCGA-33-4586 TCGA-33-4589 TCGA-34-2604 TCGA-34-2605 
        1311         1966          428         1948          958          881 
TCGA-34-2608 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-37-3789 TCGA-37-3792 
        1000          428          941          552           13           12 
TCGA-37-4130 TCGA-37-4133 TCGA-37-4135 TCGA-37-5819 TCGA-39-5016 TCGA-39-5019 
         247          238          207          103         2253         1361 
TCGA-39-5027 TCGA-39-5029 TCGA-39-5031 TCGA-39-5034 TCGA-39-5036 TCGA-39-5037 
        1849          740          833         1107         1084         1086 
TCGA-39-5039 TCGA-43-2576 TCGA-43-2578 TCGA-43-3920 TCGA-43-5668 TCGA-43-6647 
         544         1223          684         1007          349          757 
TCGA-43-6771 TCGA-43-7656 TCGA-43-7657 TCGA-43-8116 TCGA-43-8118 TCGA-43-A56V 
        1936          212          236          358         1971          366 
TCGA-46-6025 TCGA-46-6026 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 
         324          423           12          911          541         1948 
TCGA-52-7810 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 
         923          881            3          555           62           26 
TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 
          13           30           44           40           26            6 
TCGA-56-7822 TCGA-56-8503 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX 
           1           41           34           38            2           46 
TCGA-56-A4ZJ TCGA-58-8388 TCGA-58-8390 TCGA-60-2698 TCGA-60-2703 TCGA-60-2707 
          25          378          911          311         1950          661 
TCGA-60-2708 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2715 TCGA-60-2719 
        1963         1260          274         1731         1075         1297 
TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 
         983          908         1092          816          358         1973 
TCGA-63-7020 TCGA-63-7021 TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 TCGA-66-2742 
        1957         1955         1952         1967         1311          641 
TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 
          31           61           28          639          762           30 
TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2769 TCGA-66-2771 TCGA-66-2777 
          61           31           61         1947          578           61 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 
        1956          121         1954           60          790         1217 
TCGA-66-2788 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2795 
         699          699         1977          913         1952          122 
TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-8250 TCGA-68-8251 TCGA-77-6842 
        1492           83          202          244           96         1950 
TCGA-77-7141 TCGA-77-7335 TCGA-77-7463 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 
          15         1954         1954         1945         1641         1953 
TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 
        1943          293         1961         1684         1092           10 
TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6561 
        1959         1955         1963          839          713          395 
TCGA-85-6798 TCGA-85-7696 TCGA-85-7698 TCGA-85-7843 TCGA-85-8048 TCGA-85-8049 
          34           18           49           35           26           60 
TCGA-85-8070 TCGA-85-8071 TCGA-85-8276 TCGA-85-8287 TCGA-85-8350 TCGA-85-8351 
         960          428           13           13           60           55 
TCGA-85-8352 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8664 
          67           61           61           22           21            3 
TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 
         475           15           25         1973         1967         1972 
TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7766 TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE 
          13          111          289          358          244          331 
TCGA-92-7341 TCGA-92-8064 TCGA-94-7033 TCGA-94-7943 TCGA-94-A4VJ TCGA-96-A4JK 
         106          160           87          356          430          273 
TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 
         413          224          308           35          449           36 
TCGA-NC-A5HE 
        1722 

$`DEL PEAK 47(21Q22.3) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3419 TCGA-18-3421 
         370          136         2417          146           50         1331 
TCGA-18-5592 TCGA-18-5595 TCGA-21-1071 TCGA-21-1077 TCGA-21-1078 TCGA-21-1080 
          92          827         1426         1058          474         3724 
TCGA-21-1081 TCGA-21-1082 TCGA-21-5782 TCGA-21-5784 TCGA-21-A5DI TCGA-22-0940 
         284         3644          962         1268          979          608 
TCGA-22-1000 TCGA-22-1005 TCGA-22-1011 TCGA-22-4595 TCGA-22-4596 TCGA-22-4601 
        1945         1952           53          734           17         1057 
TCGA-22-4605 TCGA-22-4607 TCGA-22-5472 TCGA-22-5481 TCGA-22-5485 TCGA-22-5489 
        1946          587         1964         1952          916         1912 
TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4566 TCGA-33-4583 TCGA-33-4587 TCGA-33-6738 
          29         1940         5287         1941         1970          822 
TCGA-34-2596 TCGA-34-2600 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 
          80         1874          951         1528         2062         1715 
TCGA-34-5239 TCGA-34-5240 TCGA-34-8454 TCGA-37-3783 TCGA-37-4129 TCGA-37-4132 
         707          365          166          120          200          227 
TCGA-37-4141 TCGA-39-5011 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 
          12         1454         1947         1996         1964           52 
TCGA-39-5030 TCGA-39-5035 TCGA-39-5040 TCGA-43-2581 TCGA-43-3394 TCGA-43-5670 
          59          474         1964         1176          822          849 
TCGA-43-6143 TCGA-43-6770 TCGA-43-7658 TCGA-43-8115 TCGA-43-A474 TCGA-43-A475 
         376          310         1970          407          353          296 
TCGA-43-A56U TCGA-51-4079 TCGA-52-7811 TCGA-52-7812 TCGA-56-7221 TCGA-56-7731 
         432           12         1958         1967           30         1961 
TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 
         178           55           36           63           17           16 
TCGA-56-A4BY TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8391 TCGA-58-8393 
          30            4            4            8         2167         1058 
TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2696 
        2589         1723         1072          910          642          109 
TCGA-60-2704 TCGA-60-2706 TCGA-60-2709 TCGA-60-2710 TCGA-60-2714 TCGA-60-2716 
        1943         1958         1505         1963         1531         1475 
TCGA-60-2720 TCGA-60-2724 TCGA-63-7022 TCGA-66-2737 TCGA-66-2744 TCGA-66-2756 
          97          717         1947           61           30           30 
TCGA-66-2757 TCGA-66-2768 TCGA-66-2770 TCGA-66-2773 TCGA-66-2778 TCGA-66-2783 
          30           61          700         1946          578          759 
TCGA-66-2789 TCGA-66-2794 TCGA-68-7757 TCGA-68-A59I TCGA-68-A59J TCGA-77-6843 
        1955         1645          211          121          104         1941 
TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7142 TCGA-77-7337 
        1942         1952         1959         1968         1286         1942 
TCGA-77-7338 TCGA-77-7465 TCGA-77-8007 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 
        1952          479         1960         1945         1941         1941 
TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-A5FZ 
        1947         1946         1951         1962          833         1953 
TCGA-77-A5G1 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-85-6560 TCGA-85-7697 
        1942         1290         1280         1939          364           10 
TCGA-85-7699 TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 TCGA-85-8052 TCGA-85-8072 
           1         1965          911           60           16          513 
TCGA-85-8277 TCGA-85-8288 TCGA-85-8353 TCGA-85-8580 TCGA-85-8582 TCGA-85-A4PA 
          11           54           54          445          424         1972 
TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A512 TCGA-85-A513 TCGA-90-6837 TCGA-90-7767 
        1960           19         1987           24          758           89 
TCGA-90-7964 TCGA-90-A59Q TCGA-92-7340 TCGA-92-8063 TCGA-92-8065 TCGA-96-7544 
         428          269           82          122           70         1213 
TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-J1-A4AH 
        1344          189          211          183          256          222 
TCGA-MF-A522 TCGA-NC-A5HG TCGA-NC-A5HI 
          83         1548         1135 

  DEL PEAK 47(21Q22.3) MUTATED DEL PEAK 47(21Q22.3) WILD-TYPE 
                             1                              1 
  DEL PEAK 47(21Q22.3) MUTATED DEL PEAK 47(21Q22.3) WILD-TYPE 
                          3636                           5287 
  DEL PEAK 47(21Q22.3) MUTATED DEL PEAK 47(21Q22.3) WILD-TYPE 
                           541                            822 
[1] "1.0 - 3636.0 (541.0)" "1.0 - 5287.0 (822.0)"
[1] "hr=" "1.2"
D77V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 47(21Q22.3) MUTATED         0       44       79        1        28
  DEL PEAK 47(21Q22.3) WILD-TYPE       1       28       58        0        24
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 47(21Q22.3) MUTATED          36         28         13        5
  DEL PEAK 47(21Q22.3) WILD-TYPE        35         29          7        1
D77V3, multiclass
            clus
vv           DEL PEAK 47(21Q22.3) MUTATED DEL PEAK 47(21Q22.3) WILD-TYPE
  STAGE I                               0                              1
  STAGE IA                             44                             28
  STAGE IB                             79                             58
  STAGE II                              1                              0
  STAGE IIA                            28                             24
  STAGE IIB                            36                             35
  STAGE IIIA                           28                             29
  STAGE IIIB                           13                              7
  STAGE IV                              5                              1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 47(21Q22.3) MUTATED    55 145  22  13
  DEL PEAK 47(21Q22.3) WILD-TYPE  43 109  26   7
D77V4, multiclass
    clus
vv   DEL PEAK 47(21Q22.3) MUTATED DEL PEAK 47(21Q22.3) WILD-TYPE
  T1                           55                             43
  T2                          145                            109
  T3                           22                             26
  T4                           13                              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 47(21Q22.3) MUTATED   150  61  19   2
  DEL PEAK 47(21Q22.3) WILD-TYPE 111  52  16   3
D77V5, multiclass
    clus
vv   DEL PEAK 47(21Q22.3) MUTATED DEL PEAK 47(21Q22.3) WILD-TYPE
  N0                          150                            111
  N1                           61                             52
  N2                           19                             16
  N3                            2                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A  MX
  DEL PEAK 47(21Q22.3) MUTATED   206   4   1  21
  DEL PEAK 47(21Q22.3) WILD-TYPE 152   1   0  29
D77V6, multiclass
     clus
vv    DEL PEAK 47(21Q22.3) MUTATED DEL PEAK 47(21Q22.3) WILD-TYPE
  M0                           206                            152
  M1                             4                              1
  M1A                            1                              0
  MX                            21                             29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V7, binary
                                cls
clus                               0   1
  DEL PEAK 47(21Q22.3) MUTATED    45 190
  DEL PEAK 47(21Q22.3) WILD-TYPE  62 123
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 47(21Q22.3) MUTATED     45  190
  DEL PEAK 47(21Q22.3) WILD-TYPE   62  123
        clus
vv       DEL PEAK 47(21Q22.3) MUTATED DEL PEAK 47(21Q22.3) WILD-TYPE
  FEMALE                           45                             62
  MALE                            190                            123
[1] 2 2
[1] FALSE
D77V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 47(21Q22.3) MUTATED                                       5
  DEL PEAK 47(21Q22.3) WILD-TYPE                                     7
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 47(21Q22.3) MUTATED                                        3
  DEL PEAK 47(21Q22.3) WILD-TYPE                                      3
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 47(21Q22.3) MUTATED                                         0
  DEL PEAK 47(21Q22.3) WILD-TYPE                                       1
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 47(21Q22.3) MUTATED                                                           227
  DEL PEAK 47(21Q22.3) WILD-TYPE                                                         174
D77V9, multiclass
                                                             clus
vv                                                            DEL PEAK 47(21Q22.3) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          227
                                                             clus
vv                                                            DEL PEAK 47(21Q22.3) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            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"
D77V10, binary
                                cls
clus                               0   1
  DEL PEAK 47(21Q22.3) MUTATED     7 228
  DEL PEAK 47(21Q22.3) WILD-TYPE   6 179
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 47(21Q22.3) MUTATED      7  228
  DEL PEAK 47(21Q22.3) WILD-TYPE    6  179
     clus
vv    DEL PEAK 47(21Q22.3) MUTATED DEL PEAK 47(21Q22.3) WILD-TYPE
  NO                             7                              6
  YES                          228                            179
[1] 2 2
[1] FALSE
D77V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 47(21Q22.3) MUTATED   195   4   2   8
  DEL PEAK 47(21Q22.3) WILD-TYPE 147   4   2  10
D77V12, multiclass
    clus
vv   DEL PEAK 47(21Q22.3) MUTATED DEL PEAK 47(21Q22.3) WILD-TYPE
  R0                          195                            147
  R1                            4                              4
  R2                            2                              2
  RX                            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                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 47(21Q22.3) MUTATED       3                         7   164
  DEL PEAK 47(21Q22.3) WILD-TYPE     6                        10   134
D77V13, multiclass
                           clus
vv                          DEL PEAK 47(21Q22.3) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            7
  WHITE                                              164
                           clus
vv                          DEL PEAK 47(21Q22.3) WILD-TYPE
  ASIAN                                                  6
  BLACK OR AFRICAN AMERICAN                             10
  WHITE                                                134
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V14, binary
                                cls
clus                               0   1
  DEL PEAK 47(21Q22.3) MUTATED     6 144
  DEL PEAK 47(21Q22.3) WILD-TYPE   2 123
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 47(21Q22.3) MUTATED      6  144
  DEL PEAK 47(21Q22.3) WILD-TYPE    2  123
                        clus
vv                       DEL PEAK 47(21Q22.3) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          144
                        clus
vv                       DEL PEAK 47(21Q22.3) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            123
[1] 2 2
[1] FALSE

Clustering(78) Variable = DEL PEAK 48(22Q11.21) MUTATION ANALYSIS
D78V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 48(22Q11.21) MUTATED    49  22
  DEL PEAK 48(22Q11.21) WILD-TYPE 216 101
  DEL PEAK 48(22Q11.21) MUTATED DEL PEAK 48(22Q11.21) WILD-TYPE 
                             71                             317 
  DEL PEAK 48(22Q11.21) MUTATED DEL PEAK 48(22Q11.21) WILD-TYPE 
                             22                             101 
$`DEL PEAK 48(22Q11.21) MUTATED`
TCGA-18-3407 TCGA-18-3416 TCGA-18-3417 TCGA-18-4083 TCGA-21-1071 TCGA-21-1080 
         136          862          758          187         1426         3724 
TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 TCGA-22-1016 TCGA-22-4594 TCGA-22-4601 
         329          979          608          822         1470         1057 
TCGA-22-5471 TCGA-22-5480 TCGA-22-A5C4 TCGA-33-4583 TCGA-33-4587 TCGA-37-3792 
         965         1952           29         1941         1970           12 
TCGA-37-4129 TCGA-37-4132 TCGA-39-5011 TCGA-39-5016 TCGA-39-5035 TCGA-39-5040 
         200          227         1454         2253          474         1964 
TCGA-43-2578 TCGA-43-2581 TCGA-43-6771 TCGA-43-7656 TCGA-43-A56V TCGA-52-7812 
         684         1176         1936          212          366         1967 
TCGA-56-6546 TCGA-56-7222 TCGA-58-A46M TCGA-60-2698 TCGA-63-6202 TCGA-66-2727 
          26           13         1072          311         1973         1967 
TCGA-66-2753 TCGA-66-2754 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2766 
          31           61           30          639          762           31 
TCGA-66-2771 TCGA-66-2778 TCGA-66-2782 TCGA-66-2785 TCGA-66-2790 TCGA-66-2793 
         578          578         1954           60          699         1952 
TCGA-66-2795 TCGA-68-8250 TCGA-68-A59I TCGA-77-6843 TCGA-77-7138 TCGA-77-8139 
         122          244          121         1941         1959         1951 
TCGA-77-8150 TCGA-85-6560 TCGA-85-8049 TCGA-85-8072 TCGA-85-8664 TCGA-85-8666 
        1961          364           60          513            3          475 
TCGA-85-A4CL TCGA-85-A53L TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-8063 
          15           13          244          331          269          122 
TCGA-92-8065 TCGA-98-7454 TCGA-98-8023 TCGA-MF-A522 TCGA-NC-A5HE 
          70          256          308           83         1722 

$`DEL PEAK 48(22Q11.21) WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 
         370         2464         2417          146         1415          345 
TCGA-18-3414 TCGA-18-3415 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 
         396         1810           50         1331           85         2754 
TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 
          92          827         3636         3016         2134         1852 
TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 
        1058          474          965          284         3644          267 
TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 
         962         1268         1032          223         1945          131 
TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 
        1952           53          429         1485          623         1067 
TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 
         734           17         1161          399         1946          587 
TCGA-22-4613 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 
         358         1964         1933          445         1346           24 
TCGA-22-5479 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 
        1651         1952          357          573          916         1912 
TCGA-22-5491 TCGA-22-5492 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 
        1713          506         2524         1940         2979         1311 
TCGA-33-4566 TCGA-33-4582 TCGA-33-4586 TCGA-33-4589 TCGA-33-6738 TCGA-34-2596 
        5287         1966          428         1948          822           80 
TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 
        1874          958          881         1000          951         1528 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 
        2062         1715          707          365          428          941 
TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-4130 TCGA-37-4133 
         552          166          120           13          247          238 
TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 
         207           12          103         1361         1947         1996 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 
        1964         1849           52          740           59          833 
TCGA-39-5034 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-43-2576 TCGA-43-3394 
        1107         1084         1086          544         1223          822 
TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 
        1007          349          849          376          757          310 
TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 
         236         1970          407          358         1971          353 
TCGA-43-A475 TCGA-43-A56U TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 
         296          432          324          423           12           12 
TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-56-1622 
         911          541         1948          923         1958          881 
TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-7221 TCGA-56-7223 TCGA-56-7579 
           3          555           62           30           30           44 
TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 
          40           26            6         1961            1           41 
TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 
         178           55           36           63           17           16 
TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ 
          34           38            2           46           30           25 
TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 
           4            4            8          378          911         2167 
TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46N TCGA-60-2695 TCGA-60-2696 
        1058         2589         1723          910          642          109 
TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 
        1950         1943         1958          661         1963         1505 
TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 
        1963         1260          274         1731         1531         1075 
TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 
        1475         1297           97          983          908         1092 
TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 
         717          816          358         1957         1955         1947 
TCGA-63-7023 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2755 
        1952         1311           61          641           30           28 
TCGA-66-2756 TCGA-66-2763 TCGA-66-2765 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 
          30           30           61           61           61         1947 
TCGA-66-2770 TCGA-66-2773 TCGA-66-2777 TCGA-66-2780 TCGA-66-2781 TCGA-66-2783 
         700         1946           61         1956          121          759 
TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2791 TCGA-66-2792 
         790         1217          699         1955         1977          913 
TCGA-66-2794 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 
        1645         1492           83          202          211           96 
TCGA-68-A59J TCGA-77-6842 TCGA-77-6844 TCGA-77-6845 TCGA-77-7139 TCGA-77-7141 
         104         1950         1942         1952         1968           15 
TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 
        1286         1954         1942         1952         1954          479 
TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 
        1960         1945         1641         1953         1945         1941 
TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 
        1941         1947         1946         1962          833         1943 
TCGA-77-8148 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 
         293         1684         1092           10         1953         1942 
TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB 
        1959         1955         1963         1290         1280         1939 
TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 
         839          713          395           34           18           10 
TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 
          49            1         1965           35          911           60 
TCGA-85-8048 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8276 TCGA-85-8277 
          26           16          960          428           13           11 
TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 
          13           54           60           55           67           54 
TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 
          61           61           22           21          445          424 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 
        1972         1960           25           19         1973         1967 
TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 
        1972         1987           24          111          758          289 
TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-92-7340 TCGA-92-7341 TCGA-92-8064 
          89          358          428           82          106          160 
TCGA-94-7033 TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 
          87          356          430         1213         1344          189 
TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-8021 TCGA-98-8022 TCGA-J1-A4AH 
         211          273          183          413          224          222 
TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-NC-A5HG TCGA-NC-A5HI 
          35          449           36         1548         1135 

  DEL PEAK 48(22Q11.21) MUTATED DEL PEAK 48(22Q11.21) WILD-TYPE 
                              3                               1 
  DEL PEAK 48(22Q11.21) MUTATED DEL PEAK 48(22Q11.21) WILD-TYPE 
                           3724                            5287 
  DEL PEAK 48(22Q11.21) MUTATED DEL PEAK 48(22Q11.21) WILD-TYPE 
                            513                             707 
[1] "3.0 - 3724.0 (513.0)" "1.0 - 5287.0 (707.0)"
[1] "hr=" "1"  
D78V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 48(22Q11.21) MUTATED         1       11       19        0        12
  DEL PEAK 48(22Q11.21) WILD-TYPE       0       61      118        1        40
                                 vv
clus                              STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 48(22Q11.21) MUTATED          11         14          3        2
  DEL PEAK 48(22Q11.21) WILD-TYPE        60         43         17        4
D78V3, multiclass
            clus
vv           DEL PEAK 48(22Q11.21) MUTATED DEL PEAK 48(22Q11.21) WILD-TYPE
  STAGE I                                1                               0
  STAGE IA                              11                              61
  STAGE IB                              19                             118
  STAGE II                               0                               1
  STAGE IIA                             12                              40
  STAGE IIB                             11                              60
  STAGE IIIA                            14                              43
  STAGE IIIB                             3                              17
  STAGE IV                               2                               4
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  DEL PEAK 48(22Q11.21) MUTATED    16  47   8   3
  DEL PEAK 48(22Q11.21) WILD-TYPE  82 207  40  17
D78V4, multiclass
    clus
vv   DEL PEAK 48(22Q11.21) MUTATED DEL PEAK 48(22Q11.21) WILD-TYPE
  T1                            16                              82
  T2                            47                             207
  T3                             8                              40
  T4                             3                              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 48(22Q11.21) MUTATED    41  22  10   1
  DEL PEAK 48(22Q11.21) WILD-TYPE 220  91  25   4
D78V5, multiclass
    clus
vv   DEL PEAK 48(22Q11.21) MUTATED DEL PEAK 48(22Q11.21) WILD-TYPE
  N0                            41                             220
  N1                            22                              91
  N2                            10                              25
  N3                             1                               4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               M0  M1 M1A  MX
  DEL PEAK 48(22Q11.21) MUTATED    60   2   0  11
  DEL PEAK 48(22Q11.21) WILD-TYPE 298   3   1  39
D78V6, multiclass
     clus
vv    DEL PEAK 48(22Q11.21) MUTATED DEL PEAK 48(22Q11.21) WILD-TYPE
  M0                             60                             298
  M1                              2                               3
  M1A                             0                               1
  MX                             11                              39
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V7, binary
                                 cls
clus                                0   1
  DEL PEAK 48(22Q11.21) MUTATED    17  57
  DEL PEAK 48(22Q11.21) WILD-TYPE  90 256
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 48(22Q11.21) MUTATED     17   57
  DEL PEAK 48(22Q11.21) WILD-TYPE   90  256
        clus
vv       DEL PEAK 48(22Q11.21) MUTATED DEL PEAK 48(22Q11.21) WILD-TYPE
  FEMALE                            17                              90
  MALE                              57                             256
[1] 2 2
[1] FALSE
D78V8, continuous
                                 vv
clus                              LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 48(22Q11.21) MUTATED                                       1
  DEL PEAK 48(22Q11.21) WILD-TYPE                                    11
                                 vv
clus                              LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 48(22Q11.21) MUTATED                                        1
  DEL PEAK 48(22Q11.21) WILD-TYPE                                      5
                                 vv
clus                              LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 48(22Q11.21) MUTATED                                         1
  DEL PEAK 48(22Q11.21) WILD-TYPE                                       0
                                 vv
clus                              LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 48(22Q11.21) MUTATED                                                            71
  DEL PEAK 48(22Q11.21) WILD-TYPE                                                         330
D78V9, multiclass
                                                             clus
vv                                                            DEL PEAK 48(22Q11.21) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            71
                                                             clus
vv                                                            DEL PEAK 48(22Q11.21) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    11
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                    5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             330
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V10, binary
                                 cls
clus                                0   1
  DEL PEAK 48(22Q11.21) MUTATED     4  70
  DEL PEAK 48(22Q11.21) WILD-TYPE   9 337
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 48(22Q11.21) MUTATED      4   70
  DEL PEAK 48(22Q11.21) WILD-TYPE    9  337
     clus
vv    DEL PEAK 48(22Q11.21) MUTATED DEL PEAK 48(22Q11.21) WILD-TYPE
  NO                              4                               9
  YES                            70                             337
[1] 2 2
[1] FALSE
D78V11, continuous
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 48(22Q11.21) MUTATED    58   0   2   4
  DEL PEAK 48(22Q11.21) WILD-TYPE 284   8   2  14
D78V12, multiclass
    clus
vv   DEL PEAK 48(22Q11.21) MUTATED DEL PEAK 48(22Q11.21) WILD-TYPE
  R0                            58                             284
  R1                             0                               8
  R2                             2                               2
  RX                             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                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 48(22Q11.21) MUTATED       2                         4    47
  DEL PEAK 48(22Q11.21) WILD-TYPE     7                        13   251
D78V13, multiclass
                           clus
vv                          DEL PEAK 48(22Q11.21) MUTATED
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             4
  WHITE                                                47
                           clus
vv                          DEL PEAK 48(22Q11.21) WILD-TYPE
  ASIAN                                                   7
  BLACK OR AFRICAN AMERICAN                              13
  WHITE                                                 251
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V14, binary
                                 cls
clus                                0   1
  DEL PEAK 48(22Q11.21) MUTATED     1  43
  DEL PEAK 48(22Q11.21) WILD-TYPE   7 224
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 48(22Q11.21) MUTATED      1   43
  DEL PEAK 48(22Q11.21) WILD-TYPE    7  224
                        clus
vv                       DEL PEAK 48(22Q11.21) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            43
                        clus
vv                       DEL PEAK 48(22Q11.21) WILD-TYPE
  HISPANIC OR LATINO                                   7
  NOT HISPANIC OR LATINO                             224
[1] 2 2
[1] FALSE

Clustering(79) Variable = DEL PEAK 49(22Q13.32) MUTATION ANALYSIS
D79V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 49(22Q13.32) MUTATED    61  31
  DEL PEAK 49(22Q13.32) WILD-TYPE 204  92
  DEL PEAK 49(22Q13.32) MUTATED DEL PEAK 49(22Q13.32) WILD-TYPE 
                             92                             296 
  DEL PEAK 49(22Q13.32) MUTATED DEL PEAK 49(22Q13.32) WILD-TYPE 
                             31                              92 
$`DEL PEAK 49(22Q13.32) MUTATED`
TCGA-18-3407 TCGA-18-3417 TCGA-18-4083 TCGA-21-1070 TCGA-21-1071 TCGA-21-1080 
         136          758          187         3636         1426         3724 
TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 TCGA-22-1005 TCGA-22-1016 TCGA-22-4607 
         329          979          608         1952          822          587 
TCGA-22-4613 TCGA-22-5483 TCGA-22-5492 TCGA-33-4532 TCGA-33-4566 TCGA-33-4582 
         358          573          506         2524         5287         1966 
TCGA-33-4583 TCGA-33-4587 TCGA-34-5928 TCGA-34-8454 TCGA-37-3792 TCGA-37-4129 
        1941         1970          552          166           12          200 
TCGA-37-4130 TCGA-37-4132 TCGA-37-4141 TCGA-39-5011 TCGA-39-5016 TCGA-39-5035 
         247          227           12         1454         2253          474 
TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-5668 TCGA-43-6143 
        1964         1223          684         1176          349          376 
TCGA-43-6771 TCGA-43-7658 TCGA-52-7809 TCGA-52-7812 TCGA-56-6546 TCGA-56-7222 
        1936         1970         1948         1967           26           13 
TCGA-56-A5DR TCGA-60-2695 TCGA-63-6202 TCGA-66-2727 TCGA-66-2753 TCGA-66-2754 
           4          642         1973         1967           31           61 
TCGA-66-2757 TCGA-66-2759 TCGA-66-2763 TCGA-66-2771 TCGA-66-2778 TCGA-66-2782 
          30          762           30          578          578         1954 
TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2793 TCGA-66-2800 TCGA-68-8250 
        1955          699         1977         1952         1492          244 
TCGA-68-A59I TCGA-77-7138 TCGA-77-7142 TCGA-77-7337 TCGA-77-7465 TCGA-77-8128 
         121         1959         1286         1942          479         1953 
TCGA-77-8139 TCGA-77-8144 TCGA-77-8150 TCGA-77-8153 TCGA-77-A5G6 TCGA-85-6560 
        1951          833         1961         1684         1955          364 
TCGA-85-7697 TCGA-85-7843 TCGA-85-8048 TCGA-85-8049 TCGA-85-8354 TCGA-85-8355 
          10           35           26           60           61           61 
TCGA-85-8479 TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 TCGA-85-A510 TCGA-85-A53L 
          22          424            3          475         1967           13 
TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-8063 TCGA-92-8065 TCGA-98-7454 
         244          331          269          122           70          256 
TCGA-MF-A522 TCGA-NC-A5HE 
          83         1722 

$`DEL PEAK 49(22Q13.32) WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 
         370         2464         2417          146         1415          345 
TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 
         396         1810          862           50         1331           85 
TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 
        2754           92          827         3016         2134         1852 
TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 
        1058          474          965          284         3644          267 
TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 
         962         1268         1032          223         1945          131 
TCGA-22-1011 TCGA-22-1012 TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 
          53          429         1485          623         1067         1470 
TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 
         734           17         1161         1057          399         1946 
TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 
         965         1964         1933          445         1346           24 
TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 
        1651         1952         1952          357          916         1912 
TCGA-22-5491 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4586 
        1713           29         1940         2979         1311          428 
TCGA-33-4589 TCGA-33-6738 TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 
        1948          822           80         1874          958          881 
TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 
        1000          951         1528         2062         1715          707 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-37-3783 TCGA-37-3789 TCGA-37-4133 
         365          428          941          120           13          238 
TCGA-37-4135 TCGA-37-5819 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 
         207          103         1361         1947         1996         1964 
TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 
        1849           52          740           59          833         1107 
TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 
        1084         1086          544          822         1007          849 
TCGA-43-6647 TCGA-43-6770 TCGA-43-7656 TCGA-43-7657 TCGA-43-8115 TCGA-43-8116 
         757          310          212          236          407          358 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-6025 
        1971          353          296          432          366          324 
TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7810 
         423           12           12          911          541          923 
TCGA-52-7811 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-7221 
        1958          881            3          555           62           30 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 
          30           44           40           26            6         1961 
TCGA-56-7822 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 
           1           41          178           55           36           63 
TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX 
          17           16           34           38            2           46 
TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 
          30           25            4            8          378          911 
TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N 
        2167         1058         2589         1723         1072          910 
TCGA-60-2696 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 
         109          311         1950         1943         1958          661 
TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 
        1963         1505         1963         1260          274         1731 
TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 
        1531         1075         1475         1297           97          983 
TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-7020 
         908         1092          717          816          358         1957 
TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 
        1955         1947         1952         1311           61          641 
TCGA-66-2744 TCGA-66-2755 TCGA-66-2756 TCGA-66-2758 TCGA-66-2765 TCGA-66-2766 
          30           28           30          639           61           31 
TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2773 TCGA-66-2777 
          61           61         1947          700         1946           61 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 
        1956          121          759           60          790         1217 
TCGA-66-2788 TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 TCGA-68-7755 TCGA-68-7756 
         699          913         1645          122           83          202 
TCGA-68-7757 TCGA-68-8251 TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 
         211           96          104         1950         1941         1942 
TCGA-77-6845 TCGA-77-7139 TCGA-77-7141 TCGA-77-7335 TCGA-77-7338 TCGA-77-7463 
        1952         1968           15         1954         1952         1954 
TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 
        1960         1945         1641         1945         1941         1941 
TCGA-77-8136 TCGA-77-8138 TCGA-77-8140 TCGA-77-8145 TCGA-77-8148 TCGA-77-8154 
        1947         1946         1962         1943          293         1092 
TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G7 TCGA-77-A5G8 
          10         1953         1942         1959         1963         1290 
TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6561 TCGA-85-6798 
        1280         1939          839          713          395           34 
TCGA-85-7696 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 
          18           49            1         1965          911           60 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 
          16          960          428          513           13           11 
TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 
          13           54           60           55           67           54 
TCGA-85-8481 TCGA-85-8580 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR 
          21          445           15         1972         1960           25 
TCGA-85-A50M TCGA-85-A50Z TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A5B5 
          19         1973         1972         1987           24          111 
TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-92-7340 
         758          289           89          358          428           82 
TCGA-92-7341 TCGA-92-8064 TCGA-94-7033 TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7544 
         106          160           87          356          430         1213 
TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-8021 
        1344          189          211          273          183          413 
TCGA-98-8022 TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 
         224          308          222           35          449           36 
TCGA-NC-A5HG TCGA-NC-A5HI 
        1548         1135 

  DEL PEAK 49(22Q13.32) MUTATED DEL PEAK 49(22Q13.32) WILD-TYPE 
                              3                               1 
  DEL PEAK 49(22Q13.32) MUTATED DEL PEAK 49(22Q13.32) WILD-TYPE 
                           5287                            3644 
  DEL PEAK 49(22Q13.32) MUTATED DEL PEAK 49(22Q13.32) WILD-TYPE 
                          578.0                           703.5 
[1] "3.0 - 5287.0 (578.0)" "1.0 - 3644.0 (703.5)"
[1] "hr=" "1.2"
D79V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 49(22Q13.32) MUTATED         1       16       29        0        16
  DEL PEAK 49(22Q13.32) WILD-TYPE       0       56      108        1        36
                                 vv
clus                              STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 49(22Q13.32) MUTATED          12         16          5        2
  DEL PEAK 49(22Q13.32) WILD-TYPE        59         41         15        4
D79V3, multiclass
            clus
vv           DEL PEAK 49(22Q13.32) MUTATED DEL PEAK 49(22Q13.32) WILD-TYPE
  STAGE I                                1                               0
  STAGE IA                              16                              56
  STAGE IB                              29                             108
  STAGE II                               0                               1
  STAGE IIA                             16                              36
  STAGE IIB                             12                              59
  STAGE IIIA                            16                              41
  STAGE IIIB                             5                              15
  STAGE IV                               2                               4
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  DEL PEAK 49(22Q13.32) MUTATED    24  60  11   3
  DEL PEAK 49(22Q13.32) WILD-TYPE  74 194  37  17
D79V4, multiclass
    clus
vv   DEL PEAK 49(22Q13.32) MUTATED DEL PEAK 49(22Q13.32) WILD-TYPE
  T1                            24                              74
  T2                            60                             194
  T3                            11                              37
  T4                             3                              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 49(22Q13.32) MUTATED    59  25  11   3
  DEL PEAK 49(22Q13.32) WILD-TYPE 202  88  24   2
D79V5, multiclass
    clus
vv   DEL PEAK 49(22Q13.32) MUTATED DEL PEAK 49(22Q13.32) WILD-TYPE
  N0                            59                             202
  N1                            25                              88
  N2                            11                              24
  N3                             3                               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               M0  M1 M1A  MX
  DEL PEAK 49(22Q13.32) MUTATED    84   2   0  11
  DEL PEAK 49(22Q13.32) WILD-TYPE 274   3   1  39
D79V6, multiclass
     clus
vv    DEL PEAK 49(22Q13.32) MUTATED DEL PEAK 49(22Q13.32) WILD-TYPE
  M0                             84                             274
  M1                              2                               3
  M1A                             0                               1
  MX                             11                              39
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V7, binary
                                 cls
clus                                0   1
  DEL PEAK 49(22Q13.32) MUTATED    26  72
  DEL PEAK 49(22Q13.32) WILD-TYPE  81 241
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 49(22Q13.32) MUTATED     26   72
  DEL PEAK 49(22Q13.32) WILD-TYPE   81  241
        clus
vv       DEL PEAK 49(22Q13.32) MUTATED DEL PEAK 49(22Q13.32) WILD-TYPE
  FEMALE                            26                              81
  MALE                              72                             241
[1] 2 2
[1] FALSE
D79V8, continuous
                                 vv
clus                              LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 49(22Q13.32) MUTATED                                       4
  DEL PEAK 49(22Q13.32) WILD-TYPE                                     8
                                 vv
clus                              LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 49(22Q13.32) MUTATED                                        3
  DEL PEAK 49(22Q13.32) WILD-TYPE                                      3
                                 vv
clus                              LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 49(22Q13.32) MUTATED                                         1
  DEL PEAK 49(22Q13.32) WILD-TYPE                                       0
                                 vv
clus                              LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 49(22Q13.32) MUTATED                                                            90
  DEL PEAK 49(22Q13.32) WILD-TYPE                                                         311
D79V9, multiclass
                                                             clus
vv                                                            DEL PEAK 49(22Q13.32) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            90
                                                             clus
vv                                                            DEL PEAK 49(22Q13.32) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                     8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                    3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             311
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V10, binary
                                 cls
clus                                0   1
  DEL PEAK 49(22Q13.32) MUTATED     4  94
  DEL PEAK 49(22Q13.32) WILD-TYPE   9 313
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 49(22Q13.32) MUTATED      4   94
  DEL PEAK 49(22Q13.32) WILD-TYPE    9  313
     clus
vv    DEL PEAK 49(22Q13.32) MUTATED DEL PEAK 49(22Q13.32) WILD-TYPE
  NO                              4                               9
  YES                            94                             313
[1] 2 2
[1] FALSE
D79V11, continuous
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 49(22Q13.32) MUTATED    79   2   1   5
  DEL PEAK 49(22Q13.32) WILD-TYPE 263   6   3  13
D79V12, multiclass
    clus
vv   DEL PEAK 49(22Q13.32) MUTATED DEL PEAK 49(22Q13.32) WILD-TYPE
  R0                            79                             263
  R1                             2                               6
  R2                             1                               3
  RX                             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                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 49(22Q13.32) MUTATED       3                         4    66
  DEL PEAK 49(22Q13.32) WILD-TYPE     6                        13   232
D79V13, multiclass
                           clus
vv                          DEL PEAK 49(22Q13.32) MUTATED
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                             4
  WHITE                                                66
                           clus
vv                          DEL PEAK 49(22Q13.32) WILD-TYPE
  ASIAN                                                   6
  BLACK OR AFRICAN AMERICAN                              13
  WHITE                                                 232
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V14, binary
                                 cls
clus                                0   1
  DEL PEAK 49(22Q13.32) MUTATED     1  60
  DEL PEAK 49(22Q13.32) WILD-TYPE   7 207
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 49(22Q13.32) MUTATED      1   60
  DEL PEAK 49(22Q13.32) WILD-TYPE    7  207
                        clus
vv                       DEL PEAK 49(22Q13.32) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            60
                        clus
vv                       DEL PEAK 49(22Q13.32) WILD-TYPE
  HISPANIC OR LATINO                                   7
  NOT HISPANIC OR LATINO                             207
[1] 2 2
[1] FALSE

Clustering(80) Variable = DEL PEAK 50(XP22.2) MUTATION ANALYSIS
D80V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 50(XP22.2) MUTATED    74  38
  DEL PEAK 50(XP22.2) WILD-TYPE 191  85
  DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE 
                          112                           276 
  DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE 
                           38                            85 
$`DEL PEAK 50(XP22.2) MUTATED`
TCGA-18-3407 TCGA-18-3408 TCGA-18-3412 TCGA-18-3416 TCGA-18-3417 TCGA-18-4086 
         136         2464          345          862          758           85 
TCGA-18-5592 TCGA-18-5595 TCGA-21-1080 TCGA-21-1082 TCGA-21-1083 TCGA-22-0940 
          92          827         3724         3644          267          608 
TCGA-22-0944 TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4607 TCGA-22-5473 
         223         1485          623         1067          587         1933 
TCGA-22-5477 TCGA-22-5480 TCGA-22-5483 TCGA-22-5485 TCGA-22-A5C4 TCGA-33-4532 
        1346         1952          573          916           29         2524 
TCGA-33-4566 TCGA-34-2600 TCGA-34-2605 TCGA-34-2609 TCGA-34-5927 TCGA-34-8454 
        5287         1874          881          951          941          166 
TCGA-37-3792 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5021 TCGA-39-5027 
          12          207           12          103         1947         1849 
TCGA-39-5028 TCGA-43-5668 TCGA-43-5670 TCGA-43-6770 TCGA-43-7656 TCGA-43-8118 
          52          349          849          310          212         1971 
TCGA-43-A474 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-56-7221 
         353          423           12           12          911           30 
TCGA-56-7730 TCGA-56-8624 TCGA-56-8629 TCGA-56-A5DR TCGA-58-8390 TCGA-60-2696 
           6           36           34            4          911          109 
TCGA-60-2698 TCGA-60-2703 TCGA-60-2707 TCGA-60-2710 TCGA-60-2711 TCGA-60-2713 
         311         1950          661         1963         1260         1731 
TCGA-63-7023 TCGA-66-2753 TCGA-66-2757 TCGA-66-2758 TCGA-66-2763 TCGA-66-2769 
        1952           31           30          639           30         1947 
TCGA-66-2773 TCGA-66-2781 TCGA-66-2782 TCGA-66-2786 TCGA-66-2790 TCGA-66-2792 
        1946          121         1954          790          699          913 
TCGA-66-2800 TCGA-68-7756 TCGA-77-6842 TCGA-77-6845 TCGA-77-7138 TCGA-77-7141 
        1492          202         1950         1952         1959           15 
TCGA-77-7142 TCGA-77-7338 TCGA-77-8009 TCGA-77-8130 TCGA-77-8140 TCGA-77-8144 
        1286         1952         1641         1945         1962          833 
TCGA-77-8150 TCGA-77-8154 TCGA-77-A5G3 TCGA-77-A5GA TCGA-77-A5GF TCGA-85-6561 
        1961         1092         1959         1280          839          395 
TCGA-85-7698 TCGA-85-7699 TCGA-85-8070 TCGA-85-8071 TCGA-85-8288 TCGA-85-8352 
          49            1          960          428           54           67 
TCGA-85-8354 TCGA-85-8580 TCGA-85-A4QR TCGA-85-A50M TCGA-85-A512 TCGA-90-7766 
          61          445           25           19         1987          289 
TCGA-90-7964 TCGA-92-8063 TCGA-96-7544 TCGA-96-A4JK TCGA-96-A4JL TCGA-J1-A4AH 
         428          122         1213          273          183          222 
TCGA-L3-A4E7 TCGA-LA-A446 TCGA-NC-A5HG TCGA-NC-A5HI 
          35           36         1548         1135 

$`DEL PEAK 50(XP22.2) WILD-TYPE`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3414 TCGA-18-3415 
         370         2417          146         1415          396         1810 
TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4721 TCGA-21-1070 TCGA-21-1071 
          50         1331          187         2754         3636         1426 
TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 
        3016         2134         1852         1058          474          965 
TCGA-21-1081 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI 
         284          962         1268         1032          329          979 
TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 
        1945          131         1952           53          429          822 
TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 
        1470          734           17         1161         1057          399 
TCGA-22-4605 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5474 TCGA-22-5478 
        1946          358          965         1964          445           24 
TCGA-22-5479 TCGA-22-5481 TCGA-22-5482 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 
        1651         1952          357         1912         1713          506 
TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 
        1940         2979         1311         1966         1941          428 
TCGA-33-4587 TCGA-33-4589 TCGA-33-6738 TCGA-34-2596 TCGA-34-2604 TCGA-34-2608 
        1970         1948          822           80          958         1000 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 
        1528         2062         1715          707          365          428 
TCGA-34-5928 TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 
         552          120           13          200          247          227 
TCGA-37-4133 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5022 TCGA-39-5024 
         238         1454         2253         1361         1996         1964 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 
         740           59          833         1107          474         1084 
TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 
        1086          544         1964         1223          684         1176 
TCGA-43-3394 TCGA-43-3920 TCGA-43-6143 TCGA-43-6647 TCGA-43-6771 TCGA-43-7657 
         822         1007          376          757         1936          236 
TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V 
        1970          407          358          296          432          366 
TCGA-46-6025 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 
         324          541         1948          923         1958         1967 
TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7222 
         881            3          555           62           26           13 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7731 TCGA-56-7822 
          30           44           40           26         1961            1 
TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 
          41          178           55           63           17           16 
TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK 
          38            2           46           30           25            4 
TCGA-56-A5DS TCGA-58-8388 TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L 
           8          378         2167         1058         2589         1723 
TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2704 TCGA-60-2706 TCGA-60-2708 
        1072          910          642         1943         1958         1963 
TCGA-60-2709 TCGA-60-2712 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 
        1505          274         1531         1075         1475         1297 
TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 
          97          983          908         1092          717          816 
TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-66-2727 
         358         1973         1957         1955         1947         1967 
TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2754 TCGA-66-2755 
        1311           61          641           30           61           28 
TCGA-66-2756 TCGA-66-2759 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 
          30          762           61           31           61           61 
TCGA-66-2770 TCGA-66-2771 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2783 
         700          578           61          578         1956          759 
TCGA-66-2785 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2791 TCGA-66-2793 
          60         1217          699         1955         1977         1952 
TCGA-66-2794 TCGA-66-2795 TCGA-68-7755 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 
        1645          122           83          211          244           96 
TCGA-68-A59I TCGA-68-A59J TCGA-77-6843 TCGA-77-6844 TCGA-77-7139 TCGA-77-7335 
         121          104         1941         1942         1968         1954 
TCGA-77-7337 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8128 
        1942         1954          479         1960         1945         1953 
TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8145 
        1941         1941         1947         1946         1951         1943 
TCGA-77-8148 TCGA-77-8153 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 
         293         1684           10         1953         1942         1955 
TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6560 TCGA-85-6798 
        1963         1290         1939          713          364           34 
TCGA-85-7696 TCGA-85-7697 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 
          18           10         1965           35          911           60 
TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 
          26           60           16          513           13           11 
TCGA-85-8287 TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 TCGA-85-8355 TCGA-85-8479 
          13           60           55           54           61           22 
TCGA-85-8481 TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4PA 
          21          424            3          475           15         1972 
TCGA-85-A4QQ TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L 
        1960         1973         1967         1972           24           13 
TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE 
         111          758           89          358          244          331 
TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 
         269           82          106          160           70           87 
TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-98-7454 
         356          430         1344          189          211          256 
TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-L3-A524 TCGA-MF-A522 TCGA-NC-A5HE 
         413          224          308          449           83         1722 

  DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE 
                            1                             1 
  DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE 
                         5287                          3636 
  DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE 
                        650.0                         641.5 
[1] "1.0 - 5287.0 (650.0)" "1.0 - 3636.0 (641.5)"
[1] "hr=" "1.1"
D80V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 50(XP22.2) MUTATED         0       17       43        1        21
  DEL PEAK 50(XP22.2) WILD-TYPE       1       55       94        0        31
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 50(XP22.2) MUTATED          23         12          5        1
  DEL PEAK 50(XP22.2) WILD-TYPE        48         45         15        5
D80V3, multiclass
            clus
vv           DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE
  STAGE I                              0                             1
  STAGE IA                            17                            55
  STAGE IB                            43                            94
  STAGE II                             1                             0
  STAGE IIA                           21                            31
  STAGE IIB                           23                            48
  STAGE IIIA                          12                            45
  STAGE IIIB                           5                            15
  STAGE IV                             1                             5
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 50(XP22.2) MUTATED    25  78  13   8
  DEL PEAK 50(XP22.2) WILD-TYPE  73 176  35  12
D80V4, multiclass
    clus
vv   DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE
  T1                          25                            73
  T2                          78                           176
  T3                          13                            35
  T4                           8                            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 50(XP22.2) MUTATED    82  36   5   0
  DEL PEAK 50(XP22.2) WILD-TYPE 179  77  30   5
D80V5, multiclass
    clus
vv   DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE
  N0                          82                           179
  N1                          36                            77
  N2                           5                            30
  N3                           0                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A  MX
  DEL PEAK 50(XP22.2) MUTATED   108   1   0  12
  DEL PEAK 50(XP22.2) WILD-TYPE 250   4   1  38
D80V6, multiclass
     clus
vv    DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE
  M0                          108                           250
  M1                            1                             4
  M1A                           0                             1
  MX                           12                            38
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V7, binary
                               cls
clus                              0   1
  DEL PEAK 50(XP22.2) MUTATED    27  97
  DEL PEAK 50(XP22.2) WILD-TYPE  80 216
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 50(XP22.2) MUTATED     27   97
  DEL PEAK 50(XP22.2) WILD-TYPE   80  216
        clus
vv       DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE
  FEMALE                          27                            80
  MALE                            97                           216
[1] 2 2
[1] FALSE
D80V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 50(XP22.2) MUTATED                                       2
  DEL PEAK 50(XP22.2) WILD-TYPE                                    10
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 50(XP22.2) MUTATED                                        1
  DEL PEAK 50(XP22.2) WILD-TYPE                                      5
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 50(XP22.2) MUTATED                                         0
  DEL PEAK 50(XP22.2) WILD-TYPE                                       1
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 50(XP22.2) MUTATED                                                           121
  DEL PEAK 50(XP22.2) WILD-TYPE                                                         280
D80V9, multiclass
                                                             clus
vv                                                            DEL PEAK 50(XP22.2) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         121
                                                             clus
vv                                                            DEL PEAK 50(XP22.2) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  10
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           280
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V10, binary
                               cls
clus                              0   1
  DEL PEAK 50(XP22.2) MUTATED     5 119
  DEL PEAK 50(XP22.2) WILD-TYPE   8 288
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 50(XP22.2) MUTATED      5  119
  DEL PEAK 50(XP22.2) WILD-TYPE    8  288
     clus
vv    DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE
  NO                            5                             8
  YES                         119                           288
[1] 2 2
[1] FALSE
D80V11, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 50(XP22.2) MUTATED   100   3   1   6
  DEL PEAK 50(XP22.2) WILD-TYPE 242   5   3  12
D80V12, multiclass
    clus
vv   DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE
  R0                         100                           242
  R1                           3                             5
  R2                           1                             3
  RX                           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                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 50(XP22.2) MUTATED       4                         7    83
  DEL PEAK 50(XP22.2) WILD-TYPE     5                        10   215
D80V13, multiclass
                           clus
vv                          DEL PEAK 50(XP22.2) MUTATED
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                           7
  WHITE                                              83
                           clus
vv                          DEL PEAK 50(XP22.2) WILD-TYPE
  ASIAN                                                 5
  BLACK OR AFRICAN AMERICAN                            10
  WHITE                                               215
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V14, binary
                               cls
clus                              0   1
  DEL PEAK 50(XP22.2) MUTATED     1  77
  DEL PEAK 50(XP22.2) WILD-TYPE   7 190
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 50(XP22.2) MUTATED      1   77
  DEL PEAK 50(XP22.2) WILD-TYPE    7  190
                        clus
vv                       DEL PEAK 50(XP22.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          77
                        clus
vv                       DEL PEAK 50(XP22.2) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           190
[1] 2 2
[1] FALSE

Clustering(81) Variable = DEL PEAK 51(XP21.1) MUTATION ANALYSIS
D81V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 51(XP21.1) MUTATED    77  35
  DEL PEAK 51(XP21.1) WILD-TYPE 188  88
  DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE 
                          112                           276 
  DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE 
                           35                            88 
$`DEL PEAK 51(XP21.1) MUTATED`
TCGA-18-3407 TCGA-18-3408 TCGA-18-3412 TCGA-18-3416 TCGA-18-3417 TCGA-18-3421 
         136         2464          345          862          758         1331 
TCGA-18-4086 TCGA-18-5592 TCGA-18-5595 TCGA-21-1072 TCGA-21-1080 TCGA-21-1082 
          85           92          827         3016         3724         3644 
TCGA-21-1083 TCGA-22-0940 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4607 
         267          608          623         1067         1470          587 
TCGA-22-5473 TCGA-22-5477 TCGA-22-5480 TCGA-22-5483 TCGA-22-5485 TCGA-33-4532 
        1933         1346         1952          573          916         2524 
TCGA-33-4566 TCGA-34-2605 TCGA-34-2609 TCGA-34-5927 TCGA-34-8454 TCGA-37-4135 
        5287          881          951          941          166          207 
TCGA-37-4141 TCGA-37-5819 TCGA-39-5021 TCGA-39-5027 TCGA-39-5028 TCGA-43-6770 
          12          103         1947         1849           52          310 
TCGA-43-7656 TCGA-43-8116 TCGA-43-8118 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 
         212          358         1971           12           12          911 
TCGA-52-7810 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7730 TCGA-56-8624 
         923           30           13           30            6           36 
TCGA-56-8629 TCGA-56-A4BW TCGA-56-A5DR TCGA-58-8390 TCGA-58-8391 TCGA-60-2696 
          34            2            4          911         2167          109 
TCGA-60-2698 TCGA-60-2707 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 
         311          661         1963         1260          274         1731 
TCGA-63-7023 TCGA-66-2753 TCGA-66-2757 TCGA-66-2758 TCGA-66-2763 TCGA-66-2773 
        1952           31           30          639           30         1946 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2786 TCGA-66-2792 TCGA-66-2795 
        1956          121         1954          790          913          122 
TCGA-66-2800 TCGA-68-7756 TCGA-77-6842 TCGA-77-6845 TCGA-77-7138 TCGA-77-7141 
        1492          202         1950         1952         1959           15 
TCGA-77-7142 TCGA-77-7338 TCGA-77-8009 TCGA-77-8130 TCGA-77-8140 TCGA-77-8144 
        1286         1952         1641         1945         1962          833 
TCGA-77-8150 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5GA TCGA-77-A5GF 
        1961         1092           10         1959         1280          839 
TCGA-85-6561 TCGA-85-7698 TCGA-85-7699 TCGA-85-7843 TCGA-85-8070 TCGA-85-8071 
         395           49            1           35          960          428 
TCGA-85-8288 TCGA-85-8352 TCGA-85-8354 TCGA-85-8355 TCGA-85-8580 TCGA-85-A4CL 
          54           67           61           61          445           15 
TCGA-85-A4QR TCGA-85-A50M TCGA-85-A512 TCGA-90-7766 TCGA-92-8063 TCGA-96-7544 
          25           19         1987          289          122         1213 
TCGA-96-A4JK TCGA-LA-A446 TCGA-NC-A5HG TCGA-NC-A5HI 
         273           36         1548         1135 

$`DEL PEAK 51(XP21.1) WILD-TYPE`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3414 TCGA-18-3415 
         370         2417          146         1415          396         1810 
TCGA-18-3419 TCGA-18-4083 TCGA-18-4721 TCGA-21-1070 TCGA-21-1071 TCGA-21-1075 
          50          187         2754         3636         1426         2134 
TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1081 TCGA-21-5782 
        1852         1058          474          965          284          962 
TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0944 TCGA-22-1000 
        1268         1032          329          979          223         1945 
TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 
         131         1952           53          429          822         1485 
TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 
         734           17         1161         1057          399         1946 
TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5474 TCGA-22-5478 TCGA-22-5479 
         358          965         1964          445           24         1651 
TCGA-22-5481 TCGA-22-5482 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 
        1952          357         1912         1713          506           29 
TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 
        1940         2979         1311         1966         1941          428 
TCGA-33-4587 TCGA-33-4589 TCGA-33-6738 TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 
        1970         1948          822           80         1874          958 
TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 
        1000         1528         2062         1715          707          365 
TCGA-34-5241 TCGA-34-5928 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 
         428          552          120           13           12          200 
TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 
         247          227          238         1454         2253         1361 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 
        1996         1964          740           59          833         1107 
TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 
         474         1084         1086          544         1964         1223 
TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 
         684         1176          822         1007          349          849 
TCGA-43-6143 TCGA-43-6647 TCGA-43-6771 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 
         376          757         1936          236         1970          407 
TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-6025 TCGA-46-6026 
         353          296          432          366          324          423 
TCGA-52-7622 TCGA-52-7809 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 
         541         1948         1958         1967          881            3 
TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 
         555           62           26           44           40           26 
TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8625 
        1961            1           41          178           55           63 
TCGA-56-8626 TCGA-56-8628 TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ 
          17           16           38           46           30           25 
TCGA-56-A4ZK TCGA-56-A5DS TCGA-58-8388 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L 
           4            8          378         1058         2589         1723 
TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 
        1072          910          642         1950         1943         1958 
TCGA-60-2708 TCGA-60-2709 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 
        1963         1505         1531         1075         1475         1297 
TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 
          97          983          908         1092          717          816 
TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-66-2727 
         358         1973         1957         1955         1947         1967 
TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2754 TCGA-66-2755 
        1311           61          641           30           61           28 
TCGA-66-2756 TCGA-66-2759 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 
          30          762           61           31           61           61 
TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2777 TCGA-66-2778 TCGA-66-2783 
        1947          700          578           61          578          759 
TCGA-66-2785 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 
          60         1217          699         1955          699         1977 
TCGA-66-2793 TCGA-66-2794 TCGA-68-7755 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 
        1952         1645           83          211          244           96 
TCGA-68-A59I TCGA-68-A59J TCGA-77-6843 TCGA-77-6844 TCGA-77-7139 TCGA-77-7335 
         121          104         1941         1942         1968         1954 
TCGA-77-7337 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8128 
        1942         1954          479         1960         1945         1953 
TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8145 
        1941         1941         1947         1946         1951         1943 
TCGA-77-8148 TCGA-77-8153 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 
         293         1684         1953         1942         1955         1963 
TCGA-77-A5G8 TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6560 TCGA-85-6798 TCGA-85-7696 
        1290         1939          713          364           34           18 
TCGA-85-7697 TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 
          10         1965          911           60           26           60 
TCGA-85-8052 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8350 
          16          513           13           11           13           60 
TCGA-85-8351 TCGA-85-8353 TCGA-85-8479 TCGA-85-8481 TCGA-85-8582 TCGA-85-8664 
          55           54           22           21          424            3 
TCGA-85-8666 TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 
         475         1972         1960         1973         1967         1972 
TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7767 TCGA-90-7769 
          24           13          111          758           89          358 
TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 
         428          244          331          269           82          106 
TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7545 
         160           70           87          356          430         1344 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 
         189          211          183          256          413          224 
TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-MF-A522 TCGA-NC-A5HE 
         308          222           35          449           83         1722 

  DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE 
                            1                             1 
  DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE 
                         5287                          3636 
  DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE 
                        650.0                         641.5 
[1] "1.0 - 5287.0 (650.0)" "1.0 - 3636.0 (641.5)"
[1] "hr=" "1.1"
D81V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 51(XP21.1) MUTATED         0       18       43        1        17
  DEL PEAK 51(XP21.1) WILD-TYPE       1       54       94        0        35
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 51(XP21.1) MUTATED          22         15          5        1
  DEL PEAK 51(XP21.1) WILD-TYPE        49         42         15        5
D81V3, multiclass
            clus
vv           DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE
  STAGE I                              0                             1
  STAGE IA                            18                            54
  STAGE IB                            43                            94
  STAGE II                             1                             0
  STAGE IIA                           17                            35
  STAGE IIB                           22                            49
  STAGE IIIA                          15                            42
  STAGE IIIB                           5                            15
  STAGE IV                             1                             5
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 51(XP21.1) MUTATED    25  76  15   8
  DEL PEAK 51(XP21.1) WILD-TYPE  73 178  33  12
D81V4, multiclass
    clus
vv   DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE
  T1                          25                            73
  T2                          76                           178
  T3                          15                            33
  T4                           8                            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 51(XP21.1) MUTATED    79  37   7   0
  DEL PEAK 51(XP21.1) WILD-TYPE 182  76  28   5
D81V5, multiclass
    clus
vv   DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE
  N0                          79                           182
  N1                          37                            76
  N2                           7                            28
  N3                           0                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A  MX
  DEL PEAK 51(XP21.1) MUTATED   108   1   0  11
  DEL PEAK 51(XP21.1) WILD-TYPE 250   4   1  39
D81V6, multiclass
     clus
vv    DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE
  M0                          108                           250
  M1                            1                             4
  M1A                           0                             1
  MX                           11                            39
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V7, binary
                               cls
clus                              0   1
  DEL PEAK 51(XP21.1) MUTATED    29  95
  DEL PEAK 51(XP21.1) WILD-TYPE  78 218
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 51(XP21.1) MUTATED     29   95
  DEL PEAK 51(XP21.1) WILD-TYPE   78  218
        clus
vv       DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE
  FEMALE                          29                            78
  MALE                            95                           218
[1] 2 2
[1] FALSE
D81V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 51(XP21.1) MUTATED                                       2
  DEL PEAK 51(XP21.1) WILD-TYPE                                    10
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 51(XP21.1) MUTATED                                        1
  DEL PEAK 51(XP21.1) WILD-TYPE                                      5
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 51(XP21.1) MUTATED                                         0
  DEL PEAK 51(XP21.1) WILD-TYPE                                       1
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 51(XP21.1) MUTATED                                                           121
  DEL PEAK 51(XP21.1) WILD-TYPE                                                         280
D81V9, multiclass
                                                             clus
vv                                                            DEL PEAK 51(XP21.1) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         121
                                                             clus
vv                                                            DEL PEAK 51(XP21.1) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  10
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           280
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V10, binary
                               cls
clus                              0   1
  DEL PEAK 51(XP21.1) MUTATED     4 120
  DEL PEAK 51(XP21.1) WILD-TYPE   9 287
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 51(XP21.1) MUTATED      4  120
  DEL PEAK 51(XP21.1) WILD-TYPE    9  287
     clus
vv    DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE
  NO                            4                             9
  YES                         120                           287
[1] 2 2
[1] FALSE
D81V11, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 51(XP21.1) MUTATED   102   2   0   6
  DEL PEAK 51(XP21.1) WILD-TYPE 240   6   4  12
D81V12, multiclass
    clus
vv   DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE
  R0                         102                           240
  R1                           2                             6
  R2                           0                             4
  RX                           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                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 51(XP21.1) MUTATED       3                         7    81
  DEL PEAK 51(XP21.1) WILD-TYPE     6                        10   217
D81V13, multiclass
                           clus
vv                          DEL PEAK 51(XP21.1) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           7
  WHITE                                              81
                           clus
vv                          DEL PEAK 51(XP21.1) WILD-TYPE
  ASIAN                                                 6
  BLACK OR AFRICAN AMERICAN                            10
  WHITE                                               217
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V14, binary
                               cls
clus                              0   1
  DEL PEAK 51(XP21.1) MUTATED     1  74
  DEL PEAK 51(XP21.1) WILD-TYPE   7 193
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 51(XP21.1) MUTATED      1   74
  DEL PEAK 51(XP21.1) WILD-TYPE    7  193
                        clus
vv                       DEL PEAK 51(XP21.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          74
                        clus
vv                       DEL PEAK 51(XP21.1) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           193
[1] 2 2
[1] FALSE

Clustering(82) Variable = DEL PEAK 52(XP11.3) MUTATION ANALYSIS
D82V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 52(XP11.3) MUTATED    72  38
  DEL PEAK 52(XP11.3) WILD-TYPE 193  85
  DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE 
                          110                           278 
  DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE 
                           38                            85 
$`DEL PEAK 52(XP11.3) MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3412 TCGA-18-3415 TCGA-18-3416 
         370          136         2464          345         1810          862 
TCGA-18-3417 TCGA-18-4086 TCGA-18-5592 TCGA-18-5595 TCGA-21-1072 TCGA-21-1080 
         758           85           92          827         3016         3724 
TCGA-21-1082 TCGA-21-1083 TCGA-22-0940 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 
        3644          267          608          623         1067         1470 
TCGA-22-4607 TCGA-22-4613 TCGA-22-5473 TCGA-22-5477 TCGA-22-5480 TCGA-22-5481 
         587          358         1933         1346         1952         1952 
TCGA-22-5483 TCGA-22-5485 TCGA-22-5491 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4566 
         573          916         1713           29         2524         5287 
TCGA-33-4582 TCGA-34-2600 TCGA-34-2605 TCGA-34-5927 TCGA-34-8454 TCGA-37-4135 
        1966         1874          881          941          166          207 
TCGA-37-4141 TCGA-39-5016 TCGA-39-5027 TCGA-39-5028 TCGA-43-6770 TCGA-43-7656 
          12         2253         1849           52          310          212 
TCGA-43-8116 TCGA-43-8118 TCGA-46-6025 TCGA-51-4079 TCGA-51-4080 TCGA-56-7221 
         358         1971          324           12           12           30 
TCGA-56-7222 TCGA-56-7223 TCGA-56-7582 TCGA-56-7730 TCGA-56-8624 TCGA-56-A4BW 
          13           30           26            6           36            2 
TCGA-56-A5DR TCGA-58-8390 TCGA-58-8391 TCGA-58-A46M TCGA-60-2696 TCGA-60-2707 
           4          911         2167         1072          109          661 
TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-63-7023 TCGA-66-2753 
        1963         1260          274         1731         1952           31 
TCGA-66-2757 TCGA-66-2770 TCGA-66-2773 TCGA-66-2780 TCGA-66-2782 TCGA-66-2786 
          30          700         1946         1956         1954          790 
TCGA-66-2790 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2800 TCGA-68-7756 
         699          913         1952         1645         1492          202 
TCGA-77-6842 TCGA-77-6845 TCGA-77-7138 TCGA-77-7141 TCGA-77-7142 TCGA-77-8009 
        1950         1952         1959           15         1286         1641 
TCGA-77-8133 TCGA-77-8140 TCGA-77-8144 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5G3 
        1941         1962          833         1092           10         1959 
TCGA-77-A5GA TCGA-77-A5GF TCGA-85-6561 TCGA-85-7698 TCGA-85-7699 TCGA-85-8071 
        1280          839          395           49            1          428 
TCGA-85-8288 TCGA-85-8352 TCGA-85-8354 TCGA-85-8580 TCGA-85-A4QR TCGA-85-A50M 
          54           67           61          445           25           19 
TCGA-85-A512 TCGA-90-7766 TCGA-92-8063 TCGA-96-7544 TCGA-96-A4JK TCGA-LA-A446 
        1987          289          122         1213          273           36 
TCGA-NC-A5HG TCGA-NC-A5HI 
        1548         1135 

$`DEL PEAK 52(XP11.3) WILD-TYPE`
TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3414 TCGA-18-3419 TCGA-18-3421 
        2417          146         1415          396           50         1331 
TCGA-18-4083 TCGA-18-4721 TCGA-21-1070 TCGA-21-1071 TCGA-21-1075 TCGA-21-1076 
         187         2754         3636         1426         2134         1852 
TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1081 TCGA-21-5782 TCGA-21-5784 
        1058          474          965          284          962         1268 
TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 
        1032          329          979          223         1945          131 
TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4595 
        1952           53          429          822         1485          734 
TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-5471 
          17         1161         1057          399         1946          965 
TCGA-22-5472 TCGA-22-5474 TCGA-22-5478 TCGA-22-5479 TCGA-22-5482 TCGA-22-5489 
        1964          445           24         1651          357         1912 
TCGA-22-5492 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4583 TCGA-33-4586 
         506         1940         2979         1311         1941          428 
TCGA-33-4587 TCGA-33-4589 TCGA-33-6738 TCGA-34-2596 TCGA-34-2604 TCGA-34-2608 
        1970         1948          822           80          958         1000 
TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 
         951         1528         2062         1715          707          365 
TCGA-34-5241 TCGA-34-5928 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 
         428          552          120           13           12          200 
TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-5819 TCGA-39-5011 TCGA-39-5019 
         247          227          238          103         1454         1361 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 
        1947         1996         1964          740           59          833 
TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 
        1107          474         1084         1086          544         1964 
TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 
        1223          684         1176          822         1007          349 
TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6771 TCGA-43-7657 TCGA-43-7658 
         849          376          757         1936          236         1970 
TCGA-43-8115 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-6026 
         407          353          296          432          366          423 
TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 
         911          541         1948          923         1958         1967 
TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7579 
         881            3          555           62           26           44 
TCGA-56-7580 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 
          40         1961            1           41          178           55 
TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BX 
          63           17           16           34           38           46 
TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DS TCGA-58-8388 TCGA-58-8393 
          30           25            4            8          378         1058 
TCGA-58-A46J TCGA-58-A46L TCGA-58-A46N TCGA-60-2695 TCGA-60-2698 TCGA-60-2703 
        2589         1723          910          642          311         1950 
TCGA-60-2704 TCGA-60-2706 TCGA-60-2708 TCGA-60-2709 TCGA-60-2714 TCGA-60-2715 
        1943         1958         1963         1505         1531         1075 
TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 
        1475         1297           97          983          908         1092 
TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 
         717          816          358         1973         1957         1955 
TCGA-63-7022 TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 
        1947         1967         1311           61          641           30 
TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 
          61           28           30          639          762           30 
TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2771 
          61           31           61           61         1947          578 
TCGA-66-2777 TCGA-66-2778 TCGA-66-2781 TCGA-66-2783 TCGA-66-2785 TCGA-66-2787 
          61          578          121          759           60         1217 
TCGA-66-2788 TCGA-66-2789 TCGA-66-2791 TCGA-66-2795 TCGA-68-7755 TCGA-68-7757 
         699         1955         1977          122           83          211 
TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6843 TCGA-77-6844 
         244           96          121          104         1941         1942 
TCGA-77-7139 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 
        1968         1954         1942         1952         1954          479 
TCGA-77-8007 TCGA-77-8008 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8136 
        1960         1945         1953         1945         1941         1947 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 
        1946         1951         1943          293         1961         1684 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GB 
        1953         1942         1955         1963         1290         1939 
TCGA-77-A5GH TCGA-85-6560 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7710 
         713          364           34           18           10         1965 
TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 
          35          911           60           26           60           16 
TCGA-85-8070 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8350 
         960          513           13           11           13           60 
TCGA-85-8351 TCGA-85-8353 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8582 
          55           54           61           22           21          424 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50Z 
           3          475           15         1972         1960         1973 
TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 
        1967         1972           24           13          111          758 
TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q 
          89          358          428          244          331          269 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 
          82          106          160           70           87          356 
TCGA-94-A4VJ TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 
         430         1344          189          211          183          256 
TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 
         413          224          308          222           35          449 
TCGA-MF-A522 TCGA-NC-A5HE 
          83         1722 

  DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE 
                            1                             1 
  DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE 
                         5287                          3636 
  DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE 
                        774.0                         566.5 
[1] "1.0 - 5287.0 (774.0)" "1.0 - 3636.0 (566.5)"
[1] "hr=" "1"  
D82V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 52(XP11.3) MUTATED         0       21       38        1        18
  DEL PEAK 52(XP11.3) WILD-TYPE       1       51       99        0        34
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 52(XP11.3) MUTATED          19         13          6        1
  DEL PEAK 52(XP11.3) WILD-TYPE        52         44         14        5
D82V3, multiclass
            clus
vv           DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE
  STAGE I                              0                             1
  STAGE IA                            21                            51
  STAGE IB                            38                            99
  STAGE II                             1                             0
  STAGE IIA                           18                            34
  STAGE IIB                           19                            52
  STAGE IIIA                          13                            44
  STAGE IIIB                           6                            14
  STAGE IV                             1                             5
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 52(XP11.3) MUTATED    29  68  13   9
  DEL PEAK 52(XP11.3) WILD-TYPE  69 186  35  11
D82V4, multiclass
    clus
vv   DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE
  T1                          29                            69
  T2                          68                           186
  T3                          13                            35
  T4                           9                            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 52(XP11.3) MUTATED    76  35   7   0
  DEL PEAK 52(XP11.3) WILD-TYPE 185  78  28   5
D82V5, multiclass
    clus
vv   DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE
  N0                          76                           185
  N1                          35                            78
  N2                           7                            28
  N3                           0                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A  MX
  DEL PEAK 52(XP11.3) MUTATED   104   1   0  10
  DEL PEAK 52(XP11.3) WILD-TYPE 254   4   1  40
D82V6, multiclass
     clus
vv    DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE
  M0                          104                           254
  M1                            1                             4
  M1A                           0                             1
  MX                           10                            40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V7, binary
                               cls
clus                              0   1
  DEL PEAK 52(XP11.3) MUTATED    29  90
  DEL PEAK 52(XP11.3) WILD-TYPE  78 223
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 52(XP11.3) MUTATED     29   90
  DEL PEAK 52(XP11.3) WILD-TYPE   78  223
        clus
vv       DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE
  FEMALE                          29                            78
  MALE                            90                           223
[1] 2 2
[1] FALSE
D82V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 52(XP11.3) MUTATED                                       3
  DEL PEAK 52(XP11.3) WILD-TYPE                                     9
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 52(XP11.3) MUTATED                                        1
  DEL PEAK 52(XP11.3) WILD-TYPE                                      5
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 52(XP11.3) MUTATED                                         0
  DEL PEAK 52(XP11.3) WILD-TYPE                                       1
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 52(XP11.3) MUTATED                                                           115
  DEL PEAK 52(XP11.3) WILD-TYPE                                                         286
D82V9, multiclass
                                                             clus
vv                                                            DEL PEAK 52(XP11.3) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         115
                                                             clus
vv                                                            DEL PEAK 52(XP11.3) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           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"
D82V10, binary
                               cls
clus                              0   1
  DEL PEAK 52(XP11.3) MUTATED     4 115
  DEL PEAK 52(XP11.3) WILD-TYPE   9 292
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 52(XP11.3) MUTATED      4  115
  DEL PEAK 52(XP11.3) WILD-TYPE    9  292
     clus
vv    DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE
  NO                            4                             9
  YES                         115                           292
[1] 2 2
[1] FALSE
D82V11, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 52(XP11.3) MUTATED   101   1   0   5
  DEL PEAK 52(XP11.3) WILD-TYPE 241   7   4  13
D82V12, multiclass
    clus
vv   DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE
  R0                         101                           241
  R1                           1                             7
  R2                           0                             4
  RX                           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                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 52(XP11.3) MUTATED       3                         5    79
  DEL PEAK 52(XP11.3) WILD-TYPE     6                        12   219
D82V13, multiclass
                           clus
vv                          DEL PEAK 52(XP11.3) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           5
  WHITE                                              79
                           clus
vv                          DEL PEAK 52(XP11.3) WILD-TYPE
  ASIAN                                                 6
  BLACK OR AFRICAN AMERICAN                            12
  WHITE                                               219
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V14, binary
                               cls
clus                              0   1
  DEL PEAK 52(XP11.3) MUTATED     1  69
  DEL PEAK 52(XP11.3) WILD-TYPE   7 198
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 52(XP11.3) MUTATED      1   69
  DEL PEAK 52(XP11.3) WILD-TYPE    7  198
                        clus
vv                       DEL PEAK 52(XP11.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          69
                        clus
vv                       DEL PEAK 52(XP11.3) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           198
[1] 2 2
[1] FALSE

Clustering(83) Variable = DEL PEAK 53(XQ22.3) MUTATION ANALYSIS
D83V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 53(XQ22.3) MUTATED    55  28
  DEL PEAK 53(XQ22.3) WILD-TYPE 210  95
  DEL PEAK 53(XQ22.3) MUTATED DEL PEAK 53(XQ22.3) WILD-TYPE 
                           83                           305 
  DEL PEAK 53(XQ22.3) MUTATED DEL PEAK 53(XQ22.3) WILD-TYPE 
                           28                            95 
$`DEL PEAK 53(XQ22.3) MUTATED`
TCGA-18-3406 TCGA-18-3419 TCGA-18-4086 TCGA-18-5592 TCGA-18-5595 TCGA-21-1072 
         370           50           85           92          827         3016 
TCGA-21-1080 TCGA-21-1082 TCGA-22-0940 TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 
        3724         3644          608          587          358          965 
TCGA-22-5473 TCGA-22-5481 TCGA-22-5485 TCGA-22-5491 TCGA-33-4533 TCGA-33-4582 
        1933         1952          916         1713         1940         1966 
TCGA-33-4587 TCGA-34-2600 TCGA-34-2609 TCGA-37-4135 TCGA-37-4141 TCGA-39-5027 
        1970         1874          951          207           12         1849 
TCGA-43-7656 TCGA-51-4080 TCGA-52-7810 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 
         212           12          923           30           13           30 
TCGA-56-A4BW TCGA-56-A5DR TCGA-58-8388 TCGA-58-8390 TCGA-60-2695 TCGA-60-2696 
           2            4          378          911          642          109 
TCGA-60-2712 TCGA-60-2713 TCGA-60-2719 TCGA-60-2721 TCGA-60-2724 TCGA-60-2726 
         274         1731         1297          983          717          358 
TCGA-63-7023 TCGA-66-2727 TCGA-66-2742 TCGA-66-2753 TCGA-66-2754 TCGA-66-2757 
        1952         1967          641           31           61           30 
TCGA-66-2763 TCGA-66-2766 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2786 
          30           31         1956          121         1954          790 
TCGA-66-2790 TCGA-66-2795 TCGA-68-7755 TCGA-77-6844 TCGA-77-7138 TCGA-77-7142 
         699          122           83         1942         1959         1286 
TCGA-77-7335 TCGA-77-7337 TCGA-77-8136 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 
        1954         1942         1947         1951         1962          833 
TCGA-77-8153 TCGA-77-8154 TCGA-77-A5G3 TCGA-77-A5GA TCGA-85-7699 TCGA-85-8070 
        1684         1092         1959         1280            1          960 
TCGA-85-8071 TCGA-85-8072 TCGA-85-8288 TCGA-85-8479 TCGA-85-A512 TCGA-90-7766 
         428          513           54           22         1987          289 
TCGA-94-A4VJ TCGA-96-7544 TCGA-98-8022 TCGA-NC-A5HG TCGA-NC-A5HI 
         430         1213          224         1548         1135 

$`DEL PEAK 53(XQ22.3) WILD-TYPE`
TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 
         136         2464         2417          146         1415          345 
TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3421 TCGA-18-4083 
         396         1810          862          758         1331          187 
TCGA-18-4721 TCGA-21-1070 TCGA-21-1071 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 
        2754         3636         1426         2134         1852         1058 
TCGA-21-1078 TCGA-21-1079 TCGA-21-1081 TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 
         474          965          284          267          962         1268 
TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 
        1032          329          979          223         1945          131 
TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 
        1952           53          429          822         1485          623 
TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 
        1067         1470          734           17         1161         1057 
TCGA-22-4604 TCGA-22-4605 TCGA-22-5472 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 
         399         1946         1964          445         1346           24 
TCGA-22-5479 TCGA-22-5480 TCGA-22-5482 TCGA-22-5483 TCGA-22-5489 TCGA-22-5492 
        1651         1952          357          573         1912          506 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4583 
          29         2524         2979         1311         5287         1941 
TCGA-33-4586 TCGA-33-4589 TCGA-33-6738 TCGA-34-2596 TCGA-34-2604 TCGA-34-2605 
         428         1948          822           80          958          881 
TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 
        1000         1528         2062         1715          707          365 
TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 
         428          941          552          166          120           13 
TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-5819 
          12          200          247          227          238          103 
TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 
        1454         2253         1361         1947         1996         1964 
TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 
          52          740           59          833         1107          474 
TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 
        1084         1086          544         1964         1223          684 
TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 
        1176          822         1007          349          849          376 
TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 
         757          310         1936          236         1970          407 
TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V 
         358         1971          353          296          432          366 
TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 
         324          423           12          911          541         1948 
TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 
        1958         1967          881            3          555           62 
TCGA-56-6546 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 
          26           44           40           26            6         1961 
TCGA-56-7822 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 
           1           41          178           55           36           63 
TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4BY 
          17           16           34           38           46           30 
TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DS TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J 
          25            4            8         2167         1058         2589 
TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 
        1723         1072          910          311         1950         1943 
TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 
        1958          661         1963         1505         1963         1260 
TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 
        1531         1075         1475           97          908         1092 
TCGA-60-2725 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-66-2734 
         816         1973         1957         1955         1947         1311 
TCGA-66-2737 TCGA-66-2744 TCGA-66-2755 TCGA-66-2756 TCGA-66-2758 TCGA-66-2759 
          61           30           28           30          639          762 
TCGA-66-2765 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 
          61           61           61         1947          700          578 
TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2783 TCGA-66-2785 TCGA-66-2787 
        1946           61          578          759           60         1217 
TCGA-66-2788 TCGA-66-2789 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 
         699         1955         1977          913         1952         1645 
TCGA-66-2800 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I 
        1492          202          211          244           96          121 
TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-6845 TCGA-77-7139 TCGA-77-7141 
         104         1950         1941         1952         1968           15 
TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 
        1952         1954          479         1960         1945         1641 
TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8138 TCGA-77-8145 
        1953         1945         1941         1941         1946         1943 
TCGA-77-8148 TCGA-77-8150 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 
         293         1961           10         1953         1942         1955 
TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 
        1963         1290         1939          839          713          364 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 
         395           34           18           10           49         1965 
TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 
          35          911           60           26           60           16 
TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 
          13           11           13           60           55           67 
TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 
          54           61           61           21          445          424 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR 
           3          475           15         1972         1960           25 
TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L 
          19         1973         1967         1972           24           13 
TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED 
         111          758           89          358          428          244 
TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 
         331          269           82          106          122          160 
TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 
          70           87          356         1344          189          211 
TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8023 TCGA-J1-A4AH 
         273          183          256          413          308          222 
TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE 
          35          449           36           83         1722 

  DEL PEAK 53(XQ22.3) MUTATED DEL PEAK 53(XQ22.3) WILD-TYPE 
                            1                             1 
  DEL PEAK 53(XQ22.3) MUTATED DEL PEAK 53(XQ22.3) WILD-TYPE 
                         3724                          5287 
  DEL PEAK 53(XQ22.3) MUTATED DEL PEAK 53(XQ22.3) WILD-TYPE 
                          827                           573 
[1] "1.0 - 3724.0 (827.0)" "1.0 - 5287.0 (573.0)"
[1] "hr=" "1"  
D83V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 53(XQ22.3) MUTATED         0       18       31        0         9
  DEL PEAK 53(XQ22.3) WILD-TYPE       1       54      106        1        43
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 53(XQ22.3) MUTATED          14          8          4        1
  DEL PEAK 53(XQ22.3) WILD-TYPE        57         49         16        5
D83V3, multiclass
            clus
vv           DEL PEAK 53(XQ22.3) MUTATED DEL PEAK 53(XQ22.3) WILD-TYPE
  STAGE I                              0                             1
  STAGE IA                            18                            54
  STAGE IB                            31                           106
  STAGE II                             0                             1
  STAGE IIA                            9                            43
  STAGE IIB                           14                            57
  STAGE IIIA                           8                            49
  STAGE IIIB                           4                            16
  STAGE IV                             1                             5
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 53(XQ22.3) MUTATED    24  50   9   4
  DEL PEAK 53(XQ22.3) WILD-TYPE  74 204  39  16
D83V4, multiclass
    clus
vv   DEL PEAK 53(XQ22.3) MUTATED DEL PEAK 53(XQ22.3) WILD-TYPE
  T1                          24                            74
  T2                          50                           204
  T3                           9                            39
  T4                           4                            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 53(XQ22.3) MUTATED    58  25   4   0
  DEL PEAK 53(XQ22.3) WILD-TYPE 203  88  31   5
D83V5, multiclass
    clus
vv   DEL PEAK 53(XQ22.3) MUTATED DEL PEAK 53(XQ22.3) WILD-TYPE
  N0                          58                           203
  N1                          25                            88
  N2                           4                            31
  N3                           0                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A  MX
  DEL PEAK 53(XQ22.3) MUTATED    77   1   0   6
  DEL PEAK 53(XQ22.3) WILD-TYPE 281   4   1  44
D83V6, multiclass
     clus
vv    DEL PEAK 53(XQ22.3) MUTATED DEL PEAK 53(XQ22.3) WILD-TYPE
  M0                           77                           281
  M1                            1                             4
  M1A                           0                             1
  MX                            6                            44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V7, binary
                               cls
clus                              0   1
  DEL PEAK 53(XQ22.3) MUTATED    26  61
  DEL PEAK 53(XQ22.3) WILD-TYPE  81 252
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 53(XQ22.3) MUTATED     26   61
  DEL PEAK 53(XQ22.3) WILD-TYPE   81  252
        clus
vv       DEL PEAK 53(XQ22.3) MUTATED DEL PEAK 53(XQ22.3) WILD-TYPE
  FEMALE                          26                            81
  MALE                            61                           252
[1] 2 2
[1] FALSE
D83V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 53(XQ22.3) MUTATED                                       4
  DEL PEAK 53(XQ22.3) WILD-TYPE                                     8
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 53(XQ22.3) MUTATED                                        1
  DEL PEAK 53(XQ22.3) WILD-TYPE                                      5
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 53(XQ22.3) MUTATED                                         1
  DEL PEAK 53(XQ22.3) WILD-TYPE                                       0
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 53(XQ22.3) MUTATED                                                            81
  DEL PEAK 53(XQ22.3) WILD-TYPE                                                         320
D83V9, multiclass
                                                             clus
vv                                                            DEL PEAK 53(XQ22.3) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          81
                                                             clus
vv                                                            DEL PEAK 53(XQ22.3) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           320
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V10, binary
                               cls
clus                              0   1
  DEL PEAK 53(XQ22.3) MUTATED     3  84
  DEL PEAK 53(XQ22.3) WILD-TYPE  10 323
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 53(XQ22.3) MUTATED      3   84
  DEL PEAK 53(XQ22.3) WILD-TYPE   10  323
     clus
vv    DEL PEAK 53(XQ22.3) MUTATED DEL PEAK 53(XQ22.3) WILD-TYPE
  NO                            3                            10
  YES                          84                           323
[1] 2 2
[1] FALSE
D83V11, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 53(XQ22.3) MUTATED    76   0   1   1
  DEL PEAK 53(XQ22.3) WILD-TYPE 266   8   3  17
D83V12, multiclass
    clus
vv   DEL PEAK 53(XQ22.3) MUTATED DEL PEAK 53(XQ22.3) WILD-TYPE
  R0                          76                           266
  R1                           0                             8
  R2                           1                             3
  RX                           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                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 53(XQ22.3) MUTATED       0                         5    54
  DEL PEAK 53(XQ22.3) WILD-TYPE     9                        12   244
D83V13, multiclass
                           clus
vv                          DEL PEAK 53(XQ22.3) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           5
  WHITE                                              54
                           clus
vv                          DEL PEAK 53(XQ22.3) WILD-TYPE
  ASIAN                                                 9
  BLACK OR AFRICAN AMERICAN                            12
  WHITE                                               244
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V14, binary
                               cls
clus                              0   1
  DEL PEAK 53(XQ22.3) MUTATED     0  46
  DEL PEAK 53(XQ22.3) WILD-TYPE   8 221
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 53(XQ22.3) MUTATED      0   46
  DEL PEAK 53(XQ22.3) WILD-TYPE    8  221
                        clus
vv                       DEL PEAK 53(XQ22.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          46
                        clus
vv                       DEL PEAK 53(XQ22.3) WILD-TYPE
  HISPANIC OR LATINO                                 8
  NOT HISPANIC OR LATINO                           221
[1] 2 2
[1] FALSE
